Contacts of the strand formed by residues 595 - 599 (chain B) in PDB entry 6ZGI
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 VAL 595 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295B PRO* 5.5 3.8 - - + -
314B GLN* 3.9 6.3 + - - +
315B THR* 3.3 30.7 + - + +
316B SER 3.4 24.8 + - - +
318B PHE* 4.1 20.6 - - + +
593B GLY 4.2 0.7 - - - +
594B GLY* 1.3 78.7 - - - +
596B SER* 1.3 70.0 + - - +
610B VAL* 3.8 26.0 - - + -
611B LEU 3.5 4.9 - - - +
612B TYR* 4.1 21.8 - - + -
613B GLN* 4.2 1.9 - - - -
636B TYR* 4.5 14.8 - - + -
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Residues in contact with SER 596 (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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312B ILE* 3.7 22.0 - - - -
313B TYR 3.3 11.0 - - - -
314B GLN* 3.0 18.6 + - - -
315B THR* 4.4 1.8 - - - -
595B VAL* 1.3 76.6 + - - +
597B VAL* 1.3 61.2 + - - +
610B VAL* 3.5 8.1 - - - +
611B LEU* 2.9 42.6 + - - +
613B GLN* 2.8 24.9 + - - -
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Residues in contact with VAL 597 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B PRO* 4.3 18.4 - - + +
296B LEU* 4.6 7.2 - - + +
299B THR* 3.6 32.8 - - + +
311B GLY 3.9 1.0 - - - +
312B ILE* 3.4 3.0 - - - -
313B TYR* 2.9 42.0 + - + +
315B THR* 3.6 13.5 - - + -
596B SER* 1.3 74.2 - - - +
598B ILE* 1.3 66.4 + - - +
599B THR* 5.4 3.1 - - + -
608B VAL* 4.1 26.2 - - + -
609B ALA 3.5 11.4 - - - +
610B VAL* 4.7 3.8 - - + -
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Residues in contact with ILE 598 (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 3.5 8.3 - - - +
312B ILE* 3.5 29.4 - - + -
597B VAL* 1.3 73.7 - - - +
599B THR* 1.3 63.5 + - - +
600B PRO* 4.4 1.3 - - + +
608B VAL* 3.4 7.4 - - - +
609B ALA* 2.9 51.7 + - + +
611B LEU* 4.3 12.1 - - + +
650B LEU* 3.9 26.5 - - + -
664B ILE* 4.3 26.5 - - + -
666B ILE* 3.6 19.3 - - + -
672B ALA* 4.6 8.3 - - + -
692B ILE* 4.6 10.1 - - + +
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Residues in contact with THR 599 (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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296B LEU* 4.5 11.7 - - + +
308B VAL* 3.8 10.4 - - + +
309B GLU 3.7 9.6 - - - +
310B LYS* 3.3 3.3 - - - +
311B GLY 2.9 30.4 + - - +
313B TYR* 3.6 33.2 - - + -
597B VAL* 5.1 3.1 - - + +
598B ILE* 1.3 76.9 - - - +
600B PRO* 1.3 68.4 - - - +
601B GLY* 3.1 16.6 + - - -
602B THR* 4.3 1.6 + - - -
605B SER 5.0 2.1 + - - -
608B VAL* 4.2 16.2 - - - +
664B ILE* 4.4 2.5 - - - +
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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
------------------------------------------------------------
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