Contacts of the strand formed by residues 662 - 670 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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650D VAL* 3.4 28.5 - - + +
658D GLN* 4.4 5.8 - - + -
659D TYR* 2.8 49.4 + - + -
660D SER* 3.3 22.0 + - - +
661D LYS* 1.3 87.8 - - - +
663D TYR* 1.3 62.8 + - - +
664D PHE* 5.7 0.2 - - - -
686D TRP* 4.7 22.4 - + + -
746D CYS 4.5 2.8 - - - +
747D CYS* 4.6 2.4 - - - +
748D LEU* 4.0 23.3 + - + +
750D LEU* 4.8 2.9 - - + -
808D TYR* 5.0 6.0 - - - -
809D ALA* 3.3 13.9 - - + -
810D PRO 3.6 23.6 - - - -
811D CYS* 4.5 11.4 - - + -
813D GLU* 3.9 17.7 - - + -
814D ALA* 3.6 34.3 - - + -
1007D TYR* 5.2 7.0 - - + -
1009D ALA* 5.3 0.4 - - + -
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Residues in contact with TYR 663 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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662D TRP* 1.3 77.0 - - - +
664D PHE* 1.3 66.3 + - - +
665D GLU* 4.7 5.2 - - + +
745D SER* 3.1 37.8 - - - -
746D CYS 3.8 11.7 - - - -
747D CYS* 4.3 14.6 - - - -
758D ARG* 4.1 11.3 - - + +
761D GLY* 6.2 0.2 - - - -
793D LEU 4.5 0.7 - - - +
800D PHE* 3.9 28.7 - + - -
802D PHE* 4.3 12.0 + - - +
803D LEU 4.7 3.7 + - - -
804D PRO* 4.0 18.8 - - + -
805D PRO* 3.6 28.2 - - + +
808D TYR* 4.2 15.5 - + + -
809D ALA 2.9 13.1 + - - +
810D PRO* 3.3 7.2 - - + +
811D CYS* 3.1 23.3 + - - +
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Residues in contact with PHE 664 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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662D TRP 5.7 0.2 - - - -
663D TYR* 1.3 85.7 - - - +
665D GLU* 1.3 58.2 + - - +
666D VAL* 4.1 15.9 - - + -
684D VAL* 4.6 15.3 - - + -
685D GLY 5.4 0.7 - - - -
686D TRP* 3.6 23.8 - + - -
745D SER* 2.3 29.3 + - - -
746D CYS* 3.5 34.3 + - - -
779D PRO* 3.5 22.4 - - + -
791D PHE* 3.6 35.7 - + - -
792D LEU 4.1 9.0 - - - +
793D LEU 4.2 3.8 - - - +
800D PHE* 4.8 3.1 - - - -
811D CYS* 3.7 25.8 - - + -
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Residues in contact with GLU 665 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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663D TYR* 4.7 6.1 - - + +
664D PHE* 1.3 72.8 - - - +
666D VAL* 1.3 65.5 + - - +
743D VAL* 3.9 21.1 - - + -
744D VAL 4.3 0.4 - - - -
745D SER* 3.8 18.8 - - - -
792D LEU* 3.4 31.5 + - + +
800D PHE* 4.4 18.5 - - + -
801D LYS* 6.0 2.7 - - + +
802D PHE* 5.7 6.5 - - + +
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Residues in contact with VAL 666 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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664D PHE* 4.1 9.9 - - + -
665D GLU* 1.3 80.3 - - - +
667D MET* 1.3 60.7 + - - +
684D VAL* 4.7 23.1 - - + -
742D ASP 3.8 0.9 - - - +
743D VAL* 3.4 8.9 - - - +
744D VAL* 3.4 36.9 + - + +
781D VAL* 6.2 2.9 - - + -
789D VAL* 4.7 12.3 - - + -
790D ARG 3.5 12.3 - - - +
791D PHE* 3.6 37.7 - - + -
792D LEU* 4.7 2.2 - - - +
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Residues in contact with MET 667 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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666D VAL* 1.3 75.6 - - - +
668D VAL* 1.3 60.3 + - - +
741D GLU* 5.6 3.1 - - - -
742D ASP 3.7 7.6 - - - +
743D VAL* 4.6 13.7 - - + -
789D VAL* 3.4 5.3 - - - +
790D ARG* 2.6 50.2 + - + +
792D LEU* 4.8 7.3 - - + +
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Residues in contact with VAL 668 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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667D MET* 1.3 74.9 - - - +
669D ASP* 1.3 60.8 + - - +
671D VAL* 4.7 16.8 - - + -
682D LEU* 6.4 2.0 - - + -
738D LEU* 5.0 8.1 - - + -
739D ALA 4.5 13.7 - - - +
740D PRO* 5.3 0.9 - - + -
741D GLU* 3.1 27.0 + - - +
742D ASP* 3.6 12.8 + - + +
787D VAL* 6.1 1.1 - - + -
788D LYS 4.1 6.7 - - - +
789D VAL* 4.2 8.7 - - + -
790D ARG* 5.9 0.2 - - - -
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Residues in contact with ASP 669 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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667D MET 3.9 2.4 + - - -
668D VAL* 1.3 74.9 - - - +
670D GLU* 1.3 63.8 + - + +
740D PRO* 4.8 5.0 - - - +
741D GLU* 4.5 7.5 + - - +
788D LYS* 2.9 33.5 + - + +
789D VAL* 4.7 3.1 - - - +
790D ARG* 5.4 4.3 - - + +
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Residues in contact with GLU 670 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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668D VAL 3.8 0.4 - - - -
669D ASP* 1.3 84.4 - - + +
671D VAL* 1.3 69.6 + - - +
672D VAL* 6.3 1.1 - - + -
740D PRO* 5.4 4.5 - - - -
786D GLY 4.4 3.0 - - - +
787D VAL* 3.9 3.8 - - - +
788D LYS* 3.5 25.2 + - + +
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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