Contacts of the helix formed by residues 74 - 94 (chain X) 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 VAL 74 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55X ALA* 3.3 39.0 - - + +
58X ALA* 4.3 12.6 - - + -
59X GLN* 4.0 26.9 - - + -
70X LYS* 3.6 15.7 - - - +
71X LEU 3.3 17.9 - - - +
73X SER* 1.3 79.5 + - - +
75X GLN* 1.3 66.0 + - - +
76X GLN 3.2 0.7 - - - -
77X ALA* 3.1 17.9 + - + +
78X ILE* 3.2 13.2 + - + +
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Residues in contact with GLN 75 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A GLN* 3.4 23.1 + - - +
71A LEU 4.4 1.2 + - - -
75A GLN* 3.1 68.3 - - + +
78A ILE* 3.3 29.9 - - + +
79A LYS* 4.4 9.2 - - + +
59X GLN* 4.8 1.0 - - - +
71X LEU* 3.3 14.8 + - - +
72X VAL* 3.1 19.0 + - - +
73X SER 3.1 1.0 - - - -
74X VAL* 1.3 82.2 - - - +
76X GLN* 1.3 57.3 + - - +
78X ILE* 3.4 15.7 + - - +
79X LYS 3.0 22.0 + - - -
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Residues in contact with GLN 76 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A GLN* 5.3 2.5 + - - +
79A LYS* 6.0 3.1 - - - +
72X VAL 4.4 0.6 + - - -
73X SER 3.5 10.8 + - - +
74X VAL 3.2 0.6 - - - -
75X GLN* 1.3 79.7 - - - +
77X ALA* 1.3 57.2 + - - +
79X LYS* 3.3 32.4 + - - +
80X PHE* 2.8 33.2 + - - +
137Y GLN* 2.9 35.4 - - - +
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Residues in contact with ALA 77 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51X GLY 5.1 0.2 - - - +
55X ALA* 3.7 17.8 - - + +
73X SER 4.6 0.8 + - - +
74X VAL* 3.1 17.7 + - + +
76X GLN* 1.3 75.9 - - - +
78X ILE* 1.3 61.0 + - - +
80X PHE* 4.5 3.1 - - - -
81X ASN* 2.8 45.9 + - - +
137Y GLN* 4.6 5.4 + - - +
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Residues in contact with ILE 78 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A GLN* 3.4 27.4 - - - +
71A LEU* 4.1 28.0 - - + +
72A VAL* 3.7 5.4 - - + +
75A GLN* 5.2 0.2 - - + -
52X LEU* 4.4 10.3 - - + -
55X ALA* 3.7 18.4 - - + +
56X LEU* 4.0 25.8 - - + -
59X GLN* 4.1 15.0 - - + -
74X VAL* 3.2 14.6 + - + +
75X GLN* 3.6 20.6 - - - +
77X ALA* 1.3 75.6 - - - +
79X LYS* 1.3 60.2 + - - +
82X GLY* 2.8 28.1 + - - -
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Residues in contact with LYS 79 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A VAL* 4.1 18.5 - - + +
75A GLN* 3.2 37.0 - - + +
76A GLN* 6.0 0.7 - - - -
75X GLN 3.0 17.2 + - - +
76X GLN* 3.5 30.0 + - - +
77X ALA 3.3 0.2 - - - -
78X ILE* 1.3 77.5 - - - +
80X PHE* 1.3 57.3 + - - +
83X GLY* 2.9 27.0 + - - -
161X GLN 4.3 3.1 - - - +
162X ASP* 2.5 39.9 + - - +
163X PRO* 4.6 3.0 - - + +
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Residues in contact with PHE 80 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47X THR* 6.5 0.4 - - + -
48X TYR* 3.6 25.6 - + - -
76X GLN* 2.8 24.0 + - - +
77X ALA* 4.1 2.2 - - - +
79X LYS* 1.3 73.8 - - - +
81X ASN* 1.3 73.5 + - - +
84X GLY* 2.9 22.7 + - - -
160X ASP* 4.5 6.3 - - + -
161X GLN* 3.2 37.0 - - + +
162X ASP* 5.8 0.9 - - - -
176X TRP* 4.0 21.3 - + - -
136Y ILE 5.6 0.2 - - - -
137Y GLN* 3.6 58.3 - - + +
138Y GLY 4.1 2.0 - - - -
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Residues in contact with ASN 81 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47X THR* 3.8 5.9 + - - +
48X TYR* 3.3 49.3 - - - +
51X GLY* 3.5 24.0 - - - +
52X LEU* 3.3 12.6 - - - +
77X ALA* 2.8 36.2 + - - +
80X PHE* 1.3 82.3 - - - +
82X GLY* 1.3 60.8 + - - +
84X GLY 3.2 0.5 + - - -
85X HIS* 2.9 29.1 + - - +
137Y GLN* 5.5 0.2 - - - +
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Residues in contact with GLY 82 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A VAL* 3.7 1.5 - - - +
72A VAL* 3.8 13.0 - - - -
52X LEU* 3.7 26.1 - - - +
78X ILE 2.8 18.1 + - - -
81X ASN* 1.3 75.4 - - - +
83X GLY* 1.3 61.1 + - - +
85X HIS* 3.4 2.1 + - - +
86X ILE* 3.0 34.1 + - - +
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Residues in contact with GLY 83 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A VAL* 3.9 1.8 - - - +
79X LYS 2.9 17.2 + - - -
82X GLY* 1.3 76.7 - - - +
84X GLY* 1.3 57.5 + - - +
86X ILE* 3.4 1.4 + - - +
87X ASN* 2.9 35.3 + - - +
161X GLN 3.1 21.5 - - - -
163X PRO* 3.9 19.7 - - - -
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Residues in contact with GLY 84 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48X TYR* 4.0 12.8 - - - -
80X PHE 2.9 18.9 + - - -
81X ASN 3.2 2.4 + - - -
83X GLY* 1.3 77.5 - - - +
85X HIS* 1.3 60.3 + - - +
88X HIS* 2.8 34.4 + - - +
161X GLN* 3.5 24.8 - - - +
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Residues in contact with HIS 85 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A VAL* 4.5 9.7 - - + +
16X TYR* 3.9 26.3 - + + +
17X THR 3.7 21.7 + - - -
19X PRO* 4.0 4.8 - - - +
45X HIS* 3.2 28.6 + - - -
48X TYR* 4.0 6.4 - - + +
49X VAL* 3.9 13.0 - - + +
52X LEU* 3.9 18.8 - - + +
81X ASN 2.9 16.5 + - - +
82X GLY* 3.7 7.9 - - - +
83X GLY 3.3 0.2 - - - -
84X GLY* 1.3 73.6 - - - +
86X ILE* 1.3 62.8 + - - +
89X SER* 2.6 42.8 + - - -
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Residues in contact with ILE 86 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A VAL* 3.6 23.6 - - + +
69A PRO* 3.7 33.7 - - + -
72A VAL* 4.0 9.4 - - + -
82X GLY 3.0 23.0 + - - +
83X GLY* 3.7 3.6 - - - +
85X HIS* 1.3 77.5 - - + +
87X ASN* 1.3 68.9 + - - +
89X SER* 3.7 4.4 - - - -
90X LEU* 3.0 42.6 + - + +
163X PRO* 4.2 19.1 - - + -
164X VAL 5.9 0.2 - - - +
214X GLY 4.3 12.8 - - - +
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Residues in contact with ASN 87 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83X GLY 2.9 17.8 + - - +
84X GLY 4.0 2.2 - - - +
86X ILE* 1.3 79.8 - - - +
88X HIS* 1.3 57.3 + - - +
90X LEU* 3.3 5.2 + - - +
91X PHE* 2.9 26.5 + - - +
141X TRP* 3.6 33.1 - - + +
143X TRP* 3.3 27.8 - - + -
161X GLN* 3.0 37.5 + - - +
162X ASP 3.2 11.7 + - - -
163X PRO* 3.4 18.2 - - - +
164X VAL 4.4 0.5 + - - -
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Residues in contact with HIS 88 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40X HIS* 3.0 19.5 + + - -
44X HIS* 5.0 0.4 - - - +
45X HIS* 3.6 27.8 - + + +
48X TYR* 3.4 27.8 - + - -
84X GLY* 2.8 29.2 + - - +
87X ASN* 1.3 73.2 - - - +
89X SER* 1.3 67.1 + - - +
91X PHE* 3.0 6.9 + + - +
92X TRP* 3.0 42.3 + + - +
141X TRP* 3.8 11.8 - + - -
161X GLN* 3.5 13.0 - - - -
174X ASP* 3.4 2.7 + - - -
2003X MN 2.2 37.8 + - - -
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Residues in contact with SER 89 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19X PRO* 3.8 10.6 - - - +
45X HIS* 3.4 11.3 - - - -
85X HIS* 2.6 43.6 + - - -
86X ILE* 3.7 5.2 - - - -
88X HIS* 1.3 77.4 - - - +
90X LEU* 1.3 63.4 + - - +
92X TRP* 3.6 6.8 + - - +
93X LYS* 3.6 26.6 + - - +
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Residues in contact with LEU 90 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86X ILE* 3.0 36.7 + - + +
87X ASN* 3.5 6.3 - - - +
89X SER* 1.3 76.3 - - - +
91X PHE* 1.3 61.7 + - - +
93X LYS* 3.5 1.6 + - + -
94X ASN* 3.1 13.7 + - - -
143X TRP* 4.2 19.7 - - + -
164X VAL 6.4 0.2 - - - +
169X PRO* 4.1 30.5 - - + +
207X ARG* 2.8 49.6 + - - +
214X GLY 4.8 6.1 - - - +
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Residues in contact with PHE 91 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32X ILE* 4.9 5.4 - - + -
37X MET* 6.1 0.4 - - - -
40X HIS* 4.0 18.2 - + - -
87X ASN 2.9 14.2 + - - +
88X HIS* 3.0 9.8 + + - +
90X LEU* 1.3 74.6 - - - +
92X TRP* 1.3 96.7 + + - +
94X ASN* 3.1 17.1 + - - +
95X LEU* 3.3 42.6 - - + +
141X TRP* 3.6 22.4 - + + -
143X TRP* 6.3 0.2 - - - -
172X GLY* 3.3 26.2 - - - -
173X VAL* 3.8 3.1 - - - -
174X ASP* 3.6 13.7 - - + -
179X ALA* 5.5 0.2 - - + -
191X TYR* 3.8 20.9 - - - -
195X ILE* 4.0 12.1 - - + -
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Residues in contact with TRP 92 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19X PRO* 4.7 6.3 - - + -
20X PRO 5.5 1.8 - - - +
21X LEU* 3.5 30.3 - - + -
22X PRO* 4.0 9.1 - - + +
23X TYR* 2.7 26.9 + - - +
37X MET* 3.7 24.7 - - + -
40X HIS* 3.5 38.8 - + + -
41X HIS* 3.5 33.7 + + + -
45X HIS* 2.8 31.5 + + - -
88X HIS* 3.0 34.8 + + - -
89X SER* 4.1 6.7 - - - +
90X LEU 3.5 0.2 - - - -
91X PHE* 1.3 98.7 - + - +
93X LYS* 1.3 62.6 + - + +
95X LEU* 3.3 11.6 + - + +
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Residues in contact with LYS 93 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19X PRO* 6.4 2.9 - - - -
22X PRO* 4.8 14.8 - - + -
89X SER* 3.6 13.6 + - - +
90X LEU* 3.5 2.2 + - + +
91X PHE 3.2 0.6 - - - -
92X TRP* 1.3 75.6 - - + +
94X ASN* 1.3 56.4 + - - +
95X LEU 3.2 6.1 - - - -
200X ASN* 3.2 23.0 + - - -
203X GLU* 3.4 24.0 - - - +
207X ARG* 3.6 17.7 - - - +
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Residues in contact with ASN 94 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90X LEU* 3.1 22.0 + - - +
91X PHE* 3.1 13.0 + - - +
93X LYS* 1.3 75.5 - - - +
95X LEU* 1.3 55.7 + - - +
143X TRP* 5.1 0.2 - - - -
170X VAL 4.6 0.9 - - - +
171X PHE* 3.3 19.3 - - + +
172X GLY* 3.0 37.4 + - - +
199X ILE* 3.6 10.6 - - + +
200X ASN* 2.8 32.8 + - - +
203X GLU* 4.3 4.7 - - + -
204X ALA 5.4 0.7 - - - +
207X ARG* 2.9 33.3 - - - +
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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
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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) + - + + + + + -
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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