Contacts of the strand formed by residues 310 - 313 (chain S) in PDB entry 1VYH
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 PHE 310 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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284S TRP* 3.5 13.7 - - - -
285S ALA* 2.8 49.7 + - + +
289S SER* 4.7 26.2 - - - -
291S SER* 5.3 9.9 - - - +
292S SER* 5.1 13.9 - - - -
308S GLY* 3.1 31.4 - - - -
309S PRO* 1.3 71.8 - - - +
311S LEU* 1.3 59.2 + - - +
312S LEU* 5.5 0.2 - - + -
322S MET* 3.8 18.6 - - + -
323S TRP 3.1 21.8 - - - +
324S ASP* 2.8 37.9 - - + -
325S VAL* 4.3 0.2 - - - +
331S LEU* 4.0 10.5 - - + -
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Residues in contact with LEU 311 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250S ALA* 4.6 6.5 - - + -
258S VAL* 3.7 18.6 - - + -
260S VAL* 3.9 15.5 - - + -
272S LEU* 3.7 22.7 - - + -
282S ILE* 4.3 11.2 - - + -
283S SER 3.3 15.0 - - - +
284S TRP* 4.7 11.2 - - + -
310S PHE* 1.3 74.7 - - - +
312S LEU* 1.3 66.7 + - - +
322S MET* 3.6 0.2 - - - -
323S TRP* 2.9 65.8 + - + +
325S VAL* 3.4 30.7 - - + -
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Residues in contact with LEU 312 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282S ILE* 3.6 23.6 - - - -
283S SER* 3.2 14.9 + - - +
285S ALA* 5.1 0.4 - - + -
310S PHE 5.0 0.2 - - - -
311S LEU* 1.3 82.2 - - - +
313S SER* 1.3 58.8 - - - +
314S GLY 3.6 4.3 + - - -
320S ILE* 4.2 7.0 - - + -
321S LYS 2.7 16.6 - - - +
322S MET* 3.7 23.3 - - + -
344S VAL* 3.5 32.6 - - + +
345S LEU 4.2 3.1 - - - +
346S PHE* 3.3 43.3 - - + -
353S ILE* 3.8 25.6 - - + -
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Residues in contact with SER 313 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258S VAL* 3.8 18.6 - - - -
275S HIS* 2.6 46.5 + - - -
279S VAL* 3.7 16.2 - - - -
281S CYS 3.6 6.1 - - - -
282S ILE* 4.3 2.5 - - - -
312S LEU* 1.3 67.7 - - - +
314S GLY* 1.3 59.8 + - - +
319S THR 3.2 1.4 - - - +
321S LYS* 2.8 25.5 + - - +
323S TRP* 2.9 23.9 + - - +
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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