Contacts of the strand formed by residues 705 - 711 (chain A) in PDB entry 4WGK
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 705 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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698A LYS 3.8 0.2 - - - +
699A TYR* 3.6 6.2 - - - -
700A GLU* 2.9 29.8 + - - +
703A SER* 3.0 25.7 + - - -
704A THR* 1.3 78.4 - - - +
706A TRP* 1.3 69.7 + - - +
707A GLN* 4.0 10.2 + - - +
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Residues in contact with TRP 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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697A GLU* 3.5 26.4 - - + +
698A LYS 3.5 5.4 - - - -
699A TYR* 3.4 56.6 - + + -
705A SER* 1.3 80.2 - - - +
707A GLN* 1.3 63.6 - - - +
708A ILE* 4.3 0.9 + - - +
745A ILE* 3.7 19.5 - - + -
746A TYR 4.1 0.2 - - - -
747A ARG* 3.3 68.9 - - + +
774A ALA* 3.9 17.3 - - + -
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Residues in contact with GLN 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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697A GLU* 4.1 2.2 - - - -
698A LYS* 2.8 43.1 + - + +
700A GLU* 3.6 33.6 - - - +
703A SER* 3.9 9.5 + - - -
705A SER* 4.1 7.4 + - - +
706A TRP* 1.3 77.9 - - - +
708A ILE* 1.3 67.6 + - - +
709A VAL* 3.3 6.6 + - + +
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Residues in contact with ILE 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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335A LEU* 3.6 38.0 - - + +
695A THR* 4.0 21.3 - - + -
696A VAL 3.7 3.8 - - - -
697A GLU* 3.8 22.9 - - + +
706A TRP 4.3 1.1 + - - +
707A GLN* 1.3 71.5 - - - +
709A VAL* 1.3 59.2 + - - +
710A CYS 3.3 24.9 - - - +
711A ASN* 5.3 0.9 - - + -
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Residues in contact with VAL 709 (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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335A LEU* 3.5 13.6 - - - +
336A PRO* 5.1 1.7 - - - +
696A VAL* 2.7 15.6 + - + +
698A LYS* 3.7 27.8 - - + +
707A GLN* 3.5 16.2 - - + +
708A ILE* 1.3 74.4 - - - +
710A CYS* 1.3 72.2 + - - +
714A SER* 4.6 2.1 + - - -
716A GLU* 5.5 0.7 - - - +
735A TRP* 5.6 4.3 - - + -
742A GLN* 6.1 0.2 - - - +
746A TYR* 4.6 12.8 - - + +
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Residues in contact with CYS 710 (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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335A LEU* 4.5 2.2 - - - -
694A LEU* 5.2 0.2 - - - -
695A THR* 3.2 6.1 - - - -
696A VAL* 3.0 39.2 + - + -
708A ILE* 3.3 12.6 - - - +
709A VAL* 1.3 95.5 - - - +
711A ASN* 1.3 62.3 + - - +
714A SER* 3.5 7.9 - - - +
716A GLU* 3.5 31.0 - - - -
717A THR* 3.6 17.3 - - + -
735A TRP* 3.9 18.6 - - - -
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Residues in contact with ASN 711 (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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335A LEU* 4.1 15.9 - - + +
336A PRO* 3.1 29.9 + - - +
338A GLN* 4.7 5.7 - - - +
691A GLN 6.0 0.2 + - - -
692A THR* 3.6 18.2 - - + +
694A LEU* 3.3 15.0 - - - +
695A THR* 4.9 2.7 - - + -
708A ILE* 5.3 2.9 - - + -
710A CYS* 1.3 74.7 - - - +
712A ASP* 1.3 58.0 + - - +
713A ALA* 3.0 19.3 + - - +
714A SER* 3.1 19.2 + - - -
717A THR* 2.7 26.4 + - - -
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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