Contacts of the strand formed by residues 661 - 667 (chain A) in PDB entry 5W6V
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 ARG 661 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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583A ALA 4.7 3.4 + - - -
584A VAL* 4.1 42.0 + - - +
587A GLN* 3.9 30.0 + - - +
588A PRO 3.5 1.8 + - - -
589A VAL* 3.5 18.3 - - + +
590A ILE 3.3 22.2 + - - -
659A PRO* 3.3 4.4 - - - +
660A THR* 1.3 88.8 + - - +
662A ILE* 1.3 68.6 + - - +
663A ILE* 4.7 2.2 - - + -
699A GLY 3.3 5.6 - - - +
770A ASN* 3.2 48.2 + - - +
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Residues in contact with ILE 662 (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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590A ILE* 3.7 17.0 - - + -
592A LEU* 4.2 27.4 - - + -
644A VAL* 5.3 1.8 - - + -
648A LEU* 4.4 15.7 - - + -
659A PRO* 4.8 1.8 - - + -
661A ARG* 1.3 79.4 - - - +
663A ILE* 1.3 66.3 + - - +
664A PHE* 4.6 6.5 - - + -
685A ILE* 4.3 22.2 - - + -
689A CYS* 3.9 28.3 - - - -
696A TYR* 4.9 0.2 - - - +
698A PRO* 4.0 14.6 - - + -
699A GLY 2.7 12.7 + - - +
700A ILE* 3.4 9.7 - - + +
701A THR 2.8 28.9 + - - +
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Residues in contact with ILE 663 (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 VAL* 5.3 1.8 - - + -
589A VAL* 3.9 19.1 - - + -
590A ILE 3.1 5.7 + - - +
591A PHE* 3.5 31.0 - - + +
592A LEU* 2.8 33.3 + - - +
661A ARG* 4.7 2.9 - - + -
662A ILE* 1.3 77.5 - - - +
664A PHE* 1.3 55.9 + - - +
665A TYR* 3.6 29.8 - - + +
701A THR* 3.7 6.5 - - + +
703A ILE* 4.2 13.7 - - + -
770A ASN* 3.8 12.3 - - - +
772A PHE* 3.7 33.2 - - + -
777A LEU* 5.3 0.2 - - + -
780A LEU* 4.8 6.5 - - + -
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Residues in contact with PHE 664 (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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592A LEU* 3.6 37.0 - - + -
594A ALA* 3.5 25.8 - - + -
612A VAL* 4.4 3.4 - - + -
637A ILE* 5.1 0.2 - - + -
640A LEU* 4.2 28.7 - - + -
662A ILE* 4.6 6.7 - - + -
663A ILE* 1.3 72.2 - - - +
665A TYR* 1.3 61.1 + - - +
666A ARG* 3.8 22.2 - - + -
681A GLU* 4.3 0.9 - - - -
685A ILE* 3.9 21.1 - - + -
700A ILE* 5.2 1.1 - - + -
701A THR 2.8 16.4 + - - +
702A TYR* 3.5 39.3 - + + -
703A ILE* 2.8 30.1 + - - +
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Residues in contact with TYR 665 (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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591A PHE* 4.7 1.3 - + - -
592A LEU 2.9 16.5 + - - +
593A GLY* 3.4 4.3 - - - -
594A ALA* 3.0 26.3 + - - +
663A ILE* 3.6 25.8 - - + +
664A PHE* 1.3 76.4 - - - +
666A ARG* 1.3 59.5 + - - +
703A ILE* 3.4 30.9 - - + +
705A VAL* 3.7 24.5 - - + -
763A TYR* 4.3 1.8 - + - -
777A LEU* 4.6 1.2 + - - +
780A LEU* 4.4 6.4 - - - +
781A THR* 2.6 40.1 + - + -
784A LEU* 3.6 25.0 - - + +
798A PRO* 3.8 22.4 - - + -
800A PRO* 4.9 5.4 - - + -
801A ALA* 4.5 14.9 - - + +
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Residues in contact with ARG 666 (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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594A ALA* 3.7 21.5 - - - -
595A ASP* 4.8 0.2 - - - +
596A VAL* 3.9 10.9 - - - +
635A GLU 2.8 26.1 + - - -
637A ILE* 3.8 11.4 - - - +
664A PHE* 3.8 9.4 + - + -
665A TYR* 1.3 71.7 - - - +
667A ASP* 1.3 86.0 + - - +
668A GLY 3.8 8.9 + - - -
669A VAL* 3.5 23.8 - - + +
677A ILE* 3.7 12.4 - - - +
681A GLU* 2.7 39.2 + - - -
702A TYR* 3.4 22.6 + - + +
703A ILE 2.8 14.8 + - - +
704A VAL* 3.5 5.7 - - + +
705A VAL* 2.8 32.8 + - - +
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Residues in contact with ASP 667 (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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594A ALA 2.8 20.9 + - - +
595A ASP* 3.5 16.9 - - + +
666A ARG* 1.3 101.2 + - - +
668A GLY* 1.3 75.2 + - - +
669A VAL 3.5 1.8 - - - -
705A VAL* 3.3 19.9 - - + +
707A LYS* 5.2 4.6 + - - +
797A ILE* 3.6 18.6 - - - +
801A ALA* 4.3 15.5 - - + +
805A ARG* 2.6 38.1 + - - -
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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