Contacts of the helix formed by residues 770 - 783 (chain E) in PDB entry 3V53
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 ARG 770 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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812A ALA 3.0 26.7 + - - -
813A MET* 3.4 25.7 + - - +
814A VAL 4.6 5.5 + - - -
816A ASP* 3.0 25.3 + - - +
766E LEU* 2.9 13.7 + - - +
769E ARG* 1.3 82.2 - - + +
771E ILE* 1.3 67.2 + - + +
772E ARG 3.8 0.4 - - - -
773E PRO* 3.8 7.1 - - - +
774E TRP* 3.7 24.6 - - - +
829E LEU* 3.8 21.6 - - + +
833E GLU* 3.3 41.8 + - + +
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Residues in contact with ILE 771 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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762E VAL* 5.5 7.4 - - + -
763E ASP 5.2 1.6 - - - +
766E LEU* 2.9 28.1 + - + +
767E MET* 3.8 41.1 - - + +
770E ARG* 1.3 80.4 - - + +
772E ARG* 1.3 66.2 + - - +
774E TRP* 3.3 4.9 + - - +
775E ILE* 3.1 44.2 + - + +
798E VAL* 5.4 5.6 - - + -
826E MET* 5.7 3.4 - - + -
829E LEU* 4.7 12.9 - - + +
830E LEU* 3.9 30.1 - - + -
833E GLU* 6.3 2.2 - - + -
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Residues in contact with ARG 772 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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767E MET* 3.0 21.3 + - + +
768E GLU* 4.9 5.6 - - - +
771E ILE* 1.3 78.8 - - - +
773E PRO* 1.4 62.5 - - + +
775E ILE* 3.4 5.2 + - - +
776E ASN* 2.9 32.3 + - - +
791E VAL* 4.8 3.7 - - + +
795E CYS* 4.7 17.3 - - - -
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Residues in contact with PRO 773 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
817A GLU* 5.4 0.5 - - - +
768E GLU 4.4 4.9 - - - +
769E ARG 3.4 26.5 - - - +
770E ARG* 3.8 11.2 - - - +
771E ILE 3.6 2.5 - - - +
772E ARG* 1.4 94.6 - - + +
774E TRP* 1.3 61.4 + - - +
776E ASN* 4.0 6.8 + - + +
777E LYS* 3.2 24.6 + - - +
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Residues in contact with TRP 774 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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812A ALA* 5.3 11.6 + - + +
813A MET* 6.0 1.4 - - - -
817A GLU* 6.0 1.3 - - - -
770E ARG* 3.7 23.1 - - - +
771E ILE 3.3 8.7 + - - +
772E ARG 3.2 0.6 - - - -
773E PRO* 1.3 77.9 - - - +
775E ILE* 1.3 76.7 + - + +
777E LYS* 3.4 6.6 + - - +
778E LYS* 3.3 67.8 + - + +
822E PHE* 4.0 14.6 - + - -
825E LYS* 3.7 25.8 - - + -
826E MET* 3.5 40.8 - - + -
829E LEU* 3.7 35.1 - - + +
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Residues in contact with ILE 775 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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771E ILE* 3.1 39.0 + - + +
772E ARG* 3.9 4.5 - - - +
774E TRP* 1.3 86.8 - - + +
776E ASN* 1.3 63.0 + - - +
778E LYS* 3.0 16.3 + - - +
779E ILE* 3.2 16.0 + - + +
791E VAL* 4.0 28.0 - - + +
794E VAL* 3.9 15.3 - - + -
795E CYS* 4.1 16.2 - - - +
798E VAL* 5.1 1.3 - - + -
822E PHE* 4.3 12.6 - - + -
826E MET* 3.8 32.5 - - + -
829E LEU* 6.3 0.2 - - + -
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Residues in contact with ASN 776 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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772E ARG 2.9 19.1 + - - +
773E PRO* 4.0 6.5 + - + +
775E ILE* 1.3 76.5 - - - +
777E LYS* 1.3 62.3 + - - +
779E ILE* 3.2 12.6 + - - +
780E ILE* 3.3 24.7 + - - +
786E GLU* 3.9 19.9 - - - +
787E GLU 5.4 0.3 - - - -
788E ALA* 5.4 1.4 - - - -
791E VAL* 3.7 29.6 - - + +
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Residues in contact with LYS 777 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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817A GLU* 4.0 22.4 - - + +
773E PRO 3.2 17.1 + - - +
774E TRP* 3.6 7.0 - - - +
775E ILE 3.3 0.2 - - - -
776E ASN* 1.3 79.2 - - - +
778E LYS* 1.3 70.5 + - - +
780E ILE* 3.8 17.2 + - + +
781E GLU* 3.3 22.2 + - - +
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Residues in contact with LYS 778 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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817A GLU* 5.7 1.8 + - - -
774E TRP* 3.4 67.4 + - + +
775E ILE 3.0 9.9 + - - +
777E LYS* 1.3 82.8 - - - +
779E ILE* 1.3 59.6 + - - +
781E GLU* 3.2 30.5 + - - +
782E TYR* 2.9 51.9 + - + +
822E PHE* 3.6 16.8 - - + -
825E LYS* 4.8 12.8 - - - +
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Residues in contact with ILE 779 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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775E ILE* 3.4 19.1 - - + +
776E ASN 3.2 6.8 + - - +
778E LYS* 1.3 75.9 - - - +
780E ILE* 1.3 57.9 + - - +
782E TYR* 4.4 3.4 - - + +
783E ILE* 2.7 39.8 + - + +
785E GLU 4.1 0.4 - - - +
787E GLU* 3.3 43.3 - - + +
790E LEU* 4.9 13.7 - - + -
791E VAL* 3.7 22.9 - - + +
794E VAL* 5.5 4.0 - - + -
811E VAL* 6.1 1.3 - - + -
815E LEU* 5.0 15.5 - - + -
822E PHE* 4.5 19.1 - - + -
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Residues in contact with ILE 780 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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765B ILE* 4.2 28.2 - - + +
769B ARG* 4.4 2.1 + - - -
776E ASN* 3.3 28.5 - - - +
777E LYS* 3.8 17.0 - - + +
779E ILE* 1.3 76.1 - - - +
781E GLU* 1.3 63.1 + - - +
783E ILE 3.3 17.5 - - - +
785E GLU* 3.9 15.0 + - - +
786E GLU* 3.7 29.6 - - + +
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Residues in contact with GLU 781 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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765B ILE* 6.3 0.9 - - - -
769B ARG* 2.9 17.5 + - - -
777E LYS* 3.3 11.9 + - - +
778E LYS* 3.2 42.1 + - - +
779E ILE 3.1 0.2 - - - -
780E ILE* 1.3 80.9 - - - +
782E TYR* 1.3 72.6 + - + +
825E LYS* 5.1 6.8 + - - -
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Residues in contact with TYR 782 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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769B ARG* 2.9 22.4 + - - +
778E LYS* 2.9 40.0 + - + +
779E ILE* 4.2 4.0 - - + +
781E GLU* 1.3 95.4 + - + +
783E ILE* 1.3 57.8 + - + +
815E LEU* 4.1 33.4 - - + -
818E GLU* 3.7 44.2 - - + +
821E VAL* 4.5 8.4 + - + +
822E PHE* 3.5 48.9 + + + -
825E LYS* 4.8 9.7 + - - +
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Residues in contact with ILE 783 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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765B ILE* 5.7 1.2 - - - +
769B ARG* 3.2 29.8 + - - +
779E ILE* 2.7 28.9 + - + +
780E ILE 3.3 14.0 - - - +
782E TYR* 1.3 73.8 - - + +
785E GLU 4.1 27.3 + - - +
787E GLU* 4.7 7.2 - - + -
815E LEU* 5.3 8.3 - - + -
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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