Contacts of the strand formed by residues 763 - 770 (chain A) in PDB entry 4Z4H
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 763 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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707A VAL* 4.6 3.8 - - - -
708A GLN 3.7 7.9 - - - -
709A LYS* 4.4 10.4 - - - +
749A TYR* 3.4 2.0 - - - -
750A LEU 2.9 40.7 + - - -
751A CYS* 4.6 0.4 - - - +
753A HIS* 5.5 0.4 - - - -
761A ARG 3.3 6.6 + - - -
762A PRO* 1.3 72.6 - - - +
764A HIS* 1.3 59.9 + - - +
765A TYR* 3.7 18.9 - - - -
798A SER* 2.6 29.1 + - - -
799A ILE* 3.5 12.4 - - - +
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Residues in contact with HIS 764 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A ARG* 5.6 7.0 + - - -
673A GLU* 5.9 2.5 - - + -
706A VAL 3.5 3.3 + - - +
707A VAL* 3.5 3.1 - - - +
708A GLN* 2.9 59.9 + - + +
711A HIS* 3.8 8.5 - - + -
747A ASP* 2.8 34.2 + - + +
748A PHE 3.6 9.4 - - - -
749A TYR* 3.4 47.3 + + + -
762A PRO 3.4 1.0 + - - -
763A SER* 1.3 71.9 - - - +
765A TYR* 1.3 74.4 + - - +
766A HIS* 3.8 16.9 - - + +
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Residues in contact with TYR 765 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
667A TYR* 4.3 2.2 - + - -
705A ILE* 4.2 14.4 - - + -
706A VAL 3.4 3.8 - - - -
707A VAL* 3.6 34.1 - - + -
747A ASP* 3.1 7.5 - - - +
748A PHE* 2.8 72.8 + + + +
750A LEU* 3.8 18.3 + - + +
752A SER* 4.8 0.7 + - - -
763A SER* 3.7 36.3 - - - -
764A HIS* 1.3 77.2 - - - +
766A HIS* 1.3 60.8 + - - +
767A VAL* 5.6 0.7 - - + -
783A THR* 3.4 26.4 - - + +
787A CYS* 4.2 5.0 - - - -
798A SER 3.9 1.4 + - - -
799A ILE* 3.9 5.5 - - - -
800A PRO* 3.3 23.4 - - + +
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Residues in contact with HIS 766 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A PRO* 5.3 0.2 - - + -
673A GLU* 5.7 2.4 - - + +
676A PHE* 3.5 33.3 - + + -
705A ILE* 3.4 2.5 - - - +
706A VAL* 2.8 41.7 + - + +
708A GLN* 5.4 0.4 - - - +
742A HIS* 4.3 17.0 - + + -
745A GLU* 2.7 36.5 + - + +
746A PHE 3.8 6.3 - - - -
747A ASP* 3.8 16.7 - - + +
764A HIS* 3.8 15.6 - - + +
765A TYR* 1.3 74.6 - - - +
767A VAL* 1.3 73.2 + - - +
768A LEU* 3.4 21.5 + - + +
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Residues in contact with VAL 767 (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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25A PRO* 3.8 3.5 - - - +
26A PRO* 3.4 20.8 - - + +
703A THR* 4.4 6.1 - - + -
704A PHE 3.5 6.3 - - - +
705A ILE* 4.5 8.5 - - + +
746A PHE* 2.9 43.4 + - + +
748A PHE* 5.2 5.8 - - + -
766A HIS* 1.3 80.9 - - - +
768A LEU* 1.3 58.4 + - - +
769A TRP 3.6 22.4 - - - +
770A ASP* 3.9 17.7 - - + -
779A LEU* 3.6 28.5 - - + -
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Residues in contact with LEU 768 (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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25A PRO* 3.5 24.8 - - + +
26A PRO* 3.4 11.9 - - - +
671A VAL* 6.0 0.2 - - + -
676A PHE* 3.7 55.6 - - + +
679A VAL* 5.8 1.3 - - + -
680A LEU* 3.6 35.3 - - + +
704A PHE* 2.8 18.6 + - + +
706A VAL* 3.5 30.3 - - + -
766A HIS* 3.7 18.8 - - + +
767A VAL* 1.3 73.6 - - - +
769A TRP* 1.3 63.7 + - - +
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Residues in contact with TRP 769 (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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22A ALA 3.7 15.7 - - - -
23A PHE* 3.6 20.6 - + - -
24A LYS 3.7 20.2 - - - -
26A PRO* 3.9 5.4 - - + -
680A LEU* 4.2 8.5 - - + -
684A LEU* 3.8 26.0 - - + -
688A ARG* 3.6 24.2 - - - +
702A ILE 3.5 21.1 - - - -
703A THR* 3.3 1.6 - - - -
704A PHE* 2.7 41.7 + - + -
767A VAL* 3.4 6.4 - - - +
768A LEU* 1.3 90.3 - - - +
770A ASP* 1.3 69.9 + - - +
771A ASP* 2.9 27.4 + - - -
904A IPH 4.3 0.4 + - - -
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Residues in contact with ASP 770 (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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26A PRO* 4.1 16.8 - - + +
702A ILE 3.5 1.8 - - - -
703A THR* 2.6 33.6 + - - -
746A PHE* 4.7 7.0 - - + -
767A VAL* 3.9 12.1 - - + +
769A TRP* 1.3 80.9 - - - +
771A ASP* 1.3 62.1 + - - +
772A ASN* 3.1 9.9 + - - +
773A ARG* 3.5 21.2 + - - -
774A PHE* 3.0 34.9 + - - +
779A LEU* 5.3 0.3 - - - +
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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