Contacts of the helix formed by residues 803 - 812 (chain D) 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 SER 803 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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801D HIS 3.6 2.1 + - - -
802D SER* 1.3 74.4 - - - +
804D PRO* 1.3 74.5 - - - +
805D GLN* 4.3 5.4 - - - +
806D SER* 2.6 55.3 + - - -
807D ILE* 3.2 8.0 + - - +
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Residues in contact with PRO 804 (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 PHE* 3.4 53.4 - - + +
802D SER 3.6 0.6 - - - -
803D SER* 1.3 84.4 - - - +
805D GLN* 1.3 58.8 + - + +
807D ILE* 3.0 7.3 + - + +
808D LEU* 2.8 27.5 + - - +
823D ILE* 3.9 9.9 - - + +
827D TRP* 3.3 52.5 - - + -
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Residues in contact with GLN 805 (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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825C LYS* 4.7 10.7 - - - +
749D LYS* 2.9 29.8 + - - +
753D PHE* 3.0 21.7 - - + -
803D SER* 3.2 5.8 - - - +
804D PRO* 1.3 81.4 - - + +
806D SER* 1.3 53.8 + - - +
808D LEU* 3.0 17.9 + - - +
809D ASP* 2.7 62.5 + - - +
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Residues in contact with SER 806 (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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802D SER* 3.9 8.8 - - - -
803D SER* 2.6 44.1 + - - -
805D GLN* 1.3 76.5 - - - +
807D ILE* 1.3 63.6 + - - +
809D ASP* 3.4 13.7 + - - +
810D ASP* 3.3 22.9 + - - +
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Residues in contact with ILE 807 (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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793D PHE* 5.5 2.5 - - + -
794D VAL* 4.1 17.5 - - + -
797D LYS* 3.7 41.5 - - + -
798D VAL* 4.4 6.1 - - + -
802D SER* 4.0 13.7 - - - +
803D SER 3.4 13.7 - - - +
804D PRO 3.0 6.1 + - - +
806D SER* 1.3 76.2 + - - +
808D LEU* 1.3 63.6 + - - +
810D ASP* 3.1 8.4 + - - +
811D VAL* 3.0 29.8 + - + +
823D ILE* 3.5 21.5 - - + -
826D MET* 4.4 7.2 - - + -
827D TRP* 4.3 22.2 - - + -
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Residues in contact with LEU 808 (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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825C LYS* 5.9 3.6 - - - +
749D LYS* 4.0 12.1 - - - +
753D PHE* 3.9 30.3 - - + -
804D PRO 2.8 14.6 + - - +
805D GLN* 3.3 23.3 - - - +
807D ILE* 1.3 73.1 - - - +
809D ASP* 1.3 64.2 + - - +
811D VAL* 3.1 2.0 + - - +
812D ALA* 2.8 44.0 + - + +
819D ALA* 4.5 1.3 - - + +
820D GLU* 4.2 35.4 - - + +
823D ILE* 3.8 22.8 - - + +
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Residues in contact with ASP 809 (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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825C LYS* 4.7 11.0 + - - +
828C ARG* 3.6 15.5 - - - +
805D GLN* 2.7 51.2 + - - +
806D SER* 3.6 12.0 - - - +
807D ILE 3.3 0.2 - - - -
808D LEU* 1.3 74.2 - - - +
810D ASP* 1.3 59.7 + - - +
812D ALA* 4.0 8.7 + - - +
813D MET* 3.1 24.8 - - - +
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Residues in contact with ASP 810 (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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742C ILE* 3.5 42.8 - - + +
747C THR* 4.6 6.1 - - - +
828C ARG* 3.1 31.0 + - - +
793D PHE* 3.5 27.0 - - + -
797D LYS* 4.5 9.2 + - - +
806D SER 3.3 10.3 + - - +
807D ILE* 3.1 9.9 + - - +
809D ASP* 1.3 76.8 - - - +
811D VAL* 1.3 63.6 + - - +
812D ALA 3.4 0.2 - - - -
813D MET* 3.6 14.7 + - - +
814D VAL* 4.2 0.3 - - - +
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Residues in contact with VAL 811 (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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742C ILE* 5.7 0.2 - - - -
779D ILE* 5.9 1.3 - - + -
790D LEU* 5.2 9.4 - - + -
793D PHE* 4.9 6.3 - - + -
794D VAL* 4.4 18.8 - - + -
807D ILE* 3.0 33.6 + - + +
808D LEU* 4.0 4.5 - - - +
810D ASP* 1.3 75.6 - - + +
812D ALA* 1.3 52.9 + - - +
813D MET 2.9 5.8 - - - -
814D VAL* 2.8 30.2 + - + +
815D LEU* 2.9 42.9 + - + -
819D ALA* 3.8 9.9 - - + +
822D PHE* 4.0 15.7 - - + -
823D ILE* 5.0 0.4 - - + -
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Residues in contact with ALA 812 (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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770C ARG* 5.1 0.9 + - - -
774C TRP* 5.9 1.6 + - - -
829C LEU* 5.5 4.5 - - - +
808D LEU* 2.8 27.7 + - + +
809D ASP* 4.3 6.7 - - - +
810D ASP 3.4 0.2 - - - -
811D VAL* 1.3 75.6 - - - +
813D MET* 1.3 59.2 + - + +
814D VAL 3.4 0.2 - - - -
816D ASP* 3.3 30.4 + - - +
819D ALA* 3.4 20.0 - - + +
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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