Contacts of the helix formed by residues 76 - 86 (chain B) in PDB entry 3S4Y
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 ARG 76 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B ASN* 2.9 39.2 + - - +
53B TYR* 3.7 8.5 - - - -
54B ASP* 2.9 41.6 + - - -
74B SER 4.4 2.2 - - - +
75B ILE* 1.3 74.7 - - - +
77B PRO* 1.4 76.6 - - + +
78B GLU* 2.7 35.0 + - - +
79B VAL* 3.1 19.9 + - + +
80B ARG* 3.0 21.2 + - - +
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Residues in contact with PRO 77 (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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75B ILE* 3.7 3.3 - - + +
76B ARG* 1.4 88.2 - - + +
78B GLU* 1.3 64.4 + - - +
80B ARG* 3.5 7.6 + - + +
81B GLU* 3.0 28.2 + - - +
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Residues in contact with GLU 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B TYR* 4.3 17.1 + - + +
76B ARG* 2.7 37.5 + - - +
77B PRO* 1.3 86.8 - - - +
79B VAL* 1.3 65.1 + - + +
81B GLU* 3.9 6.1 - - - +
82B TYR* 2.9 30.1 + - - +
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Residues in contact with VAL 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B ALA* 3.5 28.3 - - + +
50B ASN* 3.5 25.6 - - - +
53B TYR* 3.6 25.4 - - + -
75B ILE* 3.9 7.0 - - + -
76B ARG* 3.1 36.5 + - + +
78B GLU* 1.3 76.2 - - - +
80B ARG* 1.3 66.3 + - - +
82B TYR* 3.3 1.9 + - - +
83B TYR* 3.1 42.9 + - + -
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Residues in contact with ARG 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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72B PHE* 3.4 44.5 + - - +
75B ILE* 3.7 31.1 - - + +
76B ARG 3.0 11.1 + - - +
77B PRO* 3.8 10.1 - - + +
79B VAL* 1.3 78.3 - - - +
81B GLU* 1.3 57.4 + - - +
83B TYR* 3.4 2.6 + - - +
84B ALA* 2.9 33.3 + - + +
90B LEU* 4.1 29.3 - - + +
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Residues in contact with GLU 81 (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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77B PRO 3.0 18.1 + - - +
78B GLU* 3.9 6.7 - - - +
80B ARG* 1.3 75.0 - - - +
82B TYR* 1.3 65.6 + - - +
84B ALA* 3.8 7.9 - - - +
85B THR* 3.0 46.8 + - - +
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Residues in contact with TYR 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B TYR* 3.7 24.0 - + + +
60B ARG* 3.2 32.3 - - + +
61B GLU* 3.5 17.8 + - - +
64B LEU* 4.1 4.5 - - + -
78B GLU 2.9 19.5 + - - +
79B VAL 3.3 4.7 + - - +
81B GLU* 1.3 78.3 - - - +
83B TYR* 1.3 91.1 + + - +
85B THR* 3.4 4.6 + - - -
86B LYS* 3.1 65.8 + - + +
244B SO4 4.2 12.7 + - - -
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Residues in contact with TYR 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B ALA* 3.6 23.6 - - + -
52B LEU* 3.5 17.8 - - + +
53B TYR* 3.2 36.8 + + + -
56B THR* 4.5 2.3 + - - -
60B ARG* 5.2 2.3 - - + +
63B PHE 4.0 8.9 + - - -
64B LEU* 4.0 4.5 - - + -
65B PRO* 3.7 24.7 - - + -
68B ILE* 3.6 32.3 - - + -
79B VAL* 3.1 33.6 + - + +
80B ARG 4.2 1.8 - - - +
82B TYR* 1.3 97.2 - + - +
84B ALA* 1.3 66.0 + - - +
86B LYS* 3.3 2.9 + - - +
87B GLY 3.2 5.4 + - - -
88B CYS* 3.0 37.7 + - + +
90B LEU* 4.7 0.7 - - + -
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Residues in contact with ALA 84 (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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80B ARG* 2.9 21.9 + - + +
81B GLU* 3.8 10.8 - - - +
83B TYR* 1.3 77.4 - - - +
85B THR* 1.3 57.6 + - - +
87B GLY* 3.0 20.8 + - - -
88B CYS 4.1 10.6 - - - +
90B LEU* 4.1 13.3 - - + +
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Residues in contact with THR 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B GLU* 3.0 39.9 + - - +
82B TYR* 3.7 4.9 - - - -
84B ALA* 1.3 76.6 - - - +
86B LYS* 1.3 69.5 + - - +
87B GLY* 3.4 3.5 + - - -
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Residues in contact with LYS 86 (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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61B GLU* 3.8 33.5 + - + +
64B LEU* 3.8 32.6 - - + +
82B TYR* 3.1 60.5 + - + +
83B TYR 3.8 5.2 - - - +
84B ALA 3.2 0.6 - - - -
85B THR* 1.3 84.7 - - + +
87B GLY* 1.3 58.8 + - - +
88B CYS* 3.5 2.6 + - - -
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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
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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