Contacts of the strand formed by residues 311 - 319 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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310B LYS* 1.3 79.6 - - - +
312B ILE* 1.3 59.0 + - - -
313B TYR* 3.8 5.3 - - - -
597B VAL 3.8 1.4 - - - +
599B THR* 2.9 37.0 + - - +
664B ILE* 3.5 25.6 - - - -
665B PRO* 5.7 1.6 - - - -
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Residues in contact with ILE 312 (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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311B GLY* 1.3 73.4 - - - -
313B TYR* 1.3 69.9 + - - +
596B SER* 4.0 21.5 - - - +
597B VAL 3.2 12.3 - - - +
598B ILE* 3.6 25.1 - - + -
611B LEU* 4.6 3.4 - - + -
664B ILE* 3.5 8.3 - - + +
665B PRO* 3.1 40.2 - - + +
666B ILE* 4.3 18.2 - - + +
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Residues in contact with TYR 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B THR* 5.5 4.3 - - - -
303B LEU* 3.5 39.1 - - + +
308B VAL* 4.5 7.2 - - + -
309B GLU* 2.8 44.3 + - - +
310B LYS 3.1 12.0 + - - -
311B GLY* 3.8 16.6 - - - -
312B ILE* 1.3 80.1 - - - +
314B GLN* 1.3 63.7 + - - +
315B THR* 4.5 6.1 - - + -
596B SER* 3.2 7.2 - - - -
597B VAL* 2.8 49.9 + - + +
599B THR* 4.4 9.2 - - + -
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Residues in contact with GLN 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B THR* 4.7 5.5 + - - -
303B LEU* 6.1 1.2 - - - +
313B TYR* 1.3 75.6 - - - +
315B THR* 1.3 65.0 + - - +
316B SER 4.4 9.3 + - - +
317B ASN* 4.4 17.8 + - - +
594B GLY* 4.8 5.9 - - - -
595B VAL 3.9 12.3 - - - +
596B SER* 3.8 12.0 + - - +
613B GLN* 5.0 10.0 + - - +
735C SER* 4.7 12.2 + - - -
764C ASN* 4.1 22.7 + - - +
768C THR* 4.5 16.3 + - + +
861C LEU* 6.0 2.3 - - - +
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Residues in contact with THR 315 (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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298B GLU* 3.4 23.5 + - - +
299B THR* 3.6 38.8 - - + -
302B THR* 3.4 26.7 - - - +
313B TYR* 4.0 5.6 + - + +
314B GLN* 1.3 78.7 - - - +
316B SER* 1.3 68.6 + - - +
595B VAL* 3.4 15.5 + - - +
597B VAL* 4.0 20.3 - - + +
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Residues in contact with SER 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298B GLU* 4.3 15.5 + - - -
314B GLN* 4.0 7.0 - - - +
315B THR* 1.3 83.7 + - - +
317B ASN* 1.3 76.4 + - - +
594B GLY* 3.7 2.6 - - - -
595B VAL* 2.7 44.7 + - - +
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Residues in contact with ASN 317 (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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314B GLN* 4.4 11.1 + - - +
316B SER* 1.3 92.8 + - - +
318B PHE* 1.3 66.9 + - - +
319B ARG* 6.2 0.7 - - + -
592B PHE* 6.5 0.9 - - + -
593B GLY* 3.3 9.8 - - - +
594B GLY* 3.3 19.9 + - - -
595B VAL* 4.2 4.7 - - - +
737C ASP* 2.6 42.0 + - - +
739C THR* 5.1 1.4 + - - -
764C ASN* 5.5 4.4 - - - +
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Residues in contact with PHE 318 (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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317B ASN* 1.3 78.5 - - - +
319B ARG* 1.3 81.5 + - - +
320B VAL* 5.3 4.0 - - + -
591B SER* 4.3 7.0 - - - -
592B PHE* 3.4 25.7 - - - +
593B GLY* 2.8 49.2 + - - +
594B GLY 3.5 17.0 - - - -
595B VAL* 4.5 9.6 - - + -
612B TYR* 4.4 15.9 - + + -
613B GLN 4.1 9.2 - - - -
615B VAL* 3.6 37.0 - - + -
619B GLU* 5.9 1.3 - - + -
620B VAL 5.0 14.1 - - - -
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Residues in contact with ARG 319 (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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317B ASN* 6.2 0.7 - - + -
318B PHE* 1.3 93.1 - - - +
320B VAL* 1.3 65.9 + - - +
321B GLN* 3.3 39.4 + - - +
322B PRO* 5.2 2.0 - - - +
590B CYS* 5.5 6.9 - - - +
591B SER 4.2 4.7 - - - +
592B PHE* 3.5 18.6 - - + -
740C MET* 4.9 19.3 - - - +
744C GLY 6.3 0.2 - - - -
745C ASP* 2.3 55.1 + - - +
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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