Contacts of the strand formed by residues 701 - 708 (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 GLY 701 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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662A THR 3.1 10.5 + - - -
663A ARG* 3.3 1.0 - - - -
664A ILE 2.7 31.7 + - - -
699A GLN 3.8 1.2 + - - -
700A PRO* 1.3 70.3 - - - +
702A ILE* 1.3 56.6 + - - -
771A ASP* 3.4 16.4 - - - -
772A ASN* 3.2 26.0 + - - -
904A IPH 4.9 0.2 - - - -
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Residues in contact with ILE 702 (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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664A ILE* 3.4 15.0 - - + +
666A PHE* 5.1 1.6 - - + -
684A LEU* 3.8 26.5 - - + -
687A ILE* 3.5 43.1 - - + -
688A ARG* 3.9 15.0 - - + -
700A PRO 3.8 2.0 - - - +
701A GLY* 1.3 74.4 - - - +
703A THR* 1.3 73.5 + - - +
704A PHE* 4.4 4.5 - - + +
769A TRP* 3.5 10.4 - - - -
770A ASP* 3.5 0.2 - - - -
771A ASP* 3.0 33.2 + - - +
904A IPH 3.2 34.1 - - + -
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Residues in contact with THR 703 (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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664A ILE 2.9 8.7 + - - -
665A ILE* 3.7 15.9 - - + -
666A PHE* 2.9 31.4 + - - +
702A ILE* 1.3 71.7 - - - +
704A PHE* 1.3 59.9 + - - +
705A ILE* 3.8 26.0 + - + +
767A VAL* 4.4 5.2 - - + -
769A TRP 3.3 7.6 - - - +
770A ASP* 2.6 30.9 + - + +
772A ASN* 3.0 14.9 + - - +
774A PHE* 3.5 16.9 - - + -
779A LEU* 4.7 2.9 - - + -
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Residues in contact with PHE 704 (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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666A PHE* 3.3 36.6 - + - -
668A ARG* 4.0 17.7 - - + -
679A VAL* 4.3 8.5 - - + -
680A LEU* 4.0 13.9 - - + -
683A GLU* 3.6 33.0 - - + -
684A LEU* 4.1 13.2 - - + -
687A ILE* 4.3 11.4 - - + -
702A ILE* 4.0 3.5 - - + -
703A THR* 1.3 71.9 - - - +
705A ILE* 1.3 64.5 - - - +
706A VAL* 4.1 4.9 - - + -
767A VAL* 3.5 4.0 - - - +
768A LEU* 2.8 56.1 + - + -
769A TRP* 2.7 31.9 + - + +
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Residues in contact with ILE 705 (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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665A ILE* 4.1 8.5 - - + -
666A PHE 2.9 12.9 + - - +
667A TYR* 3.4 43.1 - - + -
668A ARG* 2.6 35.3 + - - +
703A THR* 3.8 19.1 - - + -
704A PHE* 1.3 81.1 - - - +
706A VAL* 1.3 65.9 + - - +
707A VAL 3.8 0.3 + - - -
748A PHE* 6.0 0.9 - - + -
765A TYR* 4.2 14.4 - - + -
766A HIS 3.4 16.2 - - - +
767A VAL* 4.5 9.6 - - + +
779A LEU* 3.9 26.9 - - + -
783A THR* 5.0 0.7 - - - +
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Residues in contact with VAL 706 (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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668A ARG* 3.2 11.4 - - + +
671A VAL* 3.3 42.8 - - + +
676A PHE* 3.7 16.4 - - + -
679A VAL* 5.9 0.4 - - + -
704A PHE* 4.1 10.8 - - + -
705A ILE* 1.3 73.9 - - - +
707A VAL* 1.3 62.7 + - - +
708A GLN* 4.1 9.8 + - + +
764A HIS* 3.5 2.3 + - - +
765A TYR* 3.4 5.7 - - - -
766A HIS* 2.8 40.4 + - + +
768A LEU* 3.5 33.0 - - + -
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Residues in contact with VAL 707 (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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667A TYR* 3.8 29.6 - - + -
668A ARG 2.7 16.5 + - - +
669A ASP* 3.4 14.4 - - + +
670A GLY* 2.8 31.2 + - - -
705A ILE 4.3 0.9 - - - +
706A VAL* 1.3 74.3 - - - +
708A GLN* 1.3 63.4 + - - +
709A LYS 4.1 0.2 - - - -
763A SER* 4.6 3.8 - - - -
764A HIS 3.5 4.0 - - - +
765A TYR* 3.6 34.3 - - + -
799A ILE* 4.0 28.9 - - + -
800A PRO* 4.8 3.6 - - + -
803A ALA* 4.9 4.7 - - + -
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Residues in contact with GLN 708 (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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670A GLY* 4.9 4.3 - - - +
671A VAL 3.2 31.6 + - - +
672A SER* 3.4 16.4 - - - -
673A GLU* 4.1 9.8 + - - +
676A PHE* 3.8 19.0 - - - -
706A VAL* 4.1 4.3 + - + +
707A VAL* 1.3 77.2 - - - +
709A LYS* 1.3 60.7 + - - +
710A ARG 3.5 9.7 - - - +
711A HIS* 3.1 22.7 + - + +
763A SER* 4.6 0.9 - - - -
764A HIS* 2.9 58.6 + - + +
766A HIS* 5.4 0.4 - - - +
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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