Contacts of the strand formed by residues 735 - 743 (chain A) in PDB entry 6RUT
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 PHE 735 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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714A PHE 3.2 16.2 - - - +
715A ASP* 4.5 0.4 - - - -
716A SER* 3.6 7.9 + - - -
734A GLY* 1.3 79.6 - - - +
736A SER* 1.3 65.2 + - - +
737A VAL* 4.9 4.3 - - + -
769A ILE* 3.7 30.1 - - + -
770A GLN* 3.6 18.3 - - - +
771A SER* 3.1 47.3 + - - +
774A GLN* 3.9 27.6 - - + -
776A LEU* 3.5 42.4 - - + -
789A VAL* 3.8 19.5 - - + -
791A ALA* 4.4 4.0 - - + -
800A ASP* 5.9 0.4 - - - -
802A TYR* 4.9 4.9 - - - -
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Residues in contact with SER 736 (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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693A VAL* 3.9 25.6 - - - +
712A TYR 3.8 0.3 - - - +
713A ILE* 4.6 0.2 - - - +
714A PHE* 2.9 42.4 + - - +
735A PHE* 1.3 77.5 - - - +
737A VAL* 1.3 64.9 + - - +
738A ILE* 4.4 0.4 - - - +
766A GLN* 3.0 21.8 + - - +
769A ILE 3.8 8.3 - - - -
770A GLN* 4.3 3.3 - - - +
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Residues in contact with VAL 737 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
711A SER* 4.3 13.7 - - - +
712A TYR 3.1 9.2 - - - +
713A ILE* 3.6 35.2 - - + -
735A PHE* 4.9 4.0 - - + -
736A SER* 1.3 81.4 + - - +
738A ILE* 1.3 65.7 + - - +
739A THR* 5.1 0.9 - - - +
766A GLN* 3.1 7.6 + - - -
767A SER* 2.7 46.8 + - - +
769A ILE* 3.2 37.3 + - + +
779A VAL* 4.8 6.5 - - + -
809A PHE* 5.3 1.8 - - + -
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Residues in contact with ILE 738 (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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651A LEU* 4.6 10.1 - - + -
686A PHE* 5.0 3.6 - - + -
690A GLU* 4.0 20.2 - - + +
693A VAL* 3.7 32.8 - - + -
695A LEU* 6.2 0.7 - - + -
710A TRP 3.4 3.3 - - - +
711A SER* 3.7 1.0 - - - -
712A TYR* 2.9 42.6 + - + +
714A PHE* 4.1 19.7 - - + -
736A SER* 5.0 0.4 - - - +
737A VAL* 1.3 76.9 - - - +
739A THR* 1.3 74.6 + - - +
740A VAL* 4.3 7.0 - - + -
764A ALA* 4.0 12.8 - - + -
765A VAL 3.7 16.8 - - - +
766A GLN* 4.6 9.0 - - + -
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Residues in contact with THR 739 (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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709A LEU* 4.3 22.2 - - + -
710A TRP 3.3 8.0 + - - +
711A SER* 5.0 4.8 + - - +
737A VAL* 5.1 1.0 - - - +
738A ILE* 1.3 72.6 - - - +
740A VAL* 1.3 62.3 + - - +
741A SER* 5.1 1.6 - - - +
763A LEU 3.4 2.0 - - - +
764A ALA* 3.4 2.4 - - - -
765A VAL* 2.8 42.9 + - + +
767A SER* 3.2 13.8 - - - +
806A ASN 5.2 0.4 - - - +
807A GLY* 3.0 42.9 + - - -
809A PHE* 4.1 5.4 - - - -
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Residues in contact with VAL 740 (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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649A VAL* 3.7 33.9 - - + -
651A LEU* 4.6 2.5 - - + -
656A VAL* 3.7 21.8 - - + -
709A LEU* 3.7 7.9 - - - +
710A TRP* 3.0 45.1 + - + -
712A TYR* 3.7 27.4 - - + -
738A ILE* 4.3 6.5 - - + -
739A THR* 1.3 77.9 - - - +
741A SER* 1.3 62.3 + - - +
762A ALA* 4.1 7.0 - - + -
763A LEU 3.3 4.0 - - - +
764A ALA* 4.2 11.7 - - + -
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Residues in contact with SER 741 (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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709A LEU* 3.5 23.3 - - - -
710A TRP* 4.6 4.7 - - - -
739A THR* 5.4 2.5 - - - -
740A VAL* 1.3 73.3 - - - +
742A ARG* 1.3 67.6 + - - +
743A THR* 4.4 2.3 - - - +
762A ALA* 3.1 8.8 - - - +
763A LEU* 2.8 53.7 + - - +
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Residues in contact with ARG 742 (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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632A GLY 2.9 29.1 + - - -
634A ASP* 3.3 46.7 + - - +
636A ASN* 6.1 0.2 - - - +
646A TYR 5.7 0.2 - - - -
647A GLY* 4.0 7.7 - - - +
658A ARG* 3.8 31.6 - - - +
703A TYR* 2.8 27.1 + - - -
708A GLY* 3.4 25.0 + - - +
710A TRP* 3.8 21.9 - - + -
741A SER* 1.3 78.2 - - - +
743A THR* 1.3 65.2 + - - +
746A GLU* 3.8 9.4 - - - +
761A SER 3.6 5.8 - - - -
762A ALA* 4.6 0.9 - - - +
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Residues in contact with THR 743 (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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741A SER* 4.3 4.3 - - - +
742A ARG* 1.3 79.0 - - - +
744A GLY* 1.3 62.3 + - - +
746A GLU* 3.4 8.5 - - - +
760A PRO 3.7 1.0 - - - -
761A SER* 2.7 61.2 + - - +
762A ALA 3.8 3.8 + - - -
763A LEU* 3.9 31.0 - - + -
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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