Contacts of the strand formed by residues 319 - 323 (chain A) in PDB entry 3V9G
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 ASN 319 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317A GLY* 3.8 10.1 + - - -
318A LYS* 1.3 73.1 + - - +
320A PHE* 1.3 61.3 + - - +
347A LYS 4.8 0.2 + - - -
348A CYS 2.7 27.4 + - - -
349A SER 3.2 5.7 - - - +
350A ALA 3.0 27.1 + - - +
351A CYS* 4.3 2.2 - - - -
352A SER* 3.1 26.1 + - - -
353A ARG* 3.2 10.2 + - - +
478A LEU* 3.4 12.0 + - - +
479A THR* 2.8 51.5 + - - +
510A SER* 4.5 1.8 - - - +
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Residues in contact with PHE 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A LYS 5.0 0.2 - - - -
319A ASN* 1.3 77.9 - - - +
321A HIS* 1.3 68.8 + - - +
322A PHE* 3.9 9.0 - - + -
351A CYS* 4.3 0.7 - - - -
353A ARG* 3.1 42.0 - - - +
355A TYR* 4.2 8.7 - - + -
470A VAL* 3.5 16.6 - - + -
479A THR 3.7 3.8 + - - -
480A GLY* 3.3 21.1 - - - -
481A ALA 2.9 49.7 + - - -
497A LEU* 3.9 31.4 - - + -
500A ALA* 3.9 26.9 - - + -
501A ALA* 4.2 4.3 - - + -
504A PHE* 4.2 6.7 - + - -
510A SER* 4.3 1.6 - - - -
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Residues in contact with HIS 321 (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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320A PHE* 1.3 84.5 - - - +
322A PHE* 1.3 59.9 + - - +
335A GLY 3.6 25.8 - - - -
336A THR* 3.1 23.0 + - - -
339A SER* 3.7 6.6 + - - -
351A CYS* 3.6 17.0 - - + -
353A ARG 3.0 8.5 + - - +
354A LEU* 3.3 22.5 - - + +
355A TYR* 2.9 24.8 + - - -
481A ALA* 3.6 12.8 - - + -
483A PHE* 3.5 22.1 - + + -
509A LYS* 3.7 14.1 - - - -
510A SER* 3.1 27.9 + - - -
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Residues in contact with PHE 322 (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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320A PHE* 3.9 13.3 - - + -
321A HIS* 1.3 72.7 - - - +
323A VAL* 1.3 68.3 + - - +
324A HIS* 4.2 9.4 - - + -
355A TYR* 3.8 16.8 - - + -
458A TYR* 3.4 31.0 - + - -
463A TYR* 4.2 16.4 - + - -
466A THR* 3.8 25.4 - - + -
467A LEU* 3.4 33.4 - - + -
470A VAL* 3.9 16.6 - - + -
481A ALA 2.7 15.8 + - - +
482A VAL* 3.4 20.4 - - + -
483A PHE* 2.9 26.0 + - - +
489A VAL* 5.6 2.9 - - + -
493A ALA* 5.8 0.4 - - + -
497A LEU* 5.2 0.7 - - + -
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Residues in contact with VAL 323 (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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321A HIS 4.4 0.2 - - - +
322A PHE* 1.3 81.9 - - - +
324A HIS* 1.3 66.4 + - - +
327A ALA* 3.5 20.2 - - + -
332A VAL* 3.8 24.9 - - + -
354A LEU* 3.8 22.2 - - + -
355A TYR 2.9 19.0 + - - +
356A VAL* 4.5 3.4 - - + -
357A PRO* 3.2 22.5 - - + +
360A LEU* 4.5 5.4 - - + -
364A ILE* 4.5 7.6 - - + -
458A TYR* 2.6 27.7 + - - -
483A PHE* 3.8 8.1 - - + +
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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