Contacts of the strand formed by residues 662 - 670 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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650F VAL* 3.4 29.3 - - + +
658F GLN* 4.4 5.6 - - + -
659F TYR* 2.8 48.9 + - + -
660F SER* 3.3 22.1 + - - +
661F LYS* 1.3 88.3 - - - +
663F TYR* 1.3 62.6 + - - +
686F TRP* 4.7 23.2 - + + -
746F CYS 4.5 3.1 - - - +
747F CYS* 4.6 2.4 - - - +
748F LEU* 4.0 23.5 + - + +
750F LEU* 4.8 3.4 - - + -
808F TYR* 5.0 5.1 - - - -
809F ALA* 3.3 13.2 - - + -
810F PRO 3.6 24.0 - - - -
811F CYS* 4.5 12.3 - - + -
813F GLU* 3.9 17.9 - - + -
814F ALA* 3.6 34.3 - - + -
1007F TYR* 5.2 7.0 - - + -
1009F ALA* 5.3 0.9 - - + -
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Residues in contact with TYR 663 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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662F TRP* 1.3 76.2 - - - +
664F PHE* 1.3 66.8 + - - +
665F GLU* 4.7 4.4 - - + +
745F SER* 3.1 35.6 - - - -
746F CYS 3.8 11.9 - - - -
747F CYS* 4.3 13.9 - - - -
758F ARG* 4.1 11.4 - - + +
761F GLY* 6.2 0.3 - - - -
793F LEU 4.5 0.7 - - - +
800F PHE* 3.9 28.5 - + - -
802F PHE* 4.3 12.4 + - - +
803F LEU 4.7 3.7 + - - -
804F PRO* 4.0 18.4 - - + -
805F PRO* 3.6 28.7 - - + +
808F TYR* 4.2 15.5 - + + -
809F ALA 2.9 13.2 + - - +
810F PRO* 3.3 7.4 - - - +
811F CYS* 3.1 23.6 + - - +
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Residues in contact with PHE 664 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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663F TYR* 1.3 84.9 - - - +
665F GLU* 1.3 56.8 + - - +
666F VAL* 4.1 16.4 - - + -
684F VAL* 4.6 15.0 - - + -
685F GLY 5.4 0.9 - - - -
686F TRP* 3.6 24.0 - + - -
745F SER* 2.3 29.1 + - - -
746F CYS* 3.5 34.7 + - - -
779F PRO* 3.5 23.6 - - + -
791F PHE* 3.6 35.4 - + - -
792F LEU 4.1 9.2 - - - +
793F LEU 4.2 4.0 - - - +
800F PHE* 4.8 2.7 - - - -
811F CYS* 3.7 26.5 - - + -
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Residues in contact with GLU 665 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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663F TYR* 4.7 7.0 - - + +
664F PHE* 1.3 74.3 - - - +
666F VAL* 1.3 66.8 + - - +
743F VAL* 3.9 21.1 - - + -
744F VAL 4.3 0.4 - - - -
745F SER* 3.8 18.6 - - - -
792F LEU* 3.4 32.0 + - + +
800F PHE* 4.4 17.2 - - + -
801F LYS* 6.0 2.0 - - + -
802F PHE* 5.7 7.2 - - + +
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Residues in contact with VAL 666 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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664F PHE* 4.1 10.3 - - + -
665F GLU* 1.3 81.0 - - - +
667F MET* 1.3 61.1 + - - +
684F VAL* 4.7 23.3 - - + -
742F ASP 3.8 0.9 - - - +
743F VAL* 3.4 9.2 - - - +
744F VAL* 3.4 36.2 + - + +
781F VAL* 6.2 3.1 - - + -
789F VAL* 4.7 12.6 - - + -
790F ARG 3.5 12.8 - - - +
791F PHE* 3.6 37.2 - - + -
792F LEU* 4.7 2.2 - - - +
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Residues in contact with MET 667 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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666F VAL* 1.3 75.8 - - - +
668F VAL* 1.3 61.3 + - - +
741F GLU* 5.6 3.4 - - - -
742F ASP 3.7 7.6 - - - +
743F VAL* 4.6 13.5 - - + -
789F VAL* 3.4 4.8 - - - +
790F ARG* 2.6 50.9 + - + +
792F LEU* 4.8 6.7 - - + +
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Residues in contact with VAL 668 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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667F MET* 1.3 73.5 - - - +
669F ASP* 1.3 61.4 + - - +
671F VAL* 4.7 17.3 - - + -
682F LEU* 6.4 2.5 - - + -
738F LEU* 5.0 7.6 - - + -
739F ALA 4.5 13.9 - - - +
740F PRO* 5.3 0.9 - - + -
741F GLU* 3.1 27.4 + - - +
742F ASP* 3.6 12.8 + - + +
787F VAL* 6.1 0.9 - - + -
788F LYS 4.1 6.7 - - - +
789F VAL* 4.2 8.5 - - + -
790F ARG* 5.9 0.2 - - - -
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Residues in contact with ASP 669 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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667F MET 3.9 2.8 + - - -
668F VAL* 1.3 75.6 - - - +
670F GLU* 1.3 62.4 + - + +
740F PRO* 4.8 4.7 - - - +
741F GLU* 4.5 7.6 + - - +
788F LYS* 2.9 32.7 + - + +
789F VAL* 4.7 3.4 - - - +
790F ARG* 5.4 4.5 - - + +
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Residues in contact with GLU 670 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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668F VAL 3.8 0.6 - - - -
669F ASP* 1.3 84.4 - - + +
671F VAL* 1.3 68.2 + - - +
672F VAL* 6.3 1.1 - - + -
740F PRO* 5.4 4.9 - - - -
786F GLY 4.4 2.5 - - - +
787F VAL* 3.9 4.2 - - - +
788F LYS* 3.5 24.3 + - + +
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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