Contacts of the helix formed by residues 771 - 784 (chain D) in PDB entry 1V40
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 HIS 771 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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725D PRO* 4.7 5.6 - - + -
728D MET* 3.7 26.6 - - + +
729D GLN* 3.4 30.2 + - + -
732D ASP* 2.8 40.2 - - + +
767D LEU 4.4 9.5 + - - -
768D LEU* 2.9 16.2 + - - +
770D ASN* 1.3 103.1 + - + +
772D PRO* 1.3 66.0 - - - +
773D ARG 3.1 2.5 - - - -
774D LEU* 3.0 33.8 + - + +
775D VAL* 3.4 7.6 + - - +
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Residues in contact with PRO 772 (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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732D ASP* 5.5 0.2 - - - +
768D LEU 4.0 1.3 - - - +
769D ASP 4.5 6.3 - - - +
770D ASN 3.5 8.5 - - - +
771D HIS* 1.3 86.3 - - - +
773D ARG* 1.3 63.7 + - + +
775D VAL* 3.2 13.8 + - + +
776D THR* 2.9 32.4 + - - +
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Residues in contact with ARG 773 (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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729D GLN* 5.9 0.8 - - - +
732D ASP* 2.9 53.7 + - - +
733D THR* 4.5 3.8 - - - +
735D LEU* 3.8 15.5 - - + +
736D GLY* 3.2 35.9 + - - -
737D GLY* 3.7 7.7 - - - +
771D HIS 3.0 1.6 + - - -
772D PRO* 1.3 84.9 - - + +
774D LEU* 1.3 57.5 + - - +
776D THR* 3.4 9.3 + - - -
777D LEU* 3.1 23.9 + - - +
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Residues in contact with LEU 774 (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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728D MET* 3.6 32.1 - - + +
731D LEU* 4.2 14.1 - - + +
732D ASP* 4.2 19.1 - - + +
735D LEU* 4.2 18.8 - - + -
741D LEU* 5.2 2.9 - - + -
753D TRP* 3.3 50.9 + - + +
768D LEU* 4.3 6.1 - - + -
771D HIS* 3.0 27.1 + - + +
773D ARG* 1.3 75.3 - - - +
775D VAL* 1.3 64.2 + - - +
777D LEU* 3.5 5.6 + - + +
778D ARG* 3.2 20.4 + - - +
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Residues in contact with VAL 775 (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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768D LEU* 3.6 37.0 - - + +
771D HIS 3.8 7.0 - - - +
772D PRO* 3.2 13.6 + - + +
774D LEU* 1.3 75.8 - - - +
776D THR* 1.3 64.8 + - - +
778D ARG* 3.2 15.0 + - + +
779D LYS* 3.0 48.9 + - + +
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Residues in contact with THR 776 (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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772D PRO* 2.9 14.8 + - - +
773D ARG* 3.6 12.5 - - - -
774D LEU 3.3 0.2 - - - -
775D VAL* 1.3 78.6 - - - +
777D LEU* 1.3 61.6 + - - +
779D LYS* 3.2 11.4 + - + +
780D LYS* 3.0 38.4 + - + +
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Residues in contact with LEU 777 (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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735D LEU* 4.3 12.3 - - + -
739D GLU 3.5 23.8 - - - +
740D TRP* 3.6 24.5 - - + -
741D LEU* 3.5 37.7 - - + +
750D ASP* 3.7 9.2 - - + +
753D TRP* 3.7 22.0 - - + +
773D ARG 3.1 14.4 + - - +
774D LEU* 3.7 10.8 - - + +
775D VAL 3.2 0.2 - - - -
776D THR* 1.3 76.3 - - - +
778D ARG* 1.3 63.4 + - - +
780D LYS* 3.1 10.1 + - - +
781D VAL* 3.1 26.5 + - + +
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Residues in contact with ARG 778 (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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753D TRP* 3.7 9.6 - - + +
754D GLU* 3.2 17.4 + - + +
757D SER* 2.9 31.1 + - - +
758D THR* 3.1 29.9 + - - +
761D LEU* 3.4 24.3 - - - +
768D LEU* 3.6 25.1 - - - +
774D LEU 3.2 12.8 + - - +
775D VAL* 3.2 14.6 + - + +
777D LEU* 1.3 80.3 - - - +
779D LYS* 1.3 57.6 + - + +
781D VAL* 3.3 2.8 + - - +
782D GLN* 2.9 57.5 + - - +
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Residues in contact with LYS 779 (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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775D VAL* 3.0 37.3 + - + +
776D THR* 3.2 10.5 + - + +
778D ARG* 1.3 77.0 - - + +
780D LYS* 1.3 58.8 + - + +
782D GLN* 3.3 16.5 + - - +
783D ALA* 2.9 30.9 + - - +
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Residues in contact with LYS 780 (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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739D GLU* 2.9 62.9 + - + +
740D TRP* 3.7 26.3 - - + -
776D THR* 3.0 34.9 + - + +
777D LEU* 3.1 10.7 + - - +
779D LYS* 1.3 74.0 - - + +
781D VAL* 1.3 66.9 + - - +
783D ALA* 3.3 15.3 + - - +
784D ILE* 3.4 16.1 + - - +
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Residues in contact with VAL 781 (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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620D TYR* 4.6 2.2 - - + -
740D TRP* 4.0 9.4 - - + -
746D VAL* 5.0 0.4 - - + -
750D ASP* 3.8 36.1 - - + +
751D PHE* 3.7 27.6 - - + -
754D GLU* 3.9 23.1 - - + -
777D LEU* 3.1 16.5 + - + +
778D ARG 3.6 6.5 - - - +
780D LYS* 1.3 75.7 - - - +
782D GLN* 1.3 63.9 + - - +
783D ALA 3.2 0.9 + - - -
784D ILE* 3.2 21.6 + - - +
787D VAL* 3.4 21.2 - - + +
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Residues in contact with GLN 782 (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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754D GLU* 2.8 31.6 + - - +
758D THR* 4.3 0.8 + - - -
778D ARG* 2.9 51.4 + - - +
779D LYS* 3.7 20.0 - - - +
780D LYS 3.3 0.2 - - - -
781D VAL* 1.3 76.6 - - - +
783D ALA* 1.3 55.8 + - - +
788D ALA* 3.1 29.4 - - - +
791D ILE* 3.9 19.8 - - + +
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Residues in contact with ALA 783 (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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779D LYS 2.9 17.1 + - - +
780D LYS* 3.7 8.7 - - - +
781D VAL 3.1 0.4 - - - -
782D GLN* 1.3 76.5 - - - +
784D ILE* 1.3 65.5 + - - +
785D PRO* 2.9 12.3 - - - +
788D ALA* 4.5 4.6 - - - +
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Residues in contact with ILE 784 (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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624D TYR* 4.1 20.4 - - + -
740D TRP* 4.2 10.1 - - + -
746D VAL* 4.0 33.7 - - + -
751D PHE* 4.0 13.2 - - + -
780D LYS 3.4 11.4 + - - +
781D VAL* 3.2 20.9 + - - +
783D ALA* 1.3 74.6 - - - +
785D PRO* 1.3 66.1 - - + -
786D ALA* 4.2 7.2 - - + +
787D VAL* 2.8 18.9 + - + -
788D ALA 2.7 31.9 + - - -
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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