Contacts of the strand formed by residues 713 - 721 (chain A) in PDB entry 6N8Q
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 VAL 713 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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592A THR* 2.4 28.8 + - - -
593A SER* 2.9 20.3 + - - +
606A GLY* 4.0 5.6 - - - -
607A THR 3.1 10.2 + - - +
610A GLY 3.5 24.5 - - - +
611A PHE* 3.8 26.7 - - + -
627A THR* 3.6 10.5 - - + +
711A GLY 2.9 12.5 + - - +
712A PHE* 1.3 69.2 - - - +
714A ARG* 1.3 59.7 + - - +
715A THR 4.1 2.0 - - - +
716A LEU* 4.0 16.6 - - + -
735A ALA* 4.5 3.8 - - + -
736A GLY 3.8 11.4 - - - +
737A THR* 4.4 5.4 - - + +
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Residues in contact with ARG 714 (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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509A LYS* 5.8 0.9 + - - -
592A THR 3.9 6.3 - - - +
593A SER* 3.5 14.9 - - - -
712A PHE* 3.3 21.0 + - + +
713A VAL* 1.3 73.0 - - - +
715A THR* 1.3 62.2 + - - +
736A GLY 3.0 6.5 + - - +
737A THR 5.2 1.1 - - - -
738A ASN* 3.2 33.0 + - - +
775A PRO* 3.9 12.0 - - - +
776A VAL 3.7 19.3 - - - +
777A VAL* 3.5 23.4 - - - +
816A GLU* 3.1 29.5 + - - +
844A ARG* 4.9 13.3 + - - +
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Residues in contact with THR 715 (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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593A SER* 4.0 0.9 - - - -
713A VAL* 3.8 1.3 - - - +
714A ARG* 1.3 80.4 + - - +
716A LEU* 1.3 76.3 + - - +
717A TYR* 5.3 0.2 - - + -
734A TRP 4.4 0.2 - - - -
735A ALA* 3.3 5.2 - - - +
736A GLY 2.9 33.3 + - - +
776A VAL* 2.8 27.5 + - - -
777A VAL* 3.3 14.5 + - - +
778A GLY* 4.0 5.6 - - - -
779A ILE* 3.8 39.9 - - + +
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Residues in contact with LEU 716 (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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593A SER* 3.6 27.6 - - - +
594A LEU* 3.9 4.0 - - - +
595A ALA* 3.8 22.4 - - + +
604A ALA* 3.6 16.6 - - + +
605A PHE* 3.5 37.7 - - - +
611A PHE* 4.2 13.7 - - + -
713A VAL* 4.0 7.9 - - + -
715A THR* 1.3 87.5 - - - +
717A TYR* 1.3 65.3 + - - +
733A LEU* 4.5 3.4 - - + -
734A TRP 3.2 6.1 - - - +
735A ALA* 3.7 22.7 - - + -
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Residues in contact with TYR 717 (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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595A ALA* 4.5 2.0 - - - +
715A THR* 5.3 0.7 - - + -
716A LEU* 1.3 78.6 - - - +
718A PHE* 1.3 75.8 + - - +
719A ALA* 3.6 18.2 - - + -
733A LEU* 4.0 4.8 - - - +
734A TRP* 2.7 49.8 + + + +
779A ILE* 3.3 39.3 - - + +
780A LEU* 3.5 23.8 - - + +
781A VAL* 3.3 20.8 + - + -
788A PRO* 5.6 0.5 - - - +
789A LEU* 3.7 27.2 + - - +
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Residues in contact with PHE 718 (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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595A ALA* 3.8 31.6 - - + +
596A LEU 4.3 1.8 - - - -
597A HIS* 3.6 49.8 - - + -
600A TRP* 3.8 13.7 - + + -
602A LEU* 3.9 14.8 - - + -
604A ALA* 3.9 11.4 - - + -
613A LEU* 3.6 31.2 - - + -
717A TYR* 1.3 90.5 - - - +
719A ALA* 1.3 61.1 + - - +
732A SER 3.3 13.0 - - - +
733A LEU* 3.8 14.4 - - + -
747A LEU* 3.9 11.9 - - + -
789A LEU* 5.6 0.3 - - - +
792A PRO* 5.6 1.8 - - + -
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Residues in contact with ALA 719 (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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600A TRP* 3.8 5.5 - - - -
717A TYR* 3.6 20.0 - - + -
718A PHE* 1.3 77.3 - - - +
720A ASP* 1.3 59.3 + - - +
721A THR* 3.5 6.5 + - + -
732A SER* 2.3 53.3 + - - +
734A TRP* 3.8 12.3 - - - +
781A VAL* 3.9 11.9 - - + -
789A LEU* 4.0 8.3 - - + -
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Residues in contact with ASP 720 (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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600A TRP* 3.8 22.9 - - + -
719A ALA* 1.3 68.6 - - - +
721A THR* 1.3 58.4 + - - +
729A HIS* 3.2 33.6 + - - +
730A CYS* 3.4 20.4 - - - -
731A PRO* 3.7 4.2 - - - +
789A LEU* 3.9 14.3 - - + +
803A PRO* 5.7 3.3 - - - +
805A MET* 4.2 7.8 - - - +
809A HIS* 4.2 7.3 - - - -
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Residues in contact with THR 721 (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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719A ALA* 3.5 11.6 + - + -
720A ASP* 1.3 74.9 - - - +
722A TYR* 1.3 71.7 + - - +
723A LEU* 3.4 4.6 + - + +
729A HIS* 3.5 9.9 - - - -
730A CYS 3.1 28.5 + - - +
732A SER* 3.9 18.6 - - - +
734A TRP* 4.3 11.2 - - + +
781A VAL* 3.6 10.2 - - + +
789A LEU* 4.3 2.2 - - - -
809A HIS* 2.7 26.8 + - - -
824A LEU* 3.4 26.3 - - + +
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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