Contacts of the helix formed by residues 67 - 94 (chain Y) in PDB entry 1KKC
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASP 67 (chain Y).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B TYR* 3.8 0.8 + - - -
62Y ALA* 2.8 17.1 + - - +
65Y ALA* 4.1 11.3 - - + +
66Y THR* 1.3 72.7 - - - +
68Y VAL* 1.3 63.3 + - - +
69Y PRO* 3.0 15.0 - - - +
70Y LYS* 2.9 31.9 + - + +
71Y LEU* 3.0 23.3 + - - +
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Residues in contact with VAL 68 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B TYR* 3.3 38.6 + - + -
52B LEU* 4.3 10.3 - - + -
82B GLY* 3.6 22.4 - - - +
85B HIS* 4.3 10.5 - - + +
86B ILE* 3.5 26.2 - - + -
66Y THR 3.6 3.0 + - - +
67Y ASP* 1.3 71.3 - - - +
69Y PRO* 1.3 72.3 - - + +
71Y LEU* 3.1 9.8 + - + +
72Y VAL* 2.9 28.8 + - + +
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Residues in contact with PRO 69 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B ILE* 3.9 24.9 - - + -
163B PRO* 6.1 0.4 - - + -
213B LYS 5.4 7.9 - - - +
67Y ASP* 3.0 13.2 - - - +
68Y VAL* 1.3 95.3 - - + +
70Y LYS* 1.3 61.0 + - - +
72Y VAL* 3.3 2.3 + - + +
73Y SER* 3.0 25.2 + - - -
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Residues in contact with LYS 70 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58Y ALA* 4.5 22.6 - - - +
62Y ALA* 3.4 25.6 - - + -
67Y ASP* 2.9 23.2 + - - +
69Y PRO* 1.3 77.3 - - - +
71Y LEU* 1.3 61.6 + - - +
73Y SER* 2.9 25.4 + - - +
74Y VAL* 3.1 20.0 + - - +
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Residues in contact with LEU 71 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B TYR* 3.6 24.9 - - + +
52B LEU* 5.6 1.8 - - + -
56B LEU* 3.7 30.7 - - + -
78B ILE* 4.6 10.1 - - + -
59Y GLN* 3.1 39.3 - - + +
62Y ALA* 3.8 2.7 - - + -
63Y ALA* 3.4 25.6 - - + +
67Y ASP 3.0 15.7 + - - +
68Y VAL* 3.4 11.9 - - + +
70Y LYS* 1.3 77.3 - - - +
72Y VAL* 1.3 61.5 + - + +
74Y VAL* 3.0 19.5 - - - +
75Y GLN* 3.2 16.4 - - - +
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Residues in contact with VAL 72 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B ILE* 4.0 8.7 - - + +
79B LYS* 4.1 23.8 - - + +
82B GLY* 3.9 24.2 - - - -
83B GLY 4.0 0.2 - - - +
86B ILE* 3.9 16.8 - - + -
163B PRO* 3.9 30.5 - - + -
68Y VAL* 2.9 21.3 + - + +
69Y PRO 3.7 3.8 - - - +
71Y LEU* 1.3 77.7 - - + +
73Y SER* 1.3 64.2 + - - +
75Y GLN* 3.0 24.8 + - - +
76Y GLN 4.3 0.7 + - - -
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Residues in contact with SER 73 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B THR* 4.6 19.3 - - - -
69Y PRO 3.0 14.7 + - - -
70Y LYS* 2.9 33.4 + - - +
72Y VAL* 1.3 77.0 - - - +
74Y VAL* 1.3 61.3 + - - +
75Y GLN 3.2 0.7 + - - -
76Y GLN* 3.4 18.0 + - - +
77Y ALA* 4.4 0.9 + - - +
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Residues in contact with VAL 74 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55Y ALA* 3.2 36.6 - - + +
58Y ALA* 4.1 14.6 - - + -
59Y GLN* 3.7 28.7 - - + +
70Y LYS* 3.1 22.1 + - - +
71Y LEU* 3.0 23.3 - - - +
73Y SER* 1.3 76.1 + - - +
75Y GLN* 1.3 67.4 + - - +
76Y GLN 3.1 0.2 - - - -
77Y ALA* 3.0 19.0 + - + +
78Y ILE* 3.1 11.0 + - + +
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Residues in contact with GLN 75 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B LEU* 5.4 0.2 - - - +
59B GLN* 2.8 36.6 + - - -
75B GLN* 3.3 50.3 - - + +
78B ILE* 3.2 27.8 - - + +
79B LYS* 4.6 5.6 - - + +
59Y GLN* 4.2 2.3 - - - +
71Y LEU* 3.2 20.8 - - - +
72Y VAL* 3.0 14.5 + - - +
74Y VAL* 1.3 77.9 - - - +
76Y GLN* 1.3 56.6 + - - +
78Y ILE* 3.3 12.3 + - - +
79Y LYS* 2.8 31.4 + - - +
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Residues in contact with GLN 76 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B GLN* 5.7 1.0 + - - +
79B LYS* 6.0 3.3 - - - +
137X GLN* 2.9 35.6 - - - +
72Y VAL 4.3 1.0 + - - -
73Y SER 3.4 12.4 + - - +
74Y VAL 3.1 0.8 - - - -
75Y GLN* 1.3 77.4 - - - +
77Y ALA* 1.3 53.4 + - - +
79Y LYS* 3.5 29.3 + - - +
80Y PHE* 2.7 40.7 + - - +
162Y ASP* 5.7 0.2 + - - -
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Residues in contact with ALA 77 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137X GLN* 4.7 4.7 - - - +
51Y GLY 5.2 0.2 - - - +
55Y ALA* 3.8 17.7 - - + -
73Y SER 4.4 1.2 + - - +
74Y VAL* 3.0 16.3 + - + +
76Y GLN* 1.3 75.7 - - - +
78Y ILE* 1.3 59.0 + - - +
80Y PHE* 4.4 3.1 - - - +
81Y ASN* 2.7 48.3 + - - +
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Residues in contact with ILE 78 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B GLN* 3.6 21.1 - - - +
71B LEU* 4.3 21.1 - - + +
72B VAL* 3.8 10.3 - - + +
75B GLN* 5.3 0.7 - - + -
52Y LEU* 4.9 7.9 - - + -
55Y ALA* 3.7 22.0 - - + -
56Y LEU* 4.4 19.5 - - + -
59Y GLN* 4.0 18.6 - - + -
74Y VAL* 3.1 11.7 + - + +
75Y GLN* 3.6 31.4 - - - +
77Y ALA* 1.3 75.8 - - - +
79Y LYS* 1.3 56.4 + - - +
82Y GLY* 2.5 36.6 + - - +
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Residues in contact with LYS 79 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B VAL* 4.2 20.9 - - + +
75B GLN* 3.4 32.1 + - + +
76B GLN* 5.3 3.4 + - - -
75Y GLN 2.8 18.7 + - - +
76Y GLN* 3.5 28.8 + - - +
78Y ILE* 1.3 78.7 - - - +
80Y PHE* 1.3 58.3 + - - +
83Y GLY* 2.8 27.0 + - - -
161Y GLN 4.3 3.1 - - - +
162Y ASP* 3.0 37.3 + - - +
163Y PRO* 4.6 2.5 - - + +
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Residues in contact with PHE 80 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136X ILE 5.5 0.7 - - - -
137X GLN* 3.5 57.4 - - + +
138X GLY 4.2 1.3 - - - -
48Y TYR* 3.8 28.0 - + - -
76Y GLN* 2.7 24.2 + - - +
77Y ALA* 4.0 2.0 - - - +
79Y LYS* 1.3 75.2 - - - +
81Y ASN* 1.3 73.0 + - - +
84Y GLY* 3.0 23.2 + - - -
160Y ASP* 4.5 4.9 - - + -
161Y GLN* 3.3 40.4 - - + +
162Y ASP* 5.7 0.9 - - - -
176Y TRP* 4.0 20.4 - + - -
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Residues in contact with ASN 81 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47Y THR* 3.5 6.1 + - - +
48Y TYR* 3.3 40.3 - - - +
51Y GLY* 3.4 25.0 - - - +
52Y LEU* 3.4 21.0 - - - +
77Y ALA* 2.7 36.6 + - - +
80Y PHE* 1.3 86.0 - - - +
82Y GLY* 1.3 65.1 + - - +
84Y GLY* 3.2 1.0 + - - -
85Y HIS* 3.0 24.1 + - - +
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Residues in contact with GLY 82 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B VAL* 3.6 6.2 - - - +
72B VAL* 3.9 13.9 - - - -
52Y LEU* 3.7 21.8 - - - +
78Y ILE 2.5 25.0 + - - -
81Y ASN* 1.3 74.2 - - - +
83Y GLY* 1.3 61.6 + - - +
85Y HIS* 3.3 1.2 + - - +
86Y ILE* 3.1 27.7 + - - +
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Residues in contact with GLY 83 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B VAL* 4.0 1.6 - - - +
79Y LYS 2.8 17.8 + - - -
82Y GLY* 1.3 76.2 - - - +
84Y GLY* 1.3 55.9 + - - +
86Y ILE* 3.2 1.3 + - - +
87Y ASN* 2.8 35.0 + - - +
161Y GLN 3.0 22.4 - - - -
163Y PRO* 3.8 19.3 - - - -
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Residues in contact with GLY 84 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45Y HIS* 4.5 0.2 - - - -
48Y TYR* 3.9 15.9 - - - -
80Y PHE 3.0 15.2 + - - -
81Y ASN 3.2 3.7 + - - -
83Y GLY* 1.3 77.4 - - - +
85Y HIS* 1.3 61.5 + - - +
88Y HIS* 2.7 32.4 + - - +
161Y GLN* 3.6 23.7 + - - -
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Residues in contact with HIS 85 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B VAL* 4.4 7.9 - - + +
16Y TYR* 4.0 29.9 - + + +
17Y THR 3.8 17.7 + - - -
19Y PRO* 3.9 4.9 - - - +
45Y HIS* 3.0 35.6 + - + -
48Y TYR* 4.0 4.6 - - + +
49Y VAL* 3.9 13.0 - - + +
52Y LEU* 3.6 23.5 - - + +
81Y ASN 3.0 12.9 + - - +
82Y GLY 3.6 7.6 - - - +
84Y GLY* 1.3 75.9 - - - +
86Y ILE* 1.3 57.6 + - + +
89Y SER* 2.6 54.3 + - - -
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Residues in contact with ILE 86 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B VAL* 3.5 31.4 - - + +
69B PRO* 3.7 32.5 - - + -
72B VAL* 4.2 2.9 - - + -
82Y GLY 3.1 12.7 + - - +
83Y GLY 3.6 5.6 - - - +
85Y HIS* 1.3 76.9 - - + +
87Y ASN* 1.3 70.7 + - - +
89Y SER* 3.8 4.3 - - - -
90Y LEU* 3.1 42.7 + - + +
163Y PRO* 4.0 26.7 - - + -
164Y VAL 5.5 1.3 - - - +
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Residues in contact with ASN 87 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83Y GLY 2.8 16.7 + - - +
84Y GLY 4.0 1.8 - - - +
86Y ILE* 1.3 75.9 - - - +
88Y HIS* 1.3 58.2 + - - +
90Y LEU* 3.4 2.6 + - - +
91Y PHE* 2.9 26.3 + - - +
141Y TRP* 3.4 35.0 - - + +
143Y TRP* 3.3 24.6 - - + -
161Y GLN* 3.0 38.4 + - - +
162Y ASP 3.1 12.9 + - - -
163Y PRO* 3.3 22.0 - - - +
164Y VAL 4.4 0.5 + - - -
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Residues in contact with HIS 88 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40Y HIS* 2.9 28.9 + + - -
45Y HIS* 3.5 27.1 - + + +
48Y TYR* 3.2 30.5 - + - -
84Y GLY 2.7 30.0 + - - +
87Y ASN* 1.3 73.3 - - - +
89Y SER* 1.3 66.9 + - - +
91Y PHE* 3.4 6.1 - + - +
92Y TRP* 3.0 40.4 + + - +
141Y TRP* 3.6 13.0 - + - -
161Y GLN* 3.3 13.9 - - - -
174Y ASP* 3.5 1.7 + - - -
2004Y MN 2.3 28.5 + - - -
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Residues in contact with SER 89 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19Y PRO* 3.8 9.4 - - - +
45Y HIS* 3.5 10.2 - - - -
85Y HIS* 2.6 47.2 + - - -
86Y ILE* 3.8 4.9 - - - -
88Y HIS* 1.3 77.8 - - - +
90Y LEU* 1.3 63.0 + - - +
92Y TRP* 3.7 6.3 + - - +
93Y LYS* 3.6 24.9 + - - +
----------------------------------------------------------
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Residues in contact with LEU 90 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86Y ILE* 3.1 35.9 + - + +
87Y ASN 3.7 3.6 - - - +
89Y SER* 1.3 75.5 - - - +
91Y PHE* 1.3 64.3 + - - +
93Y LYS* 3.3 2.7 + - + -
94Y ASN* 3.0 13.9 + - - -
143Y TRP* 4.1 18.6 - - + -
164Y VAL* 6.2 0.4 - - + -
169Y PRO* 4.0 31.2 - - + -
207Y ARG* 2.8 54.3 + - - +
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Residues in contact with PHE 91 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32Y ILE* 5.0 5.4 - - + -
37Y MET* 6.0 0.7 - - - -
40Y HIS* 4.1 19.3 - + - -
87Y ASN 2.9 18.8 + - - +
88Y HIS* 3.1 6.7 + + - +
90Y LEU* 1.3 73.3 - - - +
92Y TRP* 1.3 97.0 + + - +
94Y ASN* 3.1 18.5 + - - +
95Y LEU* 3.3 41.3 - - + +
141Y TRP* 3.7 19.3 - + + -
143Y TRP* 5.8 0.4 - - - -
172Y GLY 3.4 21.8 - - - -
173Y VAL* 3.8 3.1 - - - -
174Y ASP* 3.6 19.1 - - + -
179Y ALA* 5.4 0.9 - - + -
191Y TYR* 3.9 20.2 - - - -
195Y ILE* 3.9 12.3 - - + -
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Residues in contact with TRP 92 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19Y PRO* 4.6 6.3 - - + -
20Y PRO 5.5 1.8 - - - +
21Y LEU* 3.4 30.1 - - + -
22Y PRO* 3.7 10.5 - - + +
23Y TYR* 2.9 31.7 + - - +
37Y MET* 3.6 26.0 - - + -
40Y HIS* 3.4 52.3 - + + -
41Y HIS* 3.4 24.8 + + + -
45Y HIS* 2.8 30.8 + + - -
88Y HIS* 3.0 30.4 + + - +
89Y SER* 4.1 6.3 - - - +
91Y PHE* 1.3 99.1 - + - +
93Y LYS* 1.3 62.6 + - + +
95Y LEU* 3.4 4.0 - - + +
----------------------------------------------------------
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Residues in contact with LYS 93 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22Y PRO* 4.8 12.3 - - + +
89Y SER 3.6 12.7 + - - +
90Y LEU* 3.3 4.1 + - + +
91Y PHE 3.1 0.8 - - - -
92Y TRP* 1.3 77.5 - - + +
94Y ASN* 1.3 56.7 + - - +
95Y LEU 3.1 6.6 + - - +
200Y ASN* 3.0 25.6 + - - -
203Y GLU* 3.5 23.0 + - + +
207Y ARG* 3.4 19.1 - - - +
----------------------------------------------------------
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Residues in contact with ASN 94 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90Y LEU* 3.0 22.4 + - - +
91Y PHE* 3.1 14.0 + - - +
93Y LYS* 1.3 75.0 - - - +
95Y LEU* 1.3 59.7 + - - +
143Y TRP* 5.1 0.6 - - - -
170Y VAL 4.6 0.7 - - - +
171Y PHE* 3.4 14.0 - - + +
172Y GLY* 2.9 44.5 + - - +
199Y ILE* 3.6 12.1 - - - +
200Y ASN* 2.8 28.2 + - - +
203Y GLU* 4.3 5.2 - - + -
204Y ALA 5.4 0.7 - - - +
207Y ARG* 3.1 28.9 - - - +
----------------------------------------------------------
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il