Contacts of the strand formed by residues 311 - 319 (chain A) in PDB entry 6VSB
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 GLY 311 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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310A LYS* 1.3 78.8 - - - +
312A ILE* 1.3 60.9 + - - -
313A TYR* 3.7 10.4 - - - -
597A VAL 3.6 1.9 - - - +
598A ILE* 3.7 0.2 - - - -
599A THR 2.9 32.0 + - - -
664A ILE* 3.6 23.8 - - - -
665A PRO* 6.1 0.4 - - - -
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Residues in contact with ILE 312 (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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311A GLY* 1.3 72.1 - - - -
313A TYR* 1.3 70.9 + - - +
596A SER* 3.7 23.3 - - - +
597A VAL 3.3 6.7 - - - +
598A ILE* 3.6 28.7 - - + -
611A LEU* 4.0 19.5 - - + -
613A GLN* 5.3 2.2 - - - +
664A ILE* 3.7 4.4 - - + +
665A PRO* 3.7 29.4 - - + +
666A ILE* 4.7 5.6 - - - +
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Residues in contact with TYR 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A THR* 4.9 11.1 - - + +
302A THR* 6.1 1.3 - - + -
303A LEU* 4.2 29.4 - - + -
308A VAL* 4.8 9.2 - - + -
309A GLU* 2.9 50.8 + - - +
310A LYS 3.0 17.0 + - - -
311A GLY* 3.7 13.7 - - - -
312A ILE* 1.3 79.2 - - - +
314A GLN* 1.3 64.7 + - - +
315A THR 3.9 0.7 + - - -
596A SER* 3.1 5.3 - - - -
597A VAL* 3.0 46.1 + - + +
599A THR* 5.4 2.7 - - - -
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Residues in contact with GLN 314 (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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302A THR* 4.3 10.6 + - - +
313A TYR* 1.3 75.6 - - - +
315A THR* 1.3 63.1 + - - +
316A SER* 4.2 6.9 + - - +
317A ASN* 4.1 19.8 + - - +
594A GLY* 4.1 16.0 - - - -
595A VAL 3.8 14.1 - - - +
596A SER* 3.8 11.2 + - - +
613A GLN* 5.1 7.2 + - - +
735B SER* 4.6 11.0 + - - -
764B ASN* 4.4 20.4 + - - +
768B THR* 4.3 14.6 + - + +
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Residues in contact with THR 315 (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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298A GLU* 2.5 55.5 + - + +
299A THR* 3.6 22.2 - - + -
302A THR* 3.3 20.4 + - - +
313A TYR 3.9 1.0 + - - +
314A GLN* 1.3 75.8 - - - +
316A SER* 1.3 67.2 + - - +
595A VAL* 3.3 17.1 + - + +
597A VAL* 5.0 8.3 - - + -
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Residues in contact with SER 316 (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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298A GLU* 2.9 24.0 + - - -
314A GLN* 3.9 7.6 - - - +
315A THR* 1.3 81.3 - - - +
317A ASN* 1.3 70.9 + - - +
594A GLY* 3.9 2.8 - - - -
595A VAL* 3.1 38.3 + - - +
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Residues in contact with ASN 317 (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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314A GLN* 4.1 11.7 + - - +
316A SER* 1.3 90.7 + - - +
318A PHE* 1.3 68.0 + - - +
319A ARG* 5.2 7.0 - - - +
592A PHE* 5.5 3.0 - - + -
593A GLY* 3.1 31.7 + - - +
594A GLY* 3.3 8.1 - - - +
595A VAL* 4.3 1.0 - - - +
737B ASP* 3.3 45.4 + - - +
764B ASN* 5.0 5.5 + - - -
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Residues in contact with PHE 318 (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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317A ASN* 1.3 79.5 - - - +
319A ARG* 1.3 80.1 + - - +
320A VAL* 5.8 2.9 - - + -
591A SER* 4.7 5.4 - - - -
592A PHE* 3.3 7.4 - - - +
593A GLY* 2.8 61.7 + - - +
594A GLY 3.5 21.3 - - - -
595A VAL* 4.1 5.8 - - + -
612A TYR* 3.7 38.1 - + + -
613A GLN 4.3 1.1 - - - -
615A VAL* 3.6 32.8 - - + -
620A VAL 4.9 14.1 - - - -
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Residues in contact with ARG 319 (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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317A ASN* 5.2 5.2 - - - +
318A PHE* 1.3 90.4 + - - +
320A VAL* 1.3 68.5 + - - +
321A GLN* 3.5 33.6 + - - +
590A CYS* 5.7 2.2 - - - +
591A SER 4.1 1.6 - - - -
592A PHE* 3.8 17.1 - - + -
737B ASP* 3.3 18.8 + - - -
739B THR* 6.0 1.0 - - - +
740B MET* 3.3 38.8 - - - +
745B ASP* 2.9 41.0 + - - +
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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