Contacts of the strand formed by residues 222 - 226 (chain W) in PDB entry 3EXG
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 GLY 222 (chain W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14W LEU* 3.9 0.2 - - - -
15W HIS* 3.0 35.4 + - - +
17W LEU* 4.4 2.8 - - - +
214W TYR* 3.3 20.3 - - - -
220W ILE 3.7 1.0 + - - -
221W PRO* 1.3 75.5 - - - +
223W LEU* 1.3 64.5 + - - +
251W ILE* 4.1 2.7 - - - -
252W LEU 2.8 15.7 - - - -
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Residues in contact with LEU 223 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12W CYS* 3.8 16.2 - - + -
13W ASP 3.3 11.7 - - - +
14W LEU* 3.9 11.4 - - + -
17W LEU* 4.0 9.2 - - + -
21W PRO* 3.6 30.7 - - + -
214W TYR* 3.4 7.2 - - - +
222W GLY* 1.3 75.7 - - - +
224W ARG* 1.3 60.2 + - - +
225W VAL* 4.3 1.1 - - + -
236W ALA* 4.2 16.6 - - + +
239W PHE* 4.1 10.8 - - + -
240W ALA* 5.6 2.5 - - + -
251W ILE* 3.5 31.4 - - + -
252W LEU 2.8 11.7 + - - +
253W MET* 3.3 14.1 - - + +
254W GLU 3.0 24.3 + - - +
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Residues in contact with ARG 224 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10W LYS* 5.7 2.1 - - - +
12W CYS* 3.2 25.1 - - - +
13W ASP* 2.8 42.9 + - - +
211W THR 4.4 5.3 + - - -
212W ASP* 3.2 25.9 + - - -
214W TYR* 3.7 29.6 + - + -
223W LEU* 1.3 74.2 - - - +
225W VAL* 1.3 63.0 + - - +
254W GLU* 3.3 35.8 + - - +
256W GLN* 3.4 36.3 + - + +
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Residues in contact with VAL 225 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10W LYS* 5.7 2.5 - - - -
12W CYS* 3.7 15.7 - - - +
223W LEU* 4.3 3.4 - - + -
224W ARG* 1.3 78.3 - - - +
226W ASP* 1.3 74.0 + - - +
227W GLY 3.8 0.2 - - - -
232W CYS* 3.7 35.4 - - + +
233W VAL* 4.1 6.3 - - + +
236W ALA* 3.6 22.9 - - + -
253W MET* 3.8 24.2 - - + -
254W GLU 2.8 7.1 + - - +
255W LEU* 3.7 16.2 - - + -
256W GLN* 3.2 32.3 + - - +
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Residues in contact with ASP 226 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10W LYS* 3.9 35.5 + - + +
12W CYS* 5.3 0.2 - - - -
225W VAL* 1.3 78.9 - - - +
227W GLY* 1.3 60.3 + - - +
228W MET* 3.0 23.5 + - - +
229W ASP* 3.3 31.5 + - - +
232W CYS* 3.7 18.4 - - - +
233W VAL* 3.5 13.0 - - - +
256W GLN* 4.3 4.0 - - - +
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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