Contacts of the strand formed by residues 2329 - 2332 (chain B) in PDB entry 1V9P
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 VAL2329 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2327B ASP* 3.8 15.3 - - - +
2328B VAL* 1.3 75.8 - - - +
2330B PHE* 1.3 70.8 + - - +
2331B GLN* 5.5 5.2 - - + -
2340B PRO* 3.9 0.5 - - - +
2341B VAL* 2.9 56.0 + - + +
2343B VAL* 4.2 18.4 - - + +
2356B ARG* 5.3 6.7 - - - +
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Residues in contact with PHE2330 (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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2328B VAL* 3.7 21.3 - - + -
2329B VAL* 1.3 82.8 - - - +
2331B GLN* 1.3 67.3 + - - +
2338B VAL* 3.5 27.8 - - + -
2339B THR 3.4 10.5 - - - -
2340B PRO* 4.4 4.9 - - + -
2341B VAL* 5.5 0.2 - - - -
2403B ILE* 4.5 8.7 - - + -
2404B ARG 3.6 25.4 - - - -
2405B TRP* 3.1 48.2 - + - -
2406B PRO* 3.9 17.0 - - + -
2410B PRO* 4.1 20.3 - - + +
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Residues in contact with GLN2331 (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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2329B VAL* 5.5 4.7 - - + -
2330B PHE* 1.3 80.1 - - - +
2332B VAL* 1.3 67.2 + - - +
2333B GLY 4.1 0.2 - - - -
2337B ARG 3.4 1.2 - - - +
2338B VAL* 3.2 1.1 - - - -
2339B THR* 2.4 48.8 + - - +
2341B VAL* 3.5 26.3 - - + +
2410B PRO* 5.4 0.9 - - - -
2411B GLU* 6.0 1.1 - - - -
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Residues in contact with VAL2332 (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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2331B GLN* 1.3 77.5 - - - +
2333B GLY* 1.3 62.6 + - - +
2336B GLY* 4.0 11.9 - - - +
2337B ARG 3.5 3.6 - - - -
2338B VAL* 3.9 23.8 - - + -
2409B CYS* 3.7 23.8 - - + -
2410B PRO* 4.4 9.2 - - + -
2411B GLU* 3.3 28.9 + - + +
2425B CYS* 4.9 0.7 - - + -
2430B CYS* 5.0 2.5 - - - -
2432B ALA* 3.2 31.8 - - + +
2701B ZN 4.7 1.8 - - - -
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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