Contacts of the helix formed by residues 95 - 100 (chain B) in PDB entry 3GA5
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 95 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70B PRO 5.2 1.6 + - - -
73B ALA* 5.3 0.2 - - - +
94B PRO* 1.3 77.7 - - - +
96B ARG* 1.3 63.8 + - - +
97B LYS* 3.6 8.6 + - - +
98B ALA* 3.1 25.2 + - - +
99B LEU* 3.2 19.4 + - - +
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Residues in contact with ARG 96 (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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279A ALA* 4.5 7.7 + - - +
282A THR 5.5 3.4 + - - -
284A TRP 5.1 0.4 + - - -
93B GLU* 5.8 0.9 + - - -
94B PRO 3.7 1.0 + - - -
95B SER* 1.3 73.3 - - - +
97B LYS* 1.3 57.8 + - - +
99B LEU* 3.3 7.2 + - - +
100B ASP* 2.9 63.6 + - - +
288B ASN* 3.2 49.5 + - - +
290B ILE* 4.5 21.0 - - - +
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Residues in contact with LYS 97 (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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280A ASP* 4.7 10.0 + - - +
95B SER* 3.1 8.4 + - - +
96B ARG* 1.3 80.2 - - - +
98B ALA* 1.3 63.9 + - - +
100B ASP* 3.4 6.1 + - - +
101B SER* 3.2 22.7 + - - -
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Residues in contact with ALA 98 (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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73B ALA* 4.1 25.8 - - + -
74B GLY* 4.4 9.9 - - - +
77B ILE* 3.1 16.7 - - + +
94B PRO* 4.1 2.7 - - + -
95B SER* 3.1 23.5 + - - +
97B LYS* 1.3 76.7 - - - +
99B LEU* 1.3 59.6 + - - +
101B SER* 2.7 28.5 + - - -
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Residues in contact with LEU 99 (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 ILE* 5.3 0.2 - - + -
89B PHE* 4.0 8.1 - - + -
93B GLU* 4.7 4.5 - - - +
94B PRO* 4.0 31.6 - - + +
95B SER 3.2 15.7 + - - +
96B ARG* 3.3 11.4 + - - +
98B ALA* 1.3 75.7 - - - +
100B ASP* 1.3 61.9 + - - +
101B SER 3.1 4.2 + - - -
102B TYR 3.4 7.3 + - - +
105B ALA* 3.8 13.1 - - + +
106B TYR 3.7 28.5 - - - +
107B TYR* 3.9 14.6 - - + -
288B ASN 5.6 2.7 - - - +
289B LYS* 2.8 27.6 + - + +
290B ILE* 3.9 30.5 - - + -
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Residues in contact with ASP 100 (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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276A LYS* 3.9 0.5 - - - +
277A GLY* 2.9 25.3 + - - -
279A ALA* 4.3 4.6 + - - +
280A ASP* 3.2 47.3 - - + +
281A GLY 4.7 2.1 + - - -
96B ARG* 2.9 60.2 + - - +
97B LYS* 3.8 3.8 - - - +
99B LEU* 1.3 76.8 - - - +
101B SER* 1.3 58.4 + - - +
102B TYR 3.2 1.3 - - - -
288B ASN* 4.8 5.4 - - - +
289B LYS* 4.4 3.2 + - - +
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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
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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