Contacts of the strand formed by residues 662 - 670 (chain B) in PDB entry 6X34
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 TRP 662 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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650B VAL* 3.4 29.1 - - + +
658B GLN* 4.4 4.9 - - + -
659B TYR* 2.8 50.2 + - + -
660B SER* 3.3 21.1 + - - +
661B LYS* 1.3 88.2 - - - +
663B TYR* 1.3 61.4 + - - +
664B PHE* 5.7 0.2 - - - -
686B TRP* 4.7 22.6 - + + -
746B CYS 4.5 3.1 - - - +
747B CYS* 4.6 2.3 - - - +
748B LEU* 4.0 23.6 + - + +
750B LEU* 4.8 3.1 - - + -
808B TYR* 5.0 5.4 - - - -
809B ALA* 3.3 14.1 - - + -
810B PRO 3.6 23.6 - - - -
811B CYS* 4.5 12.6 - - + -
813B GLU* 3.9 17.5 - - + -
814B ALA* 3.6 33.9 - - + -
1007B TYR* 5.2 7.2 - - + -
1009B ALA* 5.3 0.4 - - + -
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Residues in contact with TYR 663 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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662B TRP* 1.3 76.4 - - - +
664B PHE* 1.3 65.3 + - - +
665B GLU* 4.7 4.3 - - + +
745B SER* 3.1 35.6 - - - -
746B CYS 3.8 12.3 - - - -
747B CYS* 4.3 14.6 - - + -
758B ARG* 4.1 11.0 - - + +
761B GLY* 6.2 0.2 - - - -
793B LEU 4.5 1.0 - - - +
800B PHE* 3.9 28.7 - + - -
802B PHE* 4.3 12.4 + - - +
803B LEU 4.7 3.3 + - - -
804B PRO* 4.0 18.8 - - + -
805B PRO* 3.6 29.2 - - + +
808B TYR* 4.2 16.4 - + + -
809B ALA 2.9 13.0 + - - +
810B PRO* 3.3 7.3 - - - +
811B CYS* 3.1 23.0 + - - +
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Residues in contact with PHE 664 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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663B TYR* 1.3 84.8 - - - +
665B GLU* 1.3 57.0 + - - +
666B VAL* 4.1 15.5 - - + -
684B VAL* 4.6 15.0 - - + -
685B GLY 5.4 1.1 - - - -
686B TRP* 3.6 22.7 - + - -
745B SER* 2.3 28.6 + - - -
746B CYS* 3.5 33.4 + - - -
779B PRO* 3.5 22.2 - - + -
791B PHE* 3.6 35.4 - + - -
792B LEU 4.1 8.3 - - - +
793B LEU 4.2 3.6 - - - +
800B PHE* 4.8 3.1 - - - -
811B CYS* 3.7 26.0 - - + -
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Residues in contact with GLU 665 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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663B TYR* 4.7 6.1 - - + +
664B PHE* 1.3 73.4 - - - +
666B VAL* 1.3 66.8 + - - +
743B VAL* 3.8 21.1 - - + -
744B VAL 4.3 0.7 - - - -
745B SER* 3.8 19.3 - - - -
792B LEU* 3.4 31.2 + - + +
800B PHE* 4.4 18.3 - - + -
801B LYS* 6.0 2.0 - - + +
802B PHE* 5.7 7.0 - - + +
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Residues in contact with VAL 666 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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664B PHE* 4.1 11.0 - - + -
665B GLU* 1.3 79.8 - - - +
667B MET* 1.3 61.4 + - - +
684B VAL* 4.7 22.9 - - + -
742B ASP 3.8 0.9 - - - +
743B VAL* 3.4 8.7 - - - +
744B VAL* 3.4 37.4 + - + +
781B VAL* 6.2 2.5 - - + -
789B VAL* 4.7 13.0 - - + -
790B ARG 3.5 13.0 - - - +
791B PHE* 3.6 37.2 - - + -
792B LEU* 4.7 1.8 - - - +
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Residues in contact with MET 667 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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666B VAL* 1.3 75.9 - - - +
668B VAL* 1.3 60.0 + - - +
741B GLU* 5.6 3.4 - - - -
742B ASP 3.7 8.7 - - - +
743B VAL* 4.6 13.5 - - + -
789B VAL* 3.4 5.5 - - - +
790B ARG* 2.6 50.7 + - + +
792B LEU* 4.8 7.1 - - + +
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Residues in contact with VAL 668 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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667B MET* 1.3 74.3 - - - +
669B ASP* 1.3 59.9 + - - +
671B VAL* 4.7 18.4 - - + -
682B LEU* 6.4 2.5 - - + -
738B LEU* 5.0 8.1 - - + -
739B ALA 4.5 13.9 - - - +
740B PRO* 5.3 1.1 - - + -
741B GLU* 3.1 27.6 + - - +
742B ASP* 3.6 12.4 + - + +
787B VAL* 6.1 0.9 - - + -
788B LYS 4.1 6.3 - - - +
789B VAL* 4.2 8.5 - - + -
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Residues in contact with ASP 669 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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667B MET 3.9 2.6 + - - -
668B VAL* 1.3 74.6 - - - +
670B GLU* 1.3 63.5 + - + +
740B PRO* 4.8 4.8 - - - +
741B GLU* 4.5 7.7 + - - +
788B LYS* 2.9 32.5 + - + +
789B VAL* 5.0 3.1 - - - -
790B ARG* 5.4 3.8 - - + +
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Residues in contact with GLU 670 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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668B VAL 3.8 0.4 - - - -
669B ASP* 1.3 83.4 - - + +
671B VAL* 1.3 70.2 + - - +
672B VAL* 5.9 0.9 - - + -
740B PRO* 5.4 4.3 - - - -
786B GLY 4.4 3.1 - - - +
787B VAL* 3.9 4.0 - - - +
788B LYS* 3.5 23.8 + - + +
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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