Contacts of the helix formed by residues 287 - 292 (chain B) in PDB entry 3GSB
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 LYS 287 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B SER* 3.7 4.6 + - - +
115B GLU* 3.3 18.2 - - - +
232B ARG* 4.7 1.2 - - - +
265B THR* 4.6 10.5 + - - +
266B PRO 3.5 17.4 + - - -
267B ASP* 3.1 44.1 + - + +
268B LEU* 4.1 1.0 - - - +
286B GLY* 1.3 73.8 - - - -
288B ARG* 1.3 68.1 + - - +
289B GLU* 3.8 21.1 - - + +
290B ILE* 3.2 19.2 + - + +
291B MET* 3.1 16.8 + - - +
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Residues in contact with ARG 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A LYS* 4.3 12.5 + - - +
115B GLU* 2.9 40.5 + - + +
116B MET* 3.5 27.5 - - + +
286B GLY 3.5 2.5 + - - -
287B LYS* 1.3 69.3 - - - +
289B GLU* 1.3 63.5 + - - +
290B ILE 2.7 2.1 + - - -
291B MET* 2.7 30.9 + - - +
292B GLN* 3.0 37.0 + - - +
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Residues in contact with GLU 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B GLU* 4.4 3.7 - - - +
137B TYR* 4.2 17.6 - - + +
287B LYS* 3.8 29.1 - - + +
288B ARG* 1.3 85.7 + - - +
290B ILE* 1.3 62.9 + - + +
292B GLN* 3.8 16.2 - - - +
293B LEU* 3.7 14.9 - - - +
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Residues in contact with ILE 290 (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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133B LEU* 3.7 30.5 - - + +
137B TYR* 3.7 42.0 - - + +
241B LEU* 4.0 31.0 - - + -
267B ASP* 4.4 9.0 - - + -
268B LEU* 4.2 22.2 - - + -
287B LYS* 3.2 21.5 + - + +
288B ARG 2.7 5.5 + - - -
289B GLU* 1.3 75.6 - - + +
291B MET* 1.3 65.1 + - - +
292B GLN 3.1 3.1 + - - -
293B LEU* 3.3 19.4 + - - +
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Residues in contact with MET 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A PRO* 4.0 23.6 - - + +
116B MET* 3.5 46.2 - - + +
118B ARG* 4.2 4.9 - - + -
133B LEU* 4.0 20.4 - - - -
268B LEU* 4.5 4.0 - - + -
284B TYR* 3.4 40.8 - - + +
285B GLY* 4.0 11.0 - - - -
286B GLY* 4.0 8.1 - - - +
287B LYS 3.4 12.8 - - - +
288B ARG 2.7 12.5 + - - +
290B ILE* 1.3 72.2 - - - +
292B GLN* 1.3 62.3 + - - +
293B LEU 3.0 2.1 + - - -
294B VAL* 3.0 26.6 + - + +
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Residues in contact with GLN 292 (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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24A PRO* 5.5 0.7 - - - +
116B MET* 3.8 17.3 - - - +
288B ARG* 3.0 53.7 + - - +
289B GLU* 3.8 17.2 - - - +
290B ILE 3.1 0.4 - - - -
291B MET* 1.3 75.7 - - - +
293B LEU* 1.3 59.9 + - + +
294B VAL 3.1 1.2 + - - -
297B ALA* 3.2 20.1 - - + +
298B GLY* 3.0 25.1 + - - -
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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
------------------------------------------------------------
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