Contacts of the helix formed by residues 66 - 85 (chain B) in PDB entry 6N1G
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 SER 66 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B TYR* 3.8 22.3 + - - -
65B GLY* 1.3 75.6 - - - -
67B TYR* 1.3 68.0 + - - +
68B LEU* 3.0 6.7 - - - -
69B GLY* 2.8 16.1 + - - +
70B VAL* 3.2 13.6 + - - +
64D TYR* 2.9 46.7 + - - +
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Residues in contact with TYR 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B SER* 1.3 71.8 - - - +
68B LEU* 1.3 64.2 + - + +
70B VAL* 3.3 10.2 - - - +
71B ASN* 2.4 42.2 + - - +
214B GLY 4.9 1.6 - - - +
215B VAL* 3.1 43.7 - - + -
219B MET* 5.6 4.3 - - + -
54D SER* 5.3 0.2 - - - -
57D HIS* 4.0 16.2 - - + +
63D LYS* 3.0 50.9 + - + -
64D TYR* 2.7 32.5 - - - +
65D GLY* 2.9 24.8 - - - -
69D GLY* 3.9 19.6 - - - -
70D VAL* 4.1 2.3 - - - +
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Residues in contact with LEU 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B SER* 3.0 4.4 - - - -
67B TYR* 1.3 89.4 - - + +
69B GLY* 1.3 58.4 + - - +
71B ASN* 4.0 4.0 - - - -
72B LEU* 2.8 39.0 + - + +
211B VAL* 4.1 20.6 - - + -
215B VAL* 4.0 21.8 - - + -
68D LEU* 5.1 2.5 - - + -
69D GLY* 3.6 31.2 - - - +
72D LEU* 4.3 25.1 - - + -
73D GLY* 5.9 2.7 - - - +
76D PHE* 6.2 0.4 - - + -
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Residues in contact with GLY 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B SER* 5.0 4.2 + - - -
63B LYS* 4.4 14.3 + - - -
65B GLY* 5.2 2.9 - - - -
66B SER* 2.8 16.2 + - - +
68B LEU* 1.3 78.9 - - - +
70B VAL* 1.3 60.6 + - - +
72B LEU* 4.4 3.6 - - - -
73B GLY* 3.8 13.7 + - - -
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Residues in contact with VAL 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B SER* 4.9 21.9 - - - +
55B VAL* 5.0 17.0 - - + -
58B MET* 5.3 9.6 - - + -
63B LYS* 5.6 1.8 - - - +
65B GLY* 4.9 10.5 - - - +
66B SER 3.2 13.5 + - - +
67B TYR* 3.3 17.9 - - - +
69B GLY* 1.3 78.9 - - - +
71B ASN* 1.3 72.6 + - - +
73B GLY* 4.0 0.8 - - - -
74B PHE* 3.1 29.1 + - - +
223B TYR* 3.6 11.1 + - + +
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Residues in contact with ASN 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B TYR* 2.4 26.1 + - - +
68B LEU* 4.0 3.4 - - - +
70B VAL* 1.3 80.7 - - - +
72B LEU* 1.3 60.6 + - - +
74B PHE* 4.5 1.1 - - - -
75B GLY* 2.8 28.6 + - - -
210B VAL 4.5 0.8 - - - +
211B VAL* 3.3 32.2 - - + +
214B GLY* 2.7 33.5 + - - +
215B VAL* 2.8 10.8 + - + +
223B TYR* 3.1 37.2 + - - -
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Residues in contact with LEU 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B LEU* 2.8 28.5 + - + +
69B GLY* 4.9 3.6 - - - +
71B ASN* 1.3 74.0 - - - +
73B GLY* 1.3 58.7 + - - +
76B PHE* 2.9 78.7 + - + -
211B VAL* 3.5 24.3 - - + +
72D LEU* 5.0 13.5 - - + -
76D PHE* 4.6 15.9 - - + -
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Residues in contact with GLY 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B PHE* 4.6 13.4 - - - +
54B SER* 5.2 8.1 - - - -
69B GLY 3.8 11.4 + - - -
70B VAL 3.8 4.2 + - - -
71B ASN 3.2 0.2 - - - -
72B LEU* 1.3 78.5 - - - +
74B PHE* 1.3 58.9 + - - +
76B PHE* 4.0 6.3 - - - +
77B GLY* 2.9 23.4 + - - -
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Residues in contact with PHE 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B MET* 4.1 23.5 - - + +
48B MET* 5.5 2.7 - - + -
51B GLY* 3.7 28.4 - - - -
54B SER* 6.0 0.6 - - - -
70B VAL 3.1 20.8 + - - +
71B ASN 3.8 2.2 - - - +
73B GLY* 1.3 74.2 - - - +
75B GLY* 1.3 61.4 + - - +
77B GLY* 3.1 1.5 + - - +
78B VAL* 2.8 54.5 + - + +
210B VAL* 3.8 15.7 - - + -
223B TYR* 3.6 33.9 - + + +
225B ILE* 5.9 3.4 - - + -
229B ARG* 3.9 44.9 - - + -
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Residues in contact with GLY 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B ASN 2.8 20.0 + - - -
74B PHE* 1.3 74.1 - - - +
76B PHE* 1.3 60.3 + - - +
78B VAL* 3.5 3.5 + - - +
79B THR* 3.2 12.5 + - - -
207B GLY* 2.9 45.9 - - - -
210B VAL* 4.2 11.4 - - - +
211B VAL* 3.8 2.0 - - - -
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Residues in contact with PHE 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B LEU* 2.9 62.0 + - + +
73B GLY* 4.0 6.5 - - - +
75B GLY* 1.3 78.1 - - - +
77B GLY* 1.3 60.9 + - - +
79B THR* 3.1 14.2 + - - -
80B MET* 3.2 28.1 + - + +
204B LEU* 4.6 23.8 - - + -
208B ILE* 4.8 16.4 - - + -
211B VAL* 4.8 2.5 - - + -
76D PHE* 6.2 0.4 - + - -
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Residues in contact with GLY 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B VAL* 4.0 7.4 - - - +
47B MET* 4.3 9.9 - - - -
50B PHE* 4.0 26.9 - - - -
73B GLY 2.9 17.9 + - - -
74B PHE* 3.1 3.8 + - - -
76B PHE* 1.3 75.7 - - - +
78B VAL* 1.3 62.3 + - - +
80B MET* 3.2 7.3 + - - +
81B GLY* 3.1 17.5 + - - -
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Residues in contact with VAL 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B MET* 3.7 32.6 - - + +
74B PHE* 2.8 58.5 + - + +
75B GLY* 3.6 9.0 - - - +
77B GLY* 1.3 75.5 - - - +
79B THR* 1.3 60.6 + - - +
81B GLY* 3.5 2.9 + - - -
82B VAL* 3.3 21.8 + - + +
206B ILE* 4.8 14.4 - - + -
207B GLY* 5.0 0.7 - - - -
210B VAL* 4.7 15.3 - - + -
403B GOL 5.1 8.1 - - - +
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Residues in contact with THR 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B GLY 3.2 13.4 + - - -
76B PHE* 3.1 12.7 + - - -
77B GLY 3.1 0.6 - - - -
78B VAL* 1.3 75.0 - - - +
80B MET* 1.3 75.5 + - + +
81B GLY 3.2 0.4 - - - -
82B VAL* 3.1 5.9 + - - +
83B HIS* 2.9 29.5 + - + +
203B ALA* 2.6 41.9 + - + +
204B LEU* 3.7 20.4 + - + +
207B GLY* 3.3 10.3 + - - +
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Residues in contact with MET 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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46B VAL* 4.0 14.4 - - + -
50B PHE* 4.3 15.3 - - + -
76B PHE* 3.2 29.2 + - + +
77B GLY* 3.2 8.7 + - - +
79B THR* 1.3 93.0 - - + +
81B GLY* 1.3 53.3 + - - +
83B HIS* 3.7 14.5 - - + +
84B VAL* 2.7 38.8 + - + +
204B LEU* 5.6 4.5 - - + -
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Residues in contact with GLY 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B SER* 2.6 39.7 + - - -
46B VAL* 4.4 3.7 - - - +
47B MET* 5.2 2.2 - - - -
77B GLY 3.1 13.0 + - - -
78B VAL* 3.5 6.0 + - - -
79B THR 3.2 0.8 - - - -
80B MET* 1.3 75.2 - - - +
82B VAL* 1.3 62.7 + - - +
84B VAL* 3.3 14.2 - - - +
85B ALA* 3.4 7.6 + - - +
91B ALA* 4.5 3.2 - - - +
93B MET* 5.1 1.8 - - - -
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Residues in contact with VAL 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B VAL* 3.3 16.5 + - + +
79B THR* 3.1 8.9 + - - +
81B GLY* 1.3 74.3 - - - +
83B HIS* 1.3 65.7 + - - +
86B GLY* 3.0 25.9 + - - -
91B ALA* 3.8 16.4 - - + -
93B MET* 6.4 1.1 - - + -
203B ALA* 3.4 28.0 - - + +
206B ILE* 4.8 5.6 - - + -
403B GOL 3.0 38.1 - - - +
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Residues in contact with HIS 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B THR* 2.9 18.0 + - + +
80B MET* 3.7 16.4 - - + +
82B VAL* 1.3 80.7 - - - +
84B VAL* 1.3 64.9 + - - +
86B GLY* 4.0 2.9 + - - -
203B ALA* 4.6 6.5 - - + +
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Residues in contact with VAL 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B MET* 4.4 20.5 - - + +
43B SER* 4.0 16.2 - - - +
46B VAL* 4.8 13.5 - - + -
80B MET* 2.7 29.2 + - + +
81B GLY* 3.3 16.6 - - - +
83B HIS* 1.3 77.3 - - - +
85B ALA* 1.3 66.0 + - + +
86B GLY 3.8 1.6 + - - -
87B ARG* 5.3 0.7 + - - +
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Residues in contact with ALA 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B ALA* 3.5 41.7 - - + +
42B MET* 4.5 5.4 - - + -
43B SER* 3.6 16.4 - - - -
81B GLY 3.4 4.5 + - - +
82B VAL 3.7 2.0 - - - -
83B HIS 3.4 0.4 - - - -
84B VAL* 1.3 80.5 - - + +
86B GLY* 1.3 60.0 + - - +
87B ARG 3.5 1.6 - - - +
88B ILE* 4.5 6.5 - - - -
89B SER* 2.7 31.3 + - - +
91B ALA* 3.7 3.5 + - - -
93B MET* 5.5 0.2 - - + -
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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