Contacts of the helix formed by residues 768 - 781 (chain A) in PDB entry 1VDV
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 ASN 768 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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766A THR* 2.9 11.0 + - - +
767A GLN* 1.3 81.4 - - - +
769A ALA* 1.3 59.4 + - - +
770A MET* 3.6 7.4 + - - +
771A LYS* 2.9 38.9 + - + +
772A THR* 2.8 26.2 + - - +
801A LYS 3.9 0.2 + - - -
802A GLU 2.9 28.7 + - - +
803A THR* 4.4 2.5 - - - +
805A SER* 5.5 0.4 - - - +
806A THR* 6.3 0.9 - - + -
1075A SER 5.0 0.2 - - - -
1076A PRO* 3.3 20.7 - - + +
5101A YSH 3.2 28.9 + - - -
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Residues in contact with ALA 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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766A THR* 4.2 2.9 + - - +
767A GLN 4.0 1.6 - - - -
768A ASN* 1.3 74.5 - - - +
770A MET* 1.3 57.4 + - - +
772A THR* 3.6 2.8 - - - -
773A GLN* 2.9 30.5 + - - +
789A VAL* 3.9 24.7 - - + +
791A VAL* 4.3 14.1 - - + -
1036A THR* 5.5 2.6 - - + +
1066A THR* 5.3 11.4 - - + +
1067A SER 5.7 0.2 - - - -
1068A THR* 3.8 20.8 - - + +
1074A SER* 5.0 8.1 + - - +
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Residues in contact with MET 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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768A ASN* 3.2 3.5 - - - +
769A ALA* 1.3 78.5 - - - +
771A LYS* 1.3 79.7 + - + +
773A GLN* 3.3 14.8 + - - +
774A SER* 3.0 30.0 + - - +
1014A LEU* 6.2 0.2 - - - -
1068A THR* 4.5 2.9 - - - +
1073A ASN* 3.4 28.0 - - - +
1074A SER* 3.1 39.5 + - - +
1075A SER* 5.0 0.9 - - - -
1025B THR* 3.6 37.2 - - + +
1121B TYR* 3.7 23.1 - - + +
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Residues in contact with LYS 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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648A LEU* 4.1 16.6 - - + -
768A ASN* 2.9 35.2 + - + +
770A MET* 1.3 102.2 - - + +
772A THR* 1.3 60.9 + - - +
774A SER* 3.2 7.9 + - - +
775A PHE* 2.8 61.7 + - + +
802A GLU 5.5 0.2 - - - +
803A THR* 5.9 2.2 - - + -
806A THR* 4.5 6.5 - - + -
1014A LEU* 5.4 4.4 - - - +
1076A PRO* 5.5 1.8 - - - +
5101A YSH 3.9 36.1 + - - +
1121B TYR* 5.1 3.4 + - - -
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Residues in contact with THR 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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762A LEU* 5.2 1.3 - - + -
764A VAL* 4.3 7.9 - - + -
766A THR* 3.7 16.8 + - - +
768A ASN 2.8 22.6 + - - -
769A ALA* 3.6 8.3 - - - -
771A LYS* 1.3 77.5 - - - +
773A GLN* 1.3 62.6 + - - +
775A PHE* 4.0 0.7 - - - +
776A VAL* 3.0 34.8 + - + +
789A VAL* 3.8 22.4 - - + -
805A SER* 4.2 1.6 + - - -
806A THR* 4.1 17.9 - - - +
809A SER* 4.1 27.3 + - - +
810A VAL* 6.4 0.2 - - - -
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Residues in contact with GLN 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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769A ALA 2.9 17.1 + - - +
770A MET* 3.5 11.8 - - - +
772A THR* 1.3 78.8 - - - +
774A SER* 1.3 56.3 + - - +
776A VAL* 3.8 1.9 - - - +
777A ALA* 3.0 27.7 + - - +
784A VAL* 3.3 29.4 + - + +
787A ILE* 2.9 39.9 + - + +
789A VAL* 3.7 15.0 - - + -
1068A THR* 3.6 20.9 + - + +
1073A ASN 5.5 1.7 + - - -
1024B TYR* 3.4 34.8 + - - -
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Residues in contact with SER 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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770A MET* 3.0 16.8 + - - +
771A LYS* 3.2 19.8 + - - +
773A GLN* 1.3 74.2 - - - +
775A PHE* 1.3 71.7 + - - +
777A ALA* 3.4 1.4 + - - +
778A LYS* 2.8 30.9 + - - +
784A VAL* 4.2 23.6 - - - +
1025B THR* 5.5 6.3 - - - -
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Residues in contact with PHE 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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646A THR* 3.3 19.9 + - - +
647A GLY* 3.4 45.1 - - - -
648A LEU* 3.6 18.6 - - + -
771A LYS* 2.8 43.9 + - + +
772A THR 4.0 2.2 - - - +
774A SER* 1.3 77.3 + - - +
776A VAL* 1.3 67.0 + - - +
778A LYS* 3.3 12.6 + - + +
779A MET* 3.0 23.9 + - - +
803A THR* 5.5 2.9 - - - -
806A THR* 3.7 34.1 - - + -
810A VAL* 4.0 14.3 - - + +
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Residues in contact with VAL 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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760A MET* 4.4 4.5 - - - -
762A LEU* 4.2 16.2 - - + -
772A THR* 3.0 29.6 + - + +
773A GLN* 3.8 3.6 - - - +
775A PHE* 1.3 75.9 - - - +
777A ALA* 1.3 59.2 + - - +
779A MET* 3.3 5.2 + - - +
780A LEU* 3.0 48.5 + - + +
787A ILE* 4.2 18.6 - - + -
809A SER 4.4 0.9 - - - +
810A VAL* 4.3 20.0 - - + +
813A ALA* 3.7 26.5 - - + -
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Residues in contact with ALA 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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773A GLN 3.0 18.8 + - - +
774A SER 3.7 3.8 - - - +
776A VAL* 1.3 76.4 - - - +
778A LYS* 1.3 58.0 + - - +
780A LEU* 3.3 0.6 + - - -
781A GLY* 2.8 25.8 + - - -
782A VAL* 3.1 32.8 + - - +
784A VAL* 3.9 20.6 - - + -
787A ILE* 3.8 20.0 - - + -
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Residues in contact with LYS 778 (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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643A SER* 3.4 32.4 + - - -
645A GLU* 2.8 38.4 + - - +
646A THR* 5.2 4.0 - - - +
650A ASN* 3.5 26.0 - - - +
774A SER 2.8 19.0 + - - +
775A PHE* 3.6 14.8 - - + +
777A ALA* 1.3 77.6 - - - +
779A MET* 1.3 63.0 + - - +
781A GLY* 3.3 11.1 + - - -
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Residues in contact with MET 779 (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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640A ILE* 3.4 8.8 - - + +
641A PRO* 4.2 3.1 - - - -
642A GLY* 2.9 24.1 + - - -
643A SER 3.4 20.7 + - - +
654A VAL* 4.2 11.7 - - + -
775A PHE 3.0 16.4 + - - +
776A VAL* 3.6 2.5 - - + +
778A LYS* 1.3 76.9 - - - +
780A LEU* 1.3 81.8 + - + +
810A VAL* 3.3 45.5 - - + +
813A ALA* 3.8 9.0 - - + -
814A LEU* 3.3 39.5 - - + +
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Residues in contact with LEU 780 (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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641A PRO* 3.7 18.6 - - + +
642A GLY* 3.9 3.8 + - - -
758A GLY 4.7 5.6 - - - +
760A MET* 3.9 18.4 - - + -
776A VAL* 3.0 38.3 + - + +
777A ALA 3.9 2.9 - - - +
779A MET* 1.3 100.2 - - + +
781A GLY* 1.3 62.6 + - - +
782A VAL* 3.9 18.6 - - + +
787A ILE* 4.0 17.0 - - + -
817A TYR* 3.7 39.8 - - + -
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Residues in contact with GLY 781 (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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642A GLY* 4.0 10.1 - - - -
777A ALA 2.8 10.8 + - - -
778A LYS* 3.3 10.5 + - - -
779A MET 3.4 0.2 - - - -
780A LEU* 1.3 80.8 - - - +
782A VAL* 1.3 59.8 + - - +
783A PRO* 4.9 0.3 - - - +
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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