Contacts of the strand formed by residues 323 - 327 (chain F) in PDB entry 2GPV
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 GLU 323 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317F SER* 3.6 16.6 - - - +
320F PHE* 3.7 31.5 - - + +
321F GLU* 3.1 18.9 + - - +
322F ASP* 1.3 81.0 + - - +
324F LEU* 1.3 63.2 + - - +
325F VAL 4.1 0.2 - - - -
331F ILE* 3.8 22.8 - - + +
332F MET 3.3 5.4 - - - +
333F ASP* 4.0 23.0 + - + +
350F LEU* 4.0 6.3 - - - +
353F VAL* 5.6 0.5 - - - +
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Residues in contact with LEU 324 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313F VAL* 4.3 5.8 - - + +
317F SER* 3.4 7.2 - - - +
323F GLU* 1.3 72.2 - - - +
325F VAL* 1.3 61.9 + - - +
326F TYR* 3.3 24.5 + - + +
331F ILE* 3.3 0.8 - - - -
332F MET* 2.9 37.3 + - + +
346F ASN* 3.4 54.3 - - + +
349F ILE* 3.5 28.7 - - + -
350F LEU* 3.5 26.5 - - + -
353F VAL* 3.8 14.6 - - + -
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Residues in contact with VAL 325 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313F VAL* 3.4 9.1 - - - +
316F ARG* 3.1 51.9 + - + +
317F SER* 2.7 13.4 + - - +
320F PHE* 3.7 33.0 - - + -
324F LEU* 1.3 70.3 - - - +
326F TYR* 1.3 62.1 + - - +
327F ALA* 3.5 26.2 - - - +
328F ASP* 4.2 10.8 - - - +
330F TYR 4.1 2.7 - - - -
331F ILE* 4.1 18.8 - - + -
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Residues in contact with TYR 326 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249F ILE 4.9 0.7 - - - +
268F LEU* 3.6 17.3 - - + -
271F LEU* 3.5 22.2 - - + +
275F GLU* 3.8 2.6 - - - +
313F VAL* 3.7 18.6 - - + -
316F ARG* 3.1 18.0 + - - +
324F LEU* 3.3 20.3 + - + +
325F VAL* 1.3 73.5 - - - +
327F ALA* 1.3 63.8 + - - +
330F TYR* 3.0 16.0 + + + +
332F MET* 3.4 41.7 - - + -
342F LEU* 5.4 0.4 - - + +
346F ASN* 2.6 25.6 + - - -
349F ILE* 3.8 5.9 - - - +
505F OHT 3.2 61.6 - + + +
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Residues in contact with ALA 327 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249F ILE 3.3 23.1 - - - +
250F TYR 4.2 0.2 - - - -
251F ALA* 3.6 12.1 - - + +
271F LEU* 4.2 6.1 - - + -
316F ARG* 4.6 6.5 - - - +
325F VAL* 3.2 14.1 - - - +
326F TYR* 1.3 78.6 - - - +
328F ASP* 1.3 58.6 + - - +
329F ASP* 3.0 18.2 - - - +
330F TYR 2.7 30.3 + - - +
331F ILE* 3.8 0.5 - - - +
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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