Contacts of the strand formed by residues 662 - 670 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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650H VAL* 3.4 29.5 - - + +
658H GLN* 4.4 4.9 - - + -
659H TYR* 2.8 48.7 + - + -
660H SER* 3.3 21.3 + - - +
661H LYS* 1.3 86.5 - - - +
663H TYR* 1.3 62.7 + - - +
686H TRP* 4.7 22.5 - + + -
746H CYS 4.5 2.9 - - - +
747H CYS* 4.6 2.1 - - - +
748H LEU* 4.0 23.4 + - + +
750H LEU* 4.8 3.4 - - + -
808H TYR* 5.0 5.3 - - - -
809H ALA* 3.3 14.4 - - + -
810H PRO 3.6 23.6 - - - -
811H CYS* 4.5 12.1 - - + -
813H GLU* 3.9 17.5 - - + -
814H ALA* 3.6 32.3 - - + -
1007H TYR* 5.2 7.2 - - + -
1009H ALA* 5.3 1.3 - - + -
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Residues in contact with TYR 663 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
662H TRP* 1.3 76.6 - - - +
664H PHE* 1.3 66.0 + - - +
665H GLU* 4.7 4.7 - - + +
745H SER* 3.1 36.3 - - - -
746H CYS 3.8 11.9 - - - -
747H CYS* 4.3 14.1 - - - -
758H ARG* 4.1 11.0 - - + +
761H GLY* 6.2 0.2 - - - -
793H LEU 4.5 0.5 - - - +
800H PHE* 3.9 28.5 - + - -
802H PHE* 4.3 12.0 + - - +
803H LEU 4.7 3.5 + - - -
804H PRO* 4.0 19.1 - - + -
805H PRO* 3.6 28.2 - - + +
808H TYR* 4.2 16.2 - + + -
809H ALA 2.9 13.9 + - - +
810H PRO* 3.3 7.7 - - + +
811H CYS* 3.1 22.9 + - - +
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Residues in contact with PHE 664 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
663H TYR* 1.3 84.8 - - - +
665H GLU* 1.3 57.1 + - - +
666H VAL* 4.1 16.2 - - + -
684H VAL* 4.6 14.6 - - + -
685H GLY 5.4 0.7 - - - -
686H TRP* 3.6 23.6 - + - -
745H SER* 2.3 29.3 + - - -
746H CYS* 3.5 33.8 + - - -
779H PRO* 3.5 23.6 - - + -
791H PHE* 3.6 35.0 - + - -
792H LEU 4.1 9.6 - - - +
793H LEU 4.2 3.8 - - - +
800H PHE* 4.8 3.1 - - - -
811H CYS* 3.7 25.4 - - + -
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Residues in contact with GLU 665 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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663H TYR* 4.7 6.7 - - + +
664H PHE* 1.3 74.4 - - - +
666H VAL* 1.3 66.6 + - - +
743H VAL* 3.8 21.3 - - + -
744H VAL 4.3 0.4 - - - -
745H SER* 3.8 18.2 - - - -
792H LEU* 3.4 31.0 + - + +
800H PHE* 4.4 17.6 - - + -
801H LYS* 6.0 2.5 - - + +
802H PHE* 5.7 7.2 - - + +
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Residues in contact with VAL 666 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
664H PHE* 4.1 11.2 - - + -
665H GLU* 1.3 79.8 - - - +
667H MET* 1.3 59.8 + - - +
684H VAL* 4.7 22.7 - - + -
742H ASP 3.8 0.9 - - - +
743H VAL* 3.4 8.5 - - - +
744H VAL* 3.4 37.0 + - + +
745H SER* 5.7 0.2 - - - -
781H VAL* 6.2 2.9 - - + -
789H VAL* 4.7 12.3 - - + -
790H ARG 3.5 13.9 - - - +
791H PHE* 3.6 36.6 - - + -
792H LEU* 4.7 1.6 - - - +
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Residues in contact with MET 667 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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666H VAL* 1.3 74.3 - - - +
668H VAL* 1.3 59.6 + - - +
741H GLU* 5.6 3.4 - - - -
742H ASP 3.7 7.2 - - - +
743H VAL* 4.6 13.9 - - + -
789H VAL* 3.4 4.7 - - - +
790H ARG* 2.6 51.0 + - + +
792H LEU* 4.8 7.5 - - + +
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Residues in contact with VAL 668 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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667H MET* 1.3 74.8 - - - +
669H ASP* 1.3 60.6 + - - +
671H VAL* 4.7 17.3 - - + -
682H LEU* 6.4 2.2 - - + -
738H LEU* 5.0 7.9 - - + -
739H ALA 4.5 13.7 - - - +
740H PRO* 5.3 0.9 - - + -
741H GLU* 3.1 27.4 + - - +
742H ASP* 3.6 14.0 + - + +
787H VAL* 6.1 0.9 - - + -
788H LYS 4.1 7.0 - - - +
789H VAL* 4.2 8.7 - - + -
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Residues in contact with ASP 669 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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667H MET 3.9 2.2 + - - -
668H VAL* 1.3 74.8 - - - +
670H GLU* 1.3 63.1 + - + +
740H PRO* 4.8 4.7 - - - +
741H GLU* 4.5 8.3 + - - +
788H LYS* 2.9 34.0 + - + +
789H VAL* 4.7 3.4 - - - +
790H ARG* 5.4 3.8 - - + +
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Residues in contact with GLU 670 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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668H VAL* 3.8 0.4 - - - -
669H ASP* 1.3 84.2 - - + +
671H VAL* 1.3 68.8 + - - +
672H VAL* 5.9 1.3 - - + -
740H PRO* 5.4 4.3 - - - -
786H GLY 4.4 3.7 - - - +
787H VAL* 3.9 3.6 - - - +
788H LYS* 3.5 24.6 + - + +
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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