Contacts of the helix formed by residues 803 - 816 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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759A TRP* 5.7 0.2 - - - -
801A HIS 4.0 0.6 + - - -
802A SER* 1.3 74.4 - - - +
804A PRO* 1.3 77.4 - - - +
805A GLN* 3.6 12.6 + - - +
806A SER* 2.8 31.5 + - - -
807A ILE* 3.3 7.3 + - - +
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Residues in contact with PRO 804 (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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753A PHE* 3.5 51.6 - - + +
759A TRP* 5.6 1.1 - - + -
802A SER 3.5 0.8 - - - +
803A SER* 1.3 87.6 - - - +
805A GLN* 1.3 61.7 + - + +
807A ILE* 3.5 6.1 + - + +
808A LEU* 3.2 21.7 + - - +
823A ILE* 3.8 7.1 - - + +
827A TRP* 3.4 53.8 - - + -
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Residues in contact with GLN 805 (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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749A LYS* 3.0 32.7 + - - +
753A PHE* 3.6 13.3 - - + -
803A SER* 3.1 8.6 - - - +
804A PRO* 1.3 79.5 - - - +
806A SER* 1.3 64.2 + - - +
808A LEU* 3.5 19.9 + - - +
809A ASP* 3.1 59.1 + - - +
825E LYS* 4.9 7.5 - - - +
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Residues in contact with SER 806 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
797A LYS* 4.2 12.8 + - - -
802A SER* 4.6 6.2 + - - -
803A SER* 2.8 27.6 + - - -
805A GLN* 1.3 79.5 - - - +
807A ILE* 1.3 60.0 + - - +
809A ASP* 3.6 10.4 + - - +
810A ASP* 3.0 27.0 + - - +
828E ARG* 4.7 0.3 + - - -
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Residues in contact with ILE 807 (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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793A PHE* 5.1 3.6 - - + -
794A VAL* 4.2 20.6 - - + -
797A LYS* 4.3 22.9 - - + +
798A VAL* 4.5 17.9 - - + -
802A SER* 4.1 26.9 - - - +
803A SER 3.3 14.6 + - - +
804A PRO* 3.8 4.0 - - + +
806A SER* 1.3 73.9 - - - +
808A LEU* 1.3 67.3 + - - +
810A ASP* 2.8 19.4 + - - +
811A VAL* 2.9 31.1 + - + +
823A ILE* 4.4 10.1 - - + -
826A MET* 5.6 2.5 - - - -
827A TRP* 4.2 20.9 - - + -
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Residues in contact with LEU 808 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
749A LYS* 4.7 2.7 - - - +
753A PHE* 3.8 30.1 - - + -
804A PRO 3.2 12.4 + - - +
805A GLN* 3.6 25.6 - - - +
807A ILE* 1.3 77.1 - - - +
809A ASP* 1.3 59.6 + - - +
811A VAL* 3.3 4.3 + - - +
812A ALA* 2.9 39.5 + - + +
819A ALA* 4.1 1.9 - - - +
820A GLU* 3.8 50.5 - - + +
823A ILE* 3.9 18.7 - - + +
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Residues in contact with ASP 809 (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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805A GLN* 3.1 42.5 + - - +
806A SER* 3.6 10.5 - - - +
807A ILE 3.1 0.2 - - - -
808A LEU* 1.3 77.4 - - - +
810A ASP* 1.3 61.8 + - - +
812A ALA* 3.5 12.9 + - - +
813A MET* 3.4 16.8 - - - +
825E LYS* 4.0 29.3 + - + +
828E ARG* 3.4 19.9 + - - +
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Residues in contact with ASP 810 (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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793A PHE* 3.8 27.2 - - + -
797A LYS* 3.0 27.5 + - - -
806A SER* 3.0 16.2 + - - +
807A ILE* 2.8 7.7 + - - +
809A ASP* 1.3 75.9 - - - +
811A VAL* 1.3 62.0 + - - +
813A MET* 3.3 21.9 - - - +
814A VAL* 4.3 6.1 - - - +
742E ILE* 4.1 19.9 - - + +
828E ARG* 2.6 39.2 + - - +
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Residues in contact with VAL 811 (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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793A PHE* 5.0 4.5 - - + -
794A VAL* 4.7 17.0 - - + -
807A ILE* 2.9 37.0 + - + +
808A LEU* 3.9 5.8 - - - +
810A ASP* 1.3 74.8 - - + +
812A ALA* 1.3 57.0 + - - +
813A MET 3.0 5.2 - - - -
814A VAL* 2.9 23.5 + - + +
815A LEU* 3.0 31.4 + - + -
819A ALA* 3.6 18.5 - - + +
822A PHE* 4.4 14.6 - - + -
823A ILE* 4.4 9.9 - - + -
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Residues in contact with ALA 812 (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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808A LEU* 2.9 25.1 + - + +
809A ASP* 3.6 10.1 - - - +
811A VAL* 1.3 76.1 - - - +
813A MET* 1.3 58.4 + - - +
814A VAL 3.1 2.1 + - - -
815A LEU 4.1 0.4 - - - -
816A ASP* 3.6 22.9 + - - +
819A ALA* 3.8 10.9 - - + +
770E ARG* 3.0 17.5 + - - -
774E TRP* 5.3 11.5 - - + +
829E LEU* 6.0 0.2 - - - -
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Residues in contact with MET 813 (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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809A ASP 3.4 13.2 - - - +
810A ASP* 3.3 19.5 - - - +
811A VAL 3.0 0.6 - - - -
812A ALA* 1.3 76.6 - - - +
814A VAL* 1.3 57.3 + - + +
742E ILE* 5.4 5.2 - - + -
770E ARG* 3.4 22.4 + - - +
774E TRP* 6.0 1.3 - - - -
825E LYS 5.2 2.0 - - - +
828E ARG* 3.2 55.9 - - + +
829E LEU* 3.8 26.2 - - - -
832E TYR* 3.2 55.0 - - + -
833E GLU* 4.1 1.7 - - - +
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Residues in contact with VAL 814 (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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790A LEU* 5.8 9.4 - - + -
810A ASP 4.3 9.0 - - - +
811A VAL* 2.9 10.9 + - + +
813A MET* 1.3 82.8 - - - +
815A LEU* 1.3 76.7 + - + +
816A ASP* 3.8 7.0 + - - +
738E ILE* 5.4 8.7 - - + -
742E ILE* 5.9 0.4 - - + -
770E ARG* 4.6 4.9 + - - +
832E TYR* 3.3 26.9 - - + +
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Residues in contact with LEU 815 (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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779A ILE* 5.0 16.2 - - + -
782A TYR* 3.8 45.3 - - + +
783A ILE* 4.8 9.9 - - + -
811A VAL* 3.0 24.7 + - + +
814A VAL* 1.3 99.7 - - + +
816A ASP* 1.3 70.4 + - - +
818A GLU* 3.1 15.3 + - + +
819A ALA* 3.1 26.9 + - + +
822A PHE* 5.1 7.6 - - + -
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Residues in contact with ASP 816 (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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812A ALA* 3.6 22.0 + - - +
814A VAL 4.5 1.4 - - - +
815A LEU* 1.3 81.3 - - - +
817A GLU* 1.3 74.2 + - - +
818A GLU* 4.4 1.6 - - + +
819A ALA* 3.3 16.5 + - - +
820A GLU* 4.2 1.4 + - - +
770E ARG* 3.0 28.6 + - - +
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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