Contacts of the strand formed by residues 308 - 310 (chain A) in PDB entry 2G1O
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 TRP 308 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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200A MET* 3.3 22.7 - - + -
203A VAL* 3.8 24.9 - - + -
211A LEU* 4.3 13.5 - - + -
212A CYS* 4.1 4.5 - - + +
216A CYS* 3.6 21.4 - - + +
217A LEU 2.7 17.8 + - - +
218A ALA* 4.3 3.1 - - + -
219A LEU* 2.7 31.2 + - - +
227A ILE* 4.4 7.9 - - + -
228A SER 3.1 19.7 - - - -
229A GLY* 4.0 5.6 - - - -
230A SER 5.5 1.3 - - - +
233A SER* 3.7 28.0 + - - -
234A ILE* 4.0 20.0 - - + -
237A LEU* 4.1 24.2 - - + -
265A PHE* 4.1 25.1 - + - -
295A ILE* 5.4 1.3 - - + -
307A THR* 1.3 80.7 + - - +
309A ALA* 1.3 57.2 + - - +
310A LEU* 5.2 3.4 - - + -
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Residues in contact with ALA 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219A LEU* 3.2 10.5 - - + +
221A ASP* 4.8 12.1 - - + +
224A ALA* 5.3 5.4 - - + -
226A TYR 3.8 2.2 - - - +
227A ILE* 3.0 9.2 - - - +
228A SER* 2.7 55.9 + - - +
300A ILE* 4.3 14.1 - - + -
308A TRP* 1.3 74.6 - - - +
310A LEU* 1.3 62.9 + - - +
311A GLY 3.4 1.4 + - - +
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Residues in contact with LEU 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200A MET* 5.2 4.0 - - - -
218A ALA* 4.4 18.4 - - + -
219A LEU 2.5 15.6 + - - +
220A VAL* 3.7 20.7 - - + +
221A ASP* 3.1 21.1 + - - +
227A ILE* 3.9 22.4 - - + -
265A PHE* 4.2 16.4 - - + -
267A LEU* 3.8 30.1 - - + -
308A TRP* 5.2 3.8 - - + -
309A ALA* 1.3 72.8 - - - +
311A GLY* 1.3 64.1 + - - +
314A PHE* 3.9 41.1 - - + -
315A ILE* 4.3 2.9 - - - +
331A PHE* 4.8 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
------------------------------------------------------------
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