Contacts of the helix formed by residues 88 - 92 (chain C) in PDB entry 2W4G
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 VAL 88 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84C PHE* 3.7 10.7 + - + +
85C GLU 3.7 0.2 + - - -
87C PHE* 1.3 64.8 - - - +
89C GLU 1.3 46.9 - - - +
91C LEU* 3.3 4.9 + - - +
92C ARG* 3.1 7.1 + - - +
139C TYR* 5.2 0.2 - - + -
140C GLU* 4.3 11.0 - - + -
143C VAL* 3.7 14.8 - - + -
731M ALA* 2.3 28.8 - - + +
735M GLY* 4.5 3.4 - - - -
743M ALA 3.4 3.8 - - - +
746M LYS* 1.6 91.6 + - + +
747M LEU* 1.3 45.8 + - - +
749M GLY* 5.2 0.2 - - - -
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Residues in contact with GLU 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C ASP 3.6 0.9 - - - +
88C VAL 1.3 20.0 - - - -
90C GLY* 1.3 4.7 - - - +
92C ARG* 3.2 2.1 + - - +
93C VAL* 3.3 14.1 + - - +
720M PHE* 3.7 1.4 - - - -
745M GLU 2.7 16.6 - - - +
746M LYS 2.3 2.8 + - - -
747M LEU* 0.8 325.5 + - + +
748M LEU* 0.9 290.2 - - + +
749M GLY* 1.9 13.4 + - - +
750M SER 4.0 1.5 - - - +
753M VAL* 5.3 0.9 - - - +
755M HIS* 3.8 5.0 + - - -
758M TYR* 3.3 13.7 + - - -
760M PHE* 5.0 1.7 - - - -
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Residues in contact with GLY 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C ASP 2.9 8.9 + - - -
89C GLU* 1.3 14.8 - - - +
91C LEU* 1.3 46.2 - - - +
93C VAL* 3.3 0.3 - - - +
724M TYR 1.6 38.5 - - - +
725M ARG 2.8 5.3 - - - +
727M LEU* 3.3 22.9 - - - -
728M ASN* 3.6 9.0 - - - -
747M LEU* 0.5 161.2 + - - +
750M SER 5.6 0.2 - - - -
786M ILE* 3.5 3.1 - - - -
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Residues in contact with LEU 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C PHE 3.9 0.7 - - - +
88C VAL 3.3 8.5 - - - +
90C GLY* 1.3 61.2 - - - -
92C ARG* 1.3 53.9 + - - +
139C TYR* 2.8 27.4 + - + +
725M ARG* 1.9 60.6 + - + +
728M ASN 2.8 10.4 - - - +
729M ALA* 1.2 104.5 - - + +
731M ALA 2.9 31.6 - - - +
732M ILE* 3.6 3.8 - - - +
747M LEU* 1.5 22.7 - - + +
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Residues in contact with ARG 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88C VAL 3.1 2.3 + - - +
89C GLU 3.5 0.9 - - - +
91C LEU* 1.3 62.2 - - - +
93C VAL* 1.3 45.3 - - - -
96C LYS* 3.0 0.9 - - - +
139C TYR* 3.5 7.0 - - + -
720M PHE* 1.9 12.1 - - + +
721M LYS* 1.8 45.6 + - - +
742M LYS* 1.0 46.3 + - - +
743M ALA* 1.1 96.8 + - + +
744M SER* 1.2 119.6 - - - +
745M GLU* 0.7 190.7 - - - +
746M LYS* 2.1 9.5 - - - +
747M LEU* 2.0 23.4 - - + +
760M PHE* 3.9 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
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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