Contacts of the strand formed by residues 694 - 699 (chain A) in PDB entry 6Q6Q
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 LYS 694 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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626A SER 4.2 0.9 - - - +
627A ILE* 3.7 1.4 - - - -
628A ASP* 2.8 55.9 + - + +
631A GLU* 5.6 2.2 - - - +
691A LYS 5.8 1.1 - - - +
692A ARG* 3.4 40.9 + - - +
693A VAL* 1.3 74.5 - - - +
695A ILE* 1.3 61.1 + - - +
696A VAL* 5.2 6.1 - - + +
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Residues in contact with ILE 695 (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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615A VAL* 4.0 20.6 - - + -
616A THR 5.3 2.5 - - - +
624A ILE* 4.3 7.2 - - + -
626A SER 3.6 11.2 - - - +
627A ILE* 4.2 17.5 - - + -
675A VAL* 3.9 27.4 - - + -
693A VAL* 3.8 19.7 + - + +
694A LYS* 1.3 79.2 - - - +
696A VAL* 1.3 66.5 + - - +
697A TYR* 3.5 48.1 - - + +
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Residues in contact with VAL 696 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
624A ILE* 4.0 1.2 - - - -
625A VAL* 3.3 33.4 + - + +
626A SER* 3.2 31.1 + - - +
694A LYS* 5.2 5.2 - - + +
695A ILE* 1.3 82.9 - - - +
697A TYR* 1.3 72.9 + - - +
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Residues in contact with TYR 697 (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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616A THR 4.2 2.3 + - - -
617A SER* 3.9 10.1 - - - -
618A SER* 3.2 35.7 + - - -
619A ARG* 3.5 54.0 + - + +
622A ALA* 3.9 12.6 - - + -
623A LYS 3.4 9.4 - - - -
624A ILE* 4.6 5.6 - - + -
625A VAL* 4.4 4.4 - - - +
668A VAL* 4.2 24.0 - - + -
675A VAL* 4.9 2.5 - - + +
695A ILE* 3.5 49.8 - - + +
696A VAL* 1.3 87.6 - - - +
698A GLN* 1.3 62.2 + - - +
699A ASP 4.3 0.4 - - - -
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Residues in contact with GLN 698 (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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619A ARG* 5.1 0.2 - - - +
622A ALA* 3.7 1.8 - - - -
623A LYS* 2.8 40.8 + - + +
625A VAL* 4.0 22.0 - - + +
697A TYR* 1.3 77.0 - - - +
699A ASP* 1.3 69.8 + - - +
700A LEU* 3.3 14.1 - - - +
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Residues in contact with ASP 699 (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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619A ARG* 2.7 41.2 + - - +
621A HIS 3.6 8.5 + - - +
622A ALA* 3.4 11.4 - - - +
697A TYR 4.3 0.2 - - - -
698A GLN* 1.3 81.9 + - - +
700A LEU* 1.3 65.4 + - - +
1225A GLN* 5.4 3.5 - - - +
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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