Contacts of the helix formed by residues 77 - 89 (chain B) in PDB entry 4GSA
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 PRO 77 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48B LYS* 4.5 13.2 - - - +
49B ASP* 5.2 4.3 - - - +
75B ALA 3.2 6.7 - - - +
76B HIS* 1.3 100.6 - - + +
78B GLU* 1.3 64.2 + - + +
80B ILE* 3.7 9.7 + - + +
81B GLU* 3.2 26.5 + - - +
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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
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76B HIS* 3.1 25.1 + - + +
77B PRO* 1.3 82.6 - - + +
79B VAL* 1.3 62.8 + - - +
81B GLU* 4.1 8.8 - - - +
82B ALA* 3.4 21.8 + - - +
318B LYS* 3.6 32.8 + - + +
322B LEU* 4.0 14.7 - - + +
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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
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91A THR* 6.5 0.2 - - + -
72B CYS* 5.6 2.5 - - + -
76B HIS* 2.9 20.7 + - + +
78B GLU* 1.3 75.7 - - - +
80B ILE* 1.3 68.3 + - + +
82B ALA* 3.2 5.4 + - - +
83B LEU* 3.0 37.6 + - + +
277B GLY 4.6 15.3 - - - +
315B ALA* 4.6 14.4 - - + -
318B LYS* 4.1 17.0 - - + -
319B THR* 4.2 13.0 - - - +
322B LEU* 4.0 25.4 - - + -
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Residues in contact with ILE 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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87A MET* 3.8 35.6 - - + +
88A GLU* 3.7 31.9 - - + +
91A THR* 5.4 6.1 - - + -
75B ALA* 4.1 22.9 - - + +
76B HIS 3.0 14.1 + - - +
77B PRO* 4.1 11.2 - - + +
79B VAL* 1.3 80.8 - - + +
81B GLU* 1.3 59.0 + - + +
83B LEU* 3.6 11.9 - - + +
84B LYS* 2.8 40.2 + - + +
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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 3.2 19.9 + - - +
78B GLU* 4.3 9.7 - - - +
79B VAL 3.2 0.8 - - - -
80B ILE* 1.3 76.0 - - + +
82B ALA* 1.3 72.4 + - - +
83B LEU 3.1 0.2 - - - -
84B LYS* 3.3 17.6 + - - +
85B VAL* 3.1 39.7 + - + +
318B LYS* 5.2 4.3 + - - -
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Residues in contact with ALA 82 (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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78B GLU 3.4 18.1 + - - +
79B VAL 3.2 5.5 + - - +
81B GLU* 1.3 85.6 + - - +
83B LEU* 1.3 57.3 + - - +
85B VAL* 3.6 5.9 + - - +
86B ALA* 3.1 26.3 + - - +
314B THR* 3.6 19.5 - - + +
318B LYS* 4.2 23.3 - - + +
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Residues in contact with LEU 83 (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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87A MET* 4.1 21.3 - - + -
91A THR* 4.6 9.6 - - + -
311A LEU* 5.4 0.4 - - + -
79B VAL* 3.0 30.1 + - + +
80B ILE* 3.6 12.1 - - + +
82B ALA* 1.3 73.9 - - - +
84B LYS* 1.3 64.7 + - - +
85B VAL 3.1 1.8 - - - -
86B ALA* 3.8 2.5 - - - +
87B MET* 3.1 29.0 + - - +
279B LEU* 4.3 23.3 - - + -
311B LEU* 3.4 45.0 - - + +
314B THR* 4.0 4.9 - - + -
315B ALA* 3.9 17.7 - - + +
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Residues in contact with LYS 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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84A LYS* 3.2 50.0 + - + +
87A MET* 3.6 17.3 - - + -
88A GLU* 3.9 24.5 - - - +
80B ILE* 2.8 34.4 + - + +
81B GLU* 3.3 17.3 + - - +
83B LEU* 1.3 74.9 - - - +
85B VAL* 1.3 63.0 + - + +
87B MET* 3.5 13.0 + - - +
88B GLU* 4.1 4.7 + - - +
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Residues in contact with VAL 85 (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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81B GLU* 3.1 29.6 + - + +
82B ALA* 3.7 6.1 - - - +
84B LYS* 1.3 76.3 - - + +
86B ALA* 1.3 67.5 + - - +
88B GLU* 3.0 35.6 - - - +
89B LYS* 4.5 2.4 + - - +
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Residues in contact with ALA 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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82B ALA 3.1 17.4 + - - +
83B LEU 3.3 4.9 + - - +
85B VAL* 1.3 78.5 - - - +
87B MET* 1.3 63.0 + - - +
89B LYS* 2.9 27.1 + - - +
90B GLY 4.1 5.7 + - - +
99B LEU* 5.8 1.8 - - + -
310B PRO* 5.1 4.3 - - + +
311B LEU* 4.0 13.5 - - + -
314B THR* 3.7 24.2 - - + +
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Residues in contact with MET 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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75A ALA* 4.6 0.5 - - - +
80A ILE* 4.0 34.3 - - + +
83A LEU* 3.7 43.7 - - + -
84A LYS* 4.3 15.0 - - - +
87A MET* 4.1 20.0 - - + -
311A LEU* 5.8 0.4 - - + -
83B LEU 3.1 14.6 + - - +
84B LYS* 3.5 13.0 - - - +
86B ALA* 1.3 74.8 - - - +
88B GLU* 1.3 59.9 + - - +
89B LYS 2.9 2.0 + - - -
90B GLY* 3.1 19.7 + - - +
91B THR* 4.1 10.1 - - + -
311B LEU* 3.8 27.5 - - + +
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Residues in contact with GLU 88 (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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46A ARG* 6.1 0.2 - - - -
47A VAL 5.1 0.9 - - - +
48A LYS* 6.0 2.1 - - - +
75A ALA* 4.7 8.0 - - - +
80A ILE* 4.4 14.0 - - + +
84A LYS* 4.5 9.8 + - - +
84B LYS 4.1 8.4 + - - +
85B VAL* 3.0 36.5 + - - +
86B ALA 2.9 1.2 + - - -
87B MET* 1.3 78.4 - - - +
89B LYS* 1.3 64.5 + - + +
90B GLY 3.4 0.2 - - - -
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Residues in contact with LYS 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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45A ASP* 3.4 42.4 + - - +
46A ARG* 3.4 24.6 - - + +
47A VAL 3.1 28.7 + - - -
85B VAL 4.9 2.5 - - - +
86B ALA* 2.9 14.6 + - - +
88B GLU* 1.3 89.5 - - + +
90B GLY* 1.3 58.1 + - - +
93B PHE* 3.5 9.6 - - + -
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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