Contacts of the helix formed by residues 765 - 777 (chain A) in PDB entry 1QXP
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 GLY 765 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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746A MET* 3.2 10.1 - - - -
763A GLY 4.3 1.3 + - - -
764A PHE* 1.3 78.6 - - - +
766A ILE* 1.3 67.5 + - - -
767A ASP* 3.1 3.9 + - - -
768A THR* 3.1 14.3 + - - -
769A CYS* 2.9 21.5 + - - +
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Residues in contact with ILE 766 (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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654A ASP* 5.6 5.8 - - - +
663A ASN* 5.4 8.1 - - - +
742A ALA* 4.3 7.8 - - + +
746A MET* 2.8 25.7 - - + -
765A GLY* 1.3 70.1 - - - +
767A ASP* 1.4 63.1 - - - +
769A CYS* 3.3 2.9 - - - +
770A ARG* 2.5 40.5 + - + +
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Residues in contact with ASP 767 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
575A SER* 5.4 3.5 - - - -
577A GLU* 3.0 32.1 - - + +
651A ARG* 3.7 23.2 + - - +
663A ASN* 5.3 2.5 + - - -
666A ARG* 3.7 21.9 + - - -
765A GLY* 3.1 1.3 - - - -
766A ILE* 1.4 87.2 - - - +
768A THR* 1.3 70.7 + - - +
770A ARG* 2.9 20.3 + - - +
771A SER* 3.1 6.9 + - - -
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Residues in contact with THR 768 (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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764A PHE* 4.4 19.1 - - + -
765A GLY* 3.1 18.7 + - - +
767A ASP* 1.3 79.1 - - - +
769A CYS* 1.3 67.0 + - - +
771A SER* 3.1 8.5 + - - +
772A MET* 2.9 30.1 + - - +
852A ASP* 4.5 10.6 + - - +
856A SER* 4.1 25.8 - - - -
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Residues in contact with CYS 769 (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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742A ALA* 3.9 11.4 - - - +
745A LEU* 3.3 40.6 - - + -
746A MET* 3.4 25.1 - - + +
749A LEU* 5.3 1.6 - - - -
764A PHE* 4.4 13.2 - - - -
765A GLY 2.9 23.0 + - - +
766A ILE* 3.3 6.5 - - - +
768A THR* 1.3 75.6 - - - +
770A ARG* 1.3 71.6 + - - +
771A SER 3.1 0.2 + - - -
772A MET* 3.1 4.1 + - - +
773A VAL* 2.8 25.5 + - - +
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Residues in contact with ARG 770 (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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651A ARG* 3.3 35.8 + - - +
742A ALA* 3.5 18.0 - - + +
766A ILE* 2.5 27.2 + - + +
767A ASP* 2.9 13.2 + - - +
769A CYS* 1.3 79.5 - - - +
771A SER* 1.2 56.0 + - - +
773A VAL* 3.0 13.4 + - - +
774A ALA* 3.2 10.2 + - - +
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Residues in contact with SER 771 (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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651A ARG* 4.1 11.7 - - - +
666A ARG* 6.3 0.7 - - - -
767A ASP 3.1 7.6 + - - -
768A THR* 3.6 9.9 - - - -
770A ARG* 1.2 74.0 - - - +
772A MET* 1.4 67.4 - - - +
774A ALA* 3.7 2.9 + - - +
775A VAL* 3.5 22.3 + - - +
860A ARG* 3.6 19.7 + - - -
893A SER 2.3 35.0 + - - -
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Residues in contact with MET 772 (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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745A LEU* 3.7 28.9 - - + -
749A LEU* 4.8 13.5 - - + -
764A PHE* 5.3 5.4 - - + -
768A THR* 2.9 26.3 + - - +
769A CYS* 3.7 11.2 - - - +
771A SER* 1.4 59.5 - - - +
773A VAL* 1.4 68.5 + - - +
775A VAL* 3.1 12.0 + - - +
776A MET* 3.2 15.6 + - - +
792A LEU* 3.7 35.9 - - + -
796A ILE* 5.7 0.4 - - + -
855A ILE* 4.4 20.6 - - + -
856A SER* 4.9 14.8 - - - +
859A VAL* 4.1 25.6 - - + -
860A ARG* 6.0 2.0 - - + -
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Residues in contact with VAL 773 (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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740A VAL* 4.9 2.5 - - + +
741A SER* 4.2 2.9 - - - -
742A ALA* 4.0 13.0 - - + +
745A LEU* 4.0 27.6 - - + -
769A CYS 2.8 20.4 + - - +
770A ARG* 3.0 5.4 + - - +
772A MET* 1.4 77.9 - - - +
774A ALA* 1.3 69.8 + - - +
775A VAL 3.1 0.2 + - - -
776A MET 3.1 5.7 + - - -
777A ASP* 3.2 14.8 + - + +
782A GLY* 2.9 40.2 - - - +
783A LYS* 3.7 6.5 - - - +
784A LEU* 3.3 27.8 - - + +
892A TYR* 4.9 0.2 - - - +
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Residues in contact with ALA 774 (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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3A GLY* 4.4 0.3 - - - -
651A ARG* 4.8 4.7 - - - -
770A ARG 3.2 11.0 + - - +
771A SER* 4.0 2.9 - - - +
772A MET 3.3 0.4 - - - -
773A VAL* 1.3 81.0 - - - +
775A VAL* 1.3 59.4 + - - +
777A ASP* 2.7 24.4 + - - +
892A TYR* 3.2 44.9 + - + -
893A SER* 3.7 27.4 - - - +
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Residues in contact with VAL 775 (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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2A ALA* 3.4 6.0 - - + +
3A GLY* 3.1 23.0 + - - -
771A SER* 3.5 14.1 + - - +
772A MET* 3.1 7.5 + - - +
774A ALA* 1.3 81.2 - - - +
776A MET* 1.3 80.5 + - + +
859A VAL* 4.3 11.0 - - + +
860A ARG* 4.7 14.4 - - + +
863A ALA* 3.3 35.0 - - + -
892A TYR* 5.3 3.1 - - - +
893A SER* 4.6 17.7 - - - -
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Residues in contact with MET 776 (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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2A ALA* 4.2 17.4 - - + +
3A GLY 4.0 5.5 + - - +
772A MET 3.2 11.4 + - - +
773A VAL 3.1 2.8 + - - -
774A ALA 2.8 1.2 + - - -
775A VAL* 1.3 99.7 - - + +
777A ASP* 1.3 58.6 + - - +
778A SER* 4.1 0.5 + - - -
784A LEU* 4.0 14.9 - - + +
788A GLU* 3.7 39.5 - - + +
791A TYR* 3.2 41.1 - - + -
792A LEU* 4.3 30.5 - - + +
859A VAL* 5.1 8.5 - - + +
862A ASP* 5.6 2.5 - - - +
863A ALA* 5.5 2.5 - - - -
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Residues in contact with ASP 777 (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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3A GLY* 3.0 13.2 - - - -
4A ILE* 3.8 1.7 + - - +
773A VAL* 3.2 15.9 - - + +
774A ALA 2.7 7.9 + - - +
775A VAL 3.2 0.2 - - - -
776A MET* 1.3 78.4 - - - +
778A SER* 1.3 60.6 + - - +
779A ASP* 3.1 23.0 + - - +
780A THR 3.4 12.2 + - - -
781A THR* 3.4 20.7 + - - -
782A GLY 3.5 2.9 + - - -
783A LYS 3.1 28.1 - - - +
784A LEU* 3.9 1.3 - - + +
788A GLU* 5.9 1.6 - - - -
892A TYR* 2.7 33.3 + - - +
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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