Contacts of the strand formed by residues 690 - 695 (chain A) in PDB entry 5TO4
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 ALA 690 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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682A LEU* 3.8 18.8 - - + +
685A VAL 4.6 8.1 - - - +
687A ARG* 3.2 19.2 + - + +
688A ASP 3.4 0.2 - - - -
689A GLY* 1.3 78.3 - - - +
691A PHE* 1.3 59.3 + - - +
706A PHE* 3.0 5.2 - - - +
707A ARG* 2.9 33.8 + - + -
754A TYR* 3.2 21.9 - - + +
756A ILE* 4.3 9.2 - - + -
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Residues in contact with PHE 691 (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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668A TRP* 3.6 26.9 - + + -
682A LEU* 4.0 3.5 - - - +
689A GLY 3.9 5.8 - - - +
690A ALA* 1.3 75.9 - - - +
692A LEU* 1.3 70.5 + - - +
693A VAL* 4.6 5.4 - - + -
704A ILE* 4.7 1.6 - - + -
705A SER 3.2 12.6 - - - +
706A PHE* 3.8 1.8 - - + -
738A ILE* 3.9 15.7 - - + -
742A GLU* 3.8 20.9 - - - -
752A LEU* 3.7 52.9 - - + -
753A ARG 4.3 0.7 - - - -
754A TYR 2.8 17.6 + - - -
755A PRO* 3.3 33.4 - - + +
756A ILE* 2.8 35.5 + - - +
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Residues in contact with LEU 692 (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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668A TRP 3.4 13.5 - - - +
670A HIS* 3.7 9.2 - - + +
673A LEU* 3.8 33.4 - - + -
678A ALA* 4.0 26.7 - - + +
681A MET* 3.9 20.9 - - + -
682A LEU* 4.5 5.2 - - + -
691A PHE* 1.3 80.5 - - - +
693A VAL* 1.3 79.4 + - - +
694A ARG* 4.2 4.7 - - + +
704A ILE* 3.5 6.1 - - - +
705A SER* 2.9 43.0 + - - +
756A ILE* 3.9 11.4 - - + +
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Residues in contact with VAL 693 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
668A TRP* 2.7 36.9 + - + +
669A TYR* 3.4 8.0 - - + -
670A HIS* 2.9 29.3 + - - -
691A PHE* 4.6 3.8 - - + -
692A LEU* 1.3 81.3 - - - +
694A ARG* 1.3 65.5 + - - +
702A TYR* 4.2 11.0 - - + -
703A ALA 3.2 12.3 - - - +
704A ILE* 4.3 7.6 - - + -
734A LEU* 3.9 29.4 - - + -
738A ILE* 3.6 25.1 - - + -
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Residues in contact with ARG 694 (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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669A TYR* 4.4 5.4 - - - -
670A HIS 3.4 10.1 - - - +
673A LEU* 3.4 30.8 + - + +
674A THR 3.8 8.9 - - - -
675A ARG* 3.5 35.5 - - - +
678A ALA* 3.9 12.0 - - - +
692A LEU* 4.2 7.0 - - + -
693A VAL* 1.3 75.7 - - - +
695A LYS* 1.3 64.5 + - - +
696A ARG* 4.2 14.3 - - - +
702A TYR* 3.3 4.5 - - - +
703A ALA* 2.8 57.1 + - + +
705A SER* 2.9 15.5 + - - -
714A HIS* 3.1 32.9 + - - +
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Residues in contact with LYS 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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669A TYR* 3.5 15.5 + - - +
670A HIS 3.4 7.7 + - - -
671A ALA* 3.8 19.6 + - - +
673A LEU 4.1 14.4 + - - +
694A ARG* 1.3 76.5 + - - +
696A ARG* 1.3 67.8 + - - +
698A GLU 2.7 29.3 + - - -
699A PRO* 2.9 23.6 + - - +
700A ASN* 5.0 0.2 - - - +
701A SER 3.0 13.9 + - - +
702A TYR* 3.5 30.7 - - + -
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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