Contacts of the helix formed by residues 74 - 94 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B ALA* 3.1 38.1 - - + +
58B ALA* 3.8 16.6 - - + -
59B GLN* 3.2 35.0 - - + +
70B LYS* 3.2 9.4 + - + +
71B LEU 3.1 18.4 - - - +
73B SER* 1.3 80.0 + - - +
75B GLN* 1.3 64.0 + - - +
76B GLN 3.2 1.1 - - - -
77B ALA* 3.0 18.5 + - + +
78B ILE* 3.0 10.9 + - + +
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Residues in contact with GLN 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B LEU 4.4 2.2 - - - +
72B VAL* 3.0 24.8 + - - +
74B VAL* 1.3 80.5 - - - +
76B GLN* 1.3 86.4 + - - +
78B ILE* 3.3 3.8 + - - +
79B LYS* 3.0 38.9 + - - +
75Y GLN* 3.3 53.3 - - + +
76Y GLN* 5.8 0.8 + - - +
78Y ILE* 5.3 0.4 - - + -
79Y LYS* 3.4 37.0 + - + +
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Residues in contact with GLN 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A GLN* 2.7 39.1 - - - +
72B VAL 4.4 0.2 + - - -
73B SER 4.0 9.2 + - - +
74B VAL 3.2 0.8 - - - -
75B GLN* 1.3 98.2 + - - +
77B ALA* 1.3 56.9 + - - +
79B LYS* 3.3 25.6 + - - +
80B PHE* 2.8 31.1 + - - +
79Y LYS* 5.3 4.2 + - - -
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Residues in contact with ALA 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A GLN* 4.7 4.5 - - - -
51B GLY 5.2 0.2 - - - +
55B ALA* 3.8 17.4 - - + +
73B SER 4.7 1.3 + - - +
74B VAL* 3.0 16.1 + - + +
76B GLN* 1.3 76.5 - - - +
78B ILE* 1.3 59.1 + - - +
80B PHE* 4.6 3.4 - - - -
81B ASN* 2.9 44.4 + - - +
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Residues in contact with ILE 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B LEU* 4.7 7.6 - - + -
55B ALA* 3.8 22.4 - - + +
56B LEU* 3.9 22.7 - - + -
59B GLN* 3.4 38.8 - - + +
74B VAL* 3.0 11.5 + - + +
75B GLN 3.6 6.7 - - - +
77B ALA* 1.3 76.7 - - - +
79B LYS* 1.3 58.1 + - - +
82B GLY* 2.8 29.1 + - - +
71Y LEU* 4.2 13.2 - - + +
72Y VAL* 4.0 4.0 - - + +
75Y GLN* 3.2 36.3 - - + +
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Residues in contact with LYS 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B GLN* 3.0 33.5 + - - +
76B GLN* 3.6 25.8 + - - +
78B ILE* 1.3 76.9 - - - +
80B PHE* 1.3 61.0 + - - +
83B GLY* 2.9 25.6 + - - -
160B ASP* 5.9 1.4 + - - +
161B GLN 4.1 3.8 - - - +
162B ASP* 2.7 40.1 + - - +
163B PRO* 4.6 0.6 - - + +
72Y VAL* 4.1 26.0 - - + +
75Y GLN* 4.6 6.0 - - + +
76Y GLN* 6.0 2.9 - - - +
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Residues in contact with PHE 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A ILE 5.5 0.4 - - - -
137A GLN* 3.5 57.4 - - + +
138A GLY 4.2 0.9 - - - -
47B THR* 6.5 0.4 - - + -
48B TYR* 3.5 26.3 - + - -
76B GLN* 2.8 22.4 + - - +
77B ALA 4.1 1.6 - - - +
79B LYS* 1.3 75.6 - - - +
81B ASN* 1.3 72.4 + - - +
84B GLY* 2.9 22.9 + - - -
160B ASP* 4.7 4.3 - - + -
161B GLN* 3.2 42.4 - - + +
162B ASP* 5.8 0.4 - - - -
176B TRP* 3.9 20.9 - + - -
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Residues in contact with ASN 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B THR* 3.9 4.8 + - - +
48B TYR* 3.3 48.1 - - - +
51B GLY* 3.5 25.9 - - - +
52B LEU* 3.4 13.2 - - - +
77B ALA* 2.9 33.6 + - - +
80B PHE* 1.3 85.8 - - - +
82B GLY* 1.3 60.5 + - - +
84B GLY* 3.2 1.2 + - - -
85B HIS* 2.8 29.8 + - - +
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Residues in contact with GLY 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B LEU* 3.9 19.2 - - - +
78B ILE 2.8 23.4 + - - -
81B ASN* 1.3 73.4 - - - +
83B GLY* 1.3 63.2 + - - +
85B HIS* 3.2 3.3 + - - +
86B ILE* 2.9 27.6 + - - +
68Y VAL* 3.6 6.4 - - - +
72Y VAL* 3.9 13.9 - - - -
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Residues in contact with GLY 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B LYS 2.9 15.0 + - - -
82B GLY* 1.3 75.7 - - - +
84B GLY* 1.3 57.3 + - - +
86B ILE* 3.2 1.8 + - - +
87B ASN* 2.9 35.3 + - - +
161B GLN 3.0 23.8 - - - -
163B PRO* 3.7 20.2 - - - -
72Y VAL* 4.0 2.4 - - - +
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Residues in contact with GLY 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B HIS* 4.5 0.2 - - - -
48B TYR* 3.9 14.9 - - - -
80B PHE 2.9 17.1 + - - -
81B ASN 3.5 4.3 - - - -
82B GLY 3.2 0.2 - - - -
83B GLY* 1.3 77.2 - - - +
85B HIS* 1.3 59.4 + - - +
88B HIS* 2.8 32.4 + - - +
161B GLN* 3.5 24.4 - - - +
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Residues in contact with HIS 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B TYR* 3.8 28.1 - + + -
17B THR 3.6 22.0 + - - -
19B PRO* 4.1 3.6 - - - +
45B HIS* 3.0 36.0 + - + -
48B TYR* 4.0 4.0 - - + +
49B VAL* 3.7 13.2 - - + +
52B LEU* 3.7 23.5 - - + +
81B ASN 2.8 15.7 + - - +
82B GLY 3.2 4.9 + - - +
84B GLY* 1.3 77.9 - - - +
86B ILE* 1.3 55.2 + - - +
89B SER* 2.7 46.7 + - - -
68Y VAL* 4.3 9.3 - - + +
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Residues in contact with ILE 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B GLY 2.9 19.3 + - - +
83B GLY 3.6 4.9 - - - +
85B HIS* 1.3 74.2 - - - +
87B ASN* 1.3 72.6 + - - +
89B SER* 3.4 4.5 + - - -
90B LEU* 3.1 41.6 + - + +
163B PRO* 4.0 22.0 - - + -
164B VAL 5.8 0.4 - - - +
169B PRO* 6.3 0.2 - - + -
68Y VAL* 3.5 28.0 - - + -
69Y PRO* 3.9 27.4 - - + -
72Y VAL* 3.9 15.7 - - + -
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Residues in contact with ASN 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B GLY 2.9 15.8 + - - +
84B GLY 4.3 0.2 - - - +
86B ILE* 1.3 73.3 - - - +
88B HIS* 1.3 59.9 + - - +
90B LEU* 3.3 3.8 + - - +
91B PHE* 2.9 27.5 + - - +
141B TRP* 3.5 35.3 - - + +
143B TRP* 3.4 26.6 - - + -
161B GLN* 3.3 28.5 + - - +
162B ASP 3.2 21.2 + - - -
163B PRO* 3.3 22.3 - - - +
164B VAL 4.5 0.5 + - - -
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Residues in contact with HIS 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B HIS* 2.9 26.2 + + - -
44B HIS* 5.1 0.4 - - - +
45B HIS* 3.6 27.1 - + + +
48B TYR* 3.4 27.0 - + - -
84B GLY 2.8 25.9 + - - +
87B ASN* 1.3 76.5 - - - +
89B SER* 1.3 66.1 + - - +
91B PHE* 3.0 16.7 + + - +
92B TRP* 3.0 30.9 + + - +
141B TRP* 3.5 16.9 - + - -
161B GLN* 3.6 9.0 - - - -
174B ASP* 3.2 2.9 + - - -
2002B MN 2.1 32.8 + - - -
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Residues in contact with SER 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B PRO* 3.9 11.0 - - - +
45B HIS* 3.5 10.7 - - - -
85B HIS* 2.7 44.8 + - - -
86B ILE* 3.8 5.2 - - - -
88B HIS* 1.3 77.5 - - - +
90B LEU* 1.3 61.7 + - - +
92B TRP* 4.0 6.0 + - - +
93B LYS* 3.7 25.3 + - - +
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Residues in contact with LEU 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86B ILE* 3.1 37.5 + - + +
87B ASN 3.6 3.4 - - - +
89B SER* 1.3 74.8 - - - +
91B PHE* 1.3 62.0 + - - +
93B LYS* 3.2 1.3 + - + -
94B ASN* 2.9 19.2 + - - -
143B TRP* 4.1 26.9 - - + -
169B PRO* 4.2 21.8 - - + +
207B ARG* 2.9 50.4 + - - +
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Residues in contact with PHE 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B ILE* 5.1 4.0 - - + -
37B MET* 6.1 0.9 - - - -
40B HIS* 3.9 26.2 - + - -
87B ASN 2.9 14.4 + - - +
88B HIS* 3.3 11.0 - + - +
90B LEU* 1.3 74.2 - - - +
92B TRP* 1.3 89.7 + + - +
94B ASN* 3.0 18.2 + - - +
95B LEU* 3.2 40.3 - - + +
141B TRP* 3.8 15.5 - + + -
143B TRP* 5.7 0.6 - - - -
172B GLY 3.3 25.1 - - - -
173B VAL* 3.8 3.1 - - - -
174B ASP* 3.6 18.8 - - + -
179B ALA* 5.3 0.4 - - + -
191B TYR* 3.9 20.2 - - - -
195B ILE* 3.9 13.7 - - + -
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Residues in contact with TRP 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B PRO* 4.6 7.0 - - + -
20B PRO 5.6 1.6 - - - +
21B LEU* 3.4 28.5 - - + -
22B PRO* 3.8 10.7 - - + +
23B TYR* 2.8 25.7 + - - +
37B MET* 3.6 26.7 - - + -
40B HIS* 3.4 44.2 - + + -
41B HIS* 3.5 33.9 + + + -
45B HIS* 2.8 31.0 + + - -
88B HIS* 3.0 30.8 + + + +
89B SER* 4.1 7.6 - - - +
91B PHE* 1.3 93.5 - + - +
93B LYS* 1.3 63.5 + - + +
95B LEU* 3.3 10.8 - - + +
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Residues in contact with LYS 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B PRO* 4.8 12.3 - - + -
89B SER 3.7 12.7 + - - +
90B LEU* 3.2 2.2 + - + +
91B PHE 3.1 0.8 - - - -
92B TRP* 1.3 76.9 - - + +
94B ASN* 1.3 57.2 + - - +
95B LEU 3.2 5.8 - - - -
200B ASN* 3.2 22.9 + - - -
203B GLU* 3.4 24.2 + - + +
207B ARG* 3.5 17.7 - - - +
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Residues in contact with ASN 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B LEU* 2.9 21.6 + - - +
91B PHE* 3.0 11.6 + - - +
93B LYS* 1.3 75.5 - - - +
95B LEU* 1.3 59.7 + - - +
143B TRP* 4.9 0.2 - - - -
170B VAL 4.5 0.9 - - - +
171B PHE* 3.7 15.5 - - + +
172B GLY* 2.8 45.8 + - - +
199B ILE* 3.7 11.0 - - + +
200B ASN* 3.0 28.6 + - - +
203B GLU* 4.3 4.9 - - + -
204B ALA 5.4 0.2 - - - +
207B ARG* 3.1 30.3 - - - +
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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
------------------------------------------------------------
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