Contacts of the strand formed by residues 646 - 652 (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 TYR 646 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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391A VAL* 3.7 29.2 - - + -
392A ASN* 3.5 24.7 - - - -
394A GLN* 4.6 0.5 - - - +
396A ILE* 4.3 0.7 - - + -
546A ILE* 3.6 25.2 - - + +
632A GLY 3.2 15.3 - - - +
633A ILE* 3.8 15.3 - - + -
634A ASP 4.4 0.9 - - - +
643A LYS* 5.1 0.4 - - - -
644A ALA 3.8 10.5 - - - -
645A ASN* 1.3 77.6 + - - +
647A GLY* 1.3 58.2 + - - +
658A ARG* 5.7 2.2 - - - -
661A PHE* 3.6 41.2 + + + +
662A ASN 4.2 0.7 + - - -
663A PRO* 3.7 24.7 - - + +
666A ASP* 2.7 40.7 + - - +
742A ARG* 4.5 1.6 - - - +
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Residues in contact with GLY 647 (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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631A ALA* 3.2 5.3 - - - +
632A GLY 2.9 29.9 + - - +
646A TYR* 1.3 75.3 - - - +
648A ALA* 1.3 61.8 + - - -
658A ARG* 4.9 12.8 - - - +
659A LEU 3.4 13.0 - - - -
660A ASN* 5.1 0.7 - - - -
661A PHE* 3.8 7.9 - - - -
710A TRP* 4.2 6.1 - - - -
742A ARG* 4.0 7.0 - - - +
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Residues in contact with ALA 648 (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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396A ILE* 4.3 6.3 - - + -
629A LEU* 4.0 20.9 - - + -
630A LYS 3.5 11.0 - - - +
631A ALA* 3.9 11.9 - - + -
647A GLY* 1.3 75.0 - - - +
649A VAL* 1.3 63.7 + - - +
657A VAL 3.9 0.2 - - - +
658A ARG* 3.4 6.6 - - - +
659A LEU* 2.8 39.4 + - + +
661A PHE* 3.9 13.7 - - + -
710A TRP* 4.6 1.1 - - - -
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Residues in contact with VAL 649 (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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629A LEU* 3.5 2.4 - - - +
630A LYS 3.0 32.0 + - - +
648A ALA* 1.3 80.2 - - - +
650A VAL* 1.3 63.3 + - - +
656A VAL* 4.3 2.7 - - + -
657A VAL 3.2 9.4 - - - +
658A ARG* 4.4 5.8 - - + -
710A TRP* 3.4 48.9 - - + -
712A TYR* 3.2 18.9 + - + +
740A VAL* 3.7 28.3 - - + -
762A ALA* 3.9 18.6 - - + -
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Residues in contact with VAL 650 (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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386A SER* 3.3 33.2 - - - +
542A PHE* 4.0 12.6 - - + -
626A SER* 4.5 2.2 - - - -
627A VAL 3.4 14.6 - - - +
628A GLY 4.0 1.1 - - - -
629A LEU* 4.0 18.6 - - + +
649A VAL* 1.3 77.9 - - - +
651A LEU* 1.3 72.9 + - - +
652A THR* 5.1 0.7 - - + -
656A VAL* 3.7 4.3 - - - +
657A VAL* 3.0 57.9 + - + +
659A LEU* 5.0 3.8 - - + -
712A TYR* 3.6 5.8 + - - -
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Residues in contact with LEU 651 (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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625A PHE* 5.5 0.3 - - - -
626A SER* 3.2 5.2 - - - -
627A VAL* 2.9 42.7 + - + +
650A VAL* 1.3 78.2 - - - +
652A THR* 1.3 61.6 + - - +
655A GLY 4.0 0.2 - - - -
656A VAL* 3.9 22.0 - - + -
686A PHE* 3.6 25.6 - - + -
695A LEU* 4.3 18.3 - - + +
712A TYR* 3.7 34.7 + - + -
714A PHE* 3.7 24.5 - - + -
738A ILE* 4.6 8.1 - - + -
740A VAL* 4.6 10.8 - - + -
764A ALA* 4.7 0.7 - - + -
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Residues in contact with THR 652 (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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400A PHE* 4.1 3.4 - - + -
542A PHE* 4.5 3.6 - - + -
578A LEU* 3.6 26.0 - - + +
624A ASN* 4.0 4.3 - - - -
625A PHE 3.3 7.9 - - - +
626A SER* 3.7 20.2 - - - -
650A VAL* 4.0 1.5 + - + -
651A LEU* 1.3 76.7 - - - +
653A ARG* 1.4 65.2 + - - +
654A GLY 3.1 3.1 + - - -
655A GLY 2.7 27.6 + - - +
657A VAL* 3.6 18.7 - - + +
683A PHE* 3.3 21.8 - - - -
686A PHE* 3.6 9.0 - - - -
695A LEU* 4.2 5.5 - - - +
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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