Contacts of the strand formed by residues 711 - 714 (chain A) in PDB entry 1Q6S
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 VAL 711 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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580A SER 4.2 3.4 + - - +
581A TYR* 3.7 25.4 - - + -
582A ILE* 2.9 26.3 + - - +
604A SER* 4.8 0.7 - - - -
606A GLY* 3.4 26.5 - - - +
608A VAL* 3.9 24.0 - - + -
698A VAL* 5.0 2.5 - - + -
703A SER* 4.3 9.9 + - - +
704A LEU* 3.5 34.2 - - + +
709A GLY 3.5 2.8 + - - -
710A PRO* 1.3 73.2 - - - +
712A VAL* 1.3 63.5 + - - +
713A VAL* 3.9 9.2 - - + -
725A PHE* 5.7 0.4 - - + -
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Residues in contact with VAL 712 (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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582A ILE* 3.4 21.8 - - + +
584A THR* 3.7 27.6 - - + -
595A PHE* 3.8 20.2 - - + -
598A MET* 4.2 9.4 - - + -
599A VAL* 4.1 15.3 - - + -
604A SER* 3.5 25.4 - - - +
606A GLY 3.1 10.3 + - - +
607A VAL* 3.2 9.6 - - + +
608A VAL* 2.6 34.3 + - - +
710A PRO 4.2 0.7 - - - +
711A VAL* 1.3 72.3 - - - +
713A VAL* 1.3 57.4 + - - +
714A HIS* 5.1 0.4 - - + +
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Residues in contact with VAL 713 (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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581A TYR* 4.7 1.1 - - + -
582A ILE 2.7 13.0 + - - +
583A LEU* 3.3 6.9 - - + -
584A THR* 3.0 23.9 + - - +
608A VAL* 3.4 16.8 - - + +
610A LEU* 4.0 13.5 - - + -
711A VAL* 3.9 21.3 - - + -
712A VAL* 1.3 77.1 - - - +
714A HIS* 1.3 64.3 + - - +
722A SER* 3.4 31.0 + - - +
725A PHE* 4.1 15.9 - - + -
726A CYS* 3.9 23.3 - - - -
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Residues in contact with HIS 714 (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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584A THR* 3.0 31.9 - - + +
585A GLN 4.0 5.2 - - - +
586A GLY* 3.7 3.4 - - - -
587A PRO* 4.2 1.3 - - + -
595A PHE* 4.2 9.9 - + - -
607A VAL* 4.1 11.4 - - + -
608A VAL 2.8 17.3 + - - +
609A MET* 3.5 22.3 - - + +
610A LEU* 2.8 27.2 + - - +
611A ASN* 3.2 18.8 - - - -
621A CYS* 4.1 6.3 - - - -
624A TYR* 2.6 38.6 + + - -
712A VAL* 5.3 0.2 - - + -
713A VAL* 1.3 76.3 - - - +
715A CYS* 1.3 74.7 + - - +
722A SER* 3.2 10.9 + - - -
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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