Contacts of the strand formed by residues 703 - 707 (chain A) in PDB entry 6A69
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 THR 703 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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470A THR 2.7 15.8 + - - +
471A ALA* 3.4 17.0 - - - +
698A GLN* 4.5 14.1 - - - +
701A GLY 3.6 13.9 - - - +
702A ILE* 1.3 71.6 - - - +
704A VAL* 1.3 66.1 + - - +
705A ARG* 2.4 42.3 + - - +
763A ARG* 4.3 22.7 - - - +
790A GLN* 5.6 1.2 + - - -
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Residues in contact with VAL 704 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472A ILE* 3.9 18.4 - - + +
474A SER* 4.9 6.1 - - - -
480A LEU* 6.0 2.7 - - + -
694A ILE* 4.4 22.2 - - + +
697A CYS* 4.6 17.0 - - + -
698A GLN* 4.5 7.5 + - - +
702A ILE* 3.7 3.2 + - + +
703A THR* 1.3 72.4 - - - +
705A ARG* 1.3 69.1 + - - +
706A MET* 4.1 1.3 - - - +
724A ILE* 3.9 32.5 - - + +
763A ARG* 3.9 15.8 + - - +
835A PHE* 3.8 33.0 - - + -
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Residues in contact with ARG 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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471A ALA* 3.5 16.7 - - + +
472A ILE 3.2 11.9 + - - +
473A CYS* 3.3 21.4 - - - -
474A SER 3.3 16.2 + - - -
703A THR* 2.4 39.9 + - - +
704A VAL* 1.3 78.1 - - - +
706A MET* 1.3 66.4 + - - +
707A VAL* 3.5 6.4 + - + +
759A TRP* 3.9 25.3 + - - +
760A PRO* 3.7 28.5 - - - +
762A LEU* 3.3 28.5 + - - +
763A ARG* 3.9 18.1 - - + +
776A LEU* 5.4 7.2 - - + -
780A ILE* 5.3 8.4 - - - +
790A GLN* 5.2 7.7 + - - +
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Residues in contact with MET 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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474A SER* 4.0 9.6 - - - +
475A ASP 4.7 2.5 - - - +
476A LYS* 3.7 39.5 - - + +
480A LEU* 4.4 17.0 - - + -
704A VAL* 4.1 4.3 - - + +
705A ARG* 1.3 72.3 - - - +
707A VAL* 1.3 68.6 + - - +
708A THR* 4.9 2.9 - - + +
715A ALA* 3.5 44.6 - - + +
718A ILE* 5.0 5.4 - - + -
719A ALA* 4.3 10.3 - - + +
724A ILE* 4.2 14.9 - - + +
763A ARG 3.0 15.2 + - - +
764A VAL* 3.4 14.9 - - + +
765A LEU 3.1 21.5 + - - -
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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
----------------------------------------------------------
473A CYS* 4.7 7.2 - - + -
474A SER 3.0 12.9 + - - +
475A ASP* 2.9 31.3 - - - +
705A ARG* 3.9 9.9 - - + +
706A MET* 1.3 81.0 - - - +
708A THR* 1.3 64.7 + - - +
765A LEU* 3.7 29.4 - - + +
768A SER* 3.9 20.4 - - - +
773A LYS* 4.3 26.5 - - + -
776A LEU* 4.1 22.2 - - + -
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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