Contacts of the strand formed by residues 691 - 696 (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 SER 691 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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607B GLN* 4.1 10.1 + - - +
654B GLU* 4.7 14.1 - - - -
674B TYR* 3.5 11.5 - - - -
675B GLN* 2.9 32.8 + - - +
676B THR 5.6 1.3 - - - -
689B SER 3.5 8.7 + - - -
690B GLN* 1.3 82.8 + - - +
692B ILE* 1.3 67.3 + - - +
693B ILE* 3.7 6.5 + - - +
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Residues in contact with ILE 692 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
598B ILE* 4.6 8.5 - - + +
600B PRO* 4.5 9.9 - - + -
607B GLN* 3.7 26.8 - - + +
608B VAL* 3.8 35.0 - - - +
609B ALA* 3.9 11.4 - - + +
652B GLY 4.2 8.7 - - - +
653B ALA* 3.5 15.3 - - + -
654B GLU* 2.9 26.3 + - - +
664B ILE* 6.4 0.4 - - + -
672B ALA* 4.6 11.9 - - + -
673B SER 3.3 12.6 - - - +
674B TYR* 4.0 15.5 - - + -
691B SER* 1.3 75.2 - - - +
693B ILE* 1.3 66.9 + - - +
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Residues in contact with ILE 693 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
654B GLU* 3.1 22.7 - - - +
656B VAL* 4.2 23.1 - - + -
660B TYR* 4.1 18.4 - - + +
672B ALA* 3.2 5.2 - - - +
673B SER* 2.9 42.5 + - - +
675B GLN* 3.7 33.0 - - + -
676B THR 6.3 1.6 - - - -
691B SER* 4.1 11.2 - - - +
692B ILE* 1.3 79.9 - - - +
694B ALA* 1.3 58.2 + - - +
695B TYR* 3.9 23.4 - - + -
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Residues in contact with ALA 694 (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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643B PHE* 4.6 12.8 - - + -
650B LEU* 4.0 26.2 - - + -
653B ALA* 4.2 8.1 - - + -
654B GLU 2.7 11.9 + - - +
655B HIS* 3.3 9.6 + - - -
656B VAL* 3.2 22.8 + - - -
666B ILE* 5.9 0.2 - - + -
670B ILE* 4.5 8.5 - - + -
671B CYS 3.4 9.6 - - - +
672B ALA* 4.9 3.4 - - + -
693B ILE* 1.3 74.9 - - - +
695B TYR* 1.3 62.1 + - - +
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Residues in contact with TYR 695 (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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643B PHE* 6.5 0.2 - - - -
655B HIS* 4.7 3.8 - - - -
656B VAL* 3.7 21.1 - - + -
658B ASN 4.1 9.6 - - - +
660B TYR* 3.8 34.5 - + + +
661B GLU 2.7 29.5 + - - -
663B ASP* 3.4 21.5 + - - +
670B ILE* 3.4 9.9 - - - +
671B CYS* 2.9 44.5 + - + +
672B ALA 4.0 8.0 + - - -
673B SER* 3.8 23.1 - - - -
693B ILE* 3.9 21.5 - - + -
694B ALA* 1.3 76.2 - - - +
696B THR* 1.3 73.6 + - - +
697B MET* 4.6 1.3 - - - -
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Residues in contact with THR 696 (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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655B HIS* 5.2 7.2 - - - -
656B VAL 5.2 0.6 + - - -
658B ASN 4.4 3.7 + - - -
659B SER* 3.3 33.0 - - - +
669B GLY* 3.6 12.6 - - - +
670B ILE* 3.7 15.3 - - + +
695B TYR* 1.3 75.0 - - - +
697B MET* 1.3 73.6 + - - +
869C MET* 4.3 12.1 - - + -
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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