Contacts of the strand formed by residues 700 - 705 (chain A) in PDB entry 5VOT
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 TYR 700 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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504A ILE* 5.2 1.4 - - - +
645A ILE* 3.8 2.7 - - - -
646A ALA* 3.2 27.1 - - + -
647A TYR* 3.5 5.6 - - - -
648A GLY* 3.0 28.5 + - - -
681A VAL* 2.8 25.2 + - + -
683A VAL* 5.0 0.3 - - - +
692A ARG* 3.2 52.4 + - + +
693A VAL* 3.3 47.5 - - + +
696A SER* 3.2 20.0 - - - +
698A GLY* 3.5 3.7 - - - -
699A LYS* 1.3 80.7 + - - +
701A ALA* 1.3 70.6 + - - +
702A TYR* 4.2 13.3 - + - -
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Residues in contact with ALA 701 (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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502A ILE* 4.9 2.0 - - + -
503A MET 3.6 12.1 - - - +
504A ILE* 4.0 16.2 - - + -
639A LEU* 4.2 17.9 - - + -
645A ILE* 3.6 10.3 - - + +
646A ALA 2.6 14.5 + - - +
647A TYR* 3.1 31.6 - - + +
648A GLY 3.6 0.3 + - - -
700A TYR* 1.3 86.6 - - - +
702A TYR* 1.3 60.7 + - - +
703A LEU* 6.3 0.4 - - + -
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Residues in contact with TYR 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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502A ILE* 3.8 1.9 - - - +
503A MET* 2.9 50.0 + - + +
648A GLY 4.0 10.3 - - - -
649A THR 4.5 5.8 - - - -
650A LEU* 3.6 23.8 - - - +
683A VAL* 4.1 13.3 - - + +
686A THR* 4.1 26.9 + - + +
689A GLY* 4.0 27.1 - - - -
690A VAL* 5.7 1.3 - - + -
693A VAL* 3.6 18.3 - - + +
700A TYR* 4.2 12.1 - + - -
701A ALA* 1.3 74.1 - - - +
703A LEU* 1.3 86.7 + - - +
704A LEU* 3.5 32.5 - - + +
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Residues in contact with LEU 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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500A ILE* 4.7 10.8 - - + -
501A SER 3.7 3.6 - - - +
502A ILE* 3.6 35.4 - - + -
636A ALA* 6.3 0.2 - - + -
639A LEU* 5.3 5.4 - - + -
647A TYR* 4.5 9.6 - - + -
648A GLY 3.4 8.9 + - - +
649A THR* 3.7 30.1 - - + +
650A LEU 5.1 0.3 + - - -
655A THR* 5.1 3.9 - - + +
659A PHE* 3.5 33.0 - - + -
670A MET* 4.4 17.3 - - + -
674A MET* 4.4 10.1 - - - -
701A ALA* 6.3 0.2 - - + -
702A TYR* 1.3 92.1 - - - +
704A LEU* 1.3 65.5 + - - +
727A LEU* 5.9 1.8 - - + -
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Residues in contact with LEU 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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500A ILE* 4.8 4.6 - - - +
501A SER* 2.3 46.2 + - - +
503A MET* 3.7 46.4 - - + -
655A THR* 5.4 6.3 - - - -
686A THR* 5.0 8.1 - - + -
702A TYR* 3.5 20.6 - - + +
703A LEU* 1.3 78.1 - - - +
705A GLU* 1.3 58.0 + - - +
708A MET* 3.6 17.7 - - + -
709A ASN* 3.5 33.2 - - - +
712A ILE* 5.8 0.9 - - + -
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Residues in contact with GLU 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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450A TYR* 5.2 7.0 + - - -
480A THR* 2.6 30.6 + - - +
498A LEU* 3.3 26.6 - - + +
499A GLY 3.4 9.6 - - - +
500A ILE* 4.5 4.7 - - + +
501A SER* 2.8 9.0 + - - +
654A SER* 4.3 3.6 + - - -
655A THR* 4.9 12.5 + - - +
704A LEU* 1.3 78.0 - - - +
706A SER* 1.3 67.1 + - - +
707A THR* 3.3 8.1 + - - +
708A MET* 3.9 7.6 + - - -
709A ASN* 3.4 13.7 + - - +
730A LYS* 5.2 3.6 - - + +
732A TYR* 2.1 36.7 + - - -
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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