Contacts of the strand formed by residues 790 - 800 (chain A) in PDB entry 1DQ8
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 ASP 790 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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711A VAL* 4.0 16.6 - - + +
712A ILE 3.6 8.7 - - - +
713A PRO* 3.4 8.6 - - - +
714A ALA* 2.9 28.7 + - - +
725A THR* 3.4 8.4 - - - +
783A ALA* 3.5 0.5 - - - -
784A SER 2.7 34.5 + - - +
785A GLY* 3.4 21.5 - - - -
786A PRO* 3.7 10.2 - - - +
787A THR 5.5 0.2 + - - -
789A GLU* 1.3 85.2 + - - +
791A LEU* 1.3 59.1 + - - +
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Residues in contact with LEU 791 (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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710A ALA 3.7 1.0 - - - +
711A VAL* 3.2 4.5 - - - -
712A ILE* 2.8 45.0 + - + +
717A VAL* 4.2 14.1 - - + -
721A LEU* 5.0 0.7 - - + -
725A THR* 3.7 16.5 + - + +
728A MET* 3.6 42.8 - - + -
729A ILE* 4.1 18.4 - - + -
781A MET* 3.9 20.9 - - + -
782A GLU 3.7 2.0 - - - +
790A ASP* 1.3 72.0 - - - +
792A TYR* 1.3 74.7 + - - +
793A ILE* 3.7 1.5 + - + -
851A LEU* 3.7 18.6 - - + -
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Residues in contact with TYR 792 (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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709A GLU* 2.8 38.4 + - + +
710A ALA 3.6 3.6 - - - -
711A VAL* 3.9 20.2 - - + -
780A LEU* 5.0 4.7 - - + -
781A MET* 3.2 5.8 - - - +
782A GLU* 2.7 64.7 + - + +
784A SER* 3.9 17.6 - - - +
790A ASP 3.9 1.2 + - - -
791A LEU* 1.3 74.5 - - - +
793A ILE* 1.3 63.0 + - - +
794A SER* 3.6 33.5 - - - -
597D PRO 4.9 5.6 - - - -
598D ARG* 5.2 2.2 - - + -
599D ALA* 3.8 2.4 + - - +
641D ARG* 3.8 39.5 + - + +
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Residues in contact with ILE 793 (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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709A GLU* 3.2 4.5 - - - +
710A ALA* 2.9 48.3 + - + +
712A ILE* 4.8 1.8 - - + -
779A THR* 4.5 3.4 - - - +
780A LEU 3.3 12.8 - - - +
781A MET* 3.8 30.3 - - + -
791A LEU* 4.7 4.9 - - + +
792A TYR* 1.3 79.6 - - - +
794A SER* 1.3 72.1 - - - +
795A CYS* 4.8 0.7 - - - -
847A MET* 3.8 37.7 - - + +
850A GLU* 4.5 6.7 - - + -
851A LEU* 3.8 32.3 - - + +
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Residues in contact with SER 794 (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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708A CYS 3.1 15.7 - - - -
709A GLU* 4.2 0.9 - - - +
778A ILE 3.9 1.0 + - - +
779A THR* 3.2 6.2 - - - -
780A LEU* 3.0 45.9 + - - +
792A TYR* 3.6 23.3 - - - -
793A ILE* 1.3 76.7 - - - +
795A CYS* 1.3 63.8 + - - +
796A THR* 4.8 0.3 + - - -
847A MET* 4.3 1.1 - - - -
640D GLY* 3.3 26.6 + - - -
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Residues in contact with CYS 795 (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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707A VAL* 3.5 1.9 - - - -
708A CYS* 2.9 31.2 + - + +
777A CYS* 4.0 9.4 - - - -
778A ILE 3.5 5.6 - - - -
779A THR* 3.6 25.8 - - - -
793A ILE* 4.8 1.3 - - - -
794A SER* 1.3 74.0 - - - +
796A THR* 1.3 63.4 + - - +
797A MET 4.1 0.2 - - - -
843A CYS* 3.5 16.6 - - - +
846A VAL* 4.3 3.8 - - + -
847A MET* 3.6 40.1 - - + -
850A GLU* 3.9 12.8 - - - -
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Residues in contact with THR 796 (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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584A LEU* 4.7 4.9 - - + -
706A VAL 3.5 9.2 - - - +
707A VAL* 3.5 6.7 - - + +
777A CYS* 3.3 4.0 - - - -
778A ILE* 3.1 44.9 + - + +
780A LEU* 5.8 0.2 - - - +
794A SER* 4.8 0.5 + - - -
795A CYS* 1.3 74.8 - - - +
797A MET* 1.3 62.6 + - - +
798A PRO* 3.6 15.3 - - + +
742C MET* 5.2 0.7 - - + -
638D ILE* 3.2 35.7 - - + +
639D ALA* 3.6 0.9 - - - -
640D GLY* 2.9 27.4 + - - -
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Residues in contact with MET 797 (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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704A LYS 3.6 3.1 - - - +
705A SER* 3.4 1.4 - - - -
706A VAL* 2.8 33.9 + - - +
753A ALA* 4.5 0.9 - - + -
757A VAL* 3.7 22.7 - - + -
774A SER 3.2 27.8 - - - +
775A SER* 4.3 6.5 - - - +
776A ASN 3.5 13.0 - - - +
777A CYS* 3.7 13.5 - - + -
796A THR* 1.3 75.3 - - - +
798A PRO* 1.3 66.6 - - - +
799A SER 3.3 3.0 + - - -
800A ILE* 4.0 21.1 - - + +
842A VAL* 4.6 0.4 - - + -
843A CYS* 3.8 29.4 - - - -
846A VAL* 3.7 28.7 - - + -
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Residues in contact with PRO 798 (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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697A ASN 4.2 5.6 - - - +
698A TRP* 3.6 55.0 - - + +
701A GLY* 3.2 15.5 - - - -
702A ARG 3.3 1.6 + - - -
704A LYS 3.7 1.9 - - - +
705A SER* 2.7 31.9 + - - +
776A ASN* 3.7 8.3 - - + +
796A THR* 3.6 17.7 - - + +
797A MET* 1.3 82.4 - - - +
799A SER* 1.3 59.5 + - - +
742C MET* 5.2 5.6 - - + -
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Residues in contact with SER 799 (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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697A ASN* 3.9 13.4 + - - +
702A ARG* 3.0 31.7 - - - +
773A GLY 3.0 22.6 + - - +
774A SER* 3.2 19.5 + - - -
776A ASN* 3.2 20.6 + - - +
797A MET 3.3 1.6 + - - -
798A PRO* 1.3 82.8 - - - +
800A ILE* 1.3 65.2 + - - +
801A GLU* 3.2 8.2 + - - +
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Residues in contact with ILE 800 (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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704A LYS* 2.8 46.8 + - + +
706A VAL* 4.2 12.8 - - + -
761A TYR* 3.3 18.2 - - + +
774A SER* 3.9 17.9 - - - +
797A MET* 4.0 29.4 - - + -
799A SER* 1.3 70.8 - - - +
801A GLU* 1.3 57.8 + - - +
802A ILE* 3.6 28.1 + - + -
839A ALA* 3.4 28.5 - - + +
842A VAL* 3.9 17.9 - - + -
843A CYS* 4.2 2.5 - - + +
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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