Contacts of the helix formed by residues 805 - 817 (chain A) in PDB entry 3S51
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 805 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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672A HIS* 3.4 27.1 - - - -
754A GLU* 2.9 27.9 + - - -
803A LEU 3.4 4.2 + - - -
804A LEU* 1.3 75.0 - - - +
806A LEU* 1.3 64.2 + - - +
807A LYS* 3.9 7.1 + - - +
808A PHE* 3.1 11.6 + - - +
809A VAL* 3.1 17.3 + - - +
848A LYS* 4.3 2.0 - - - +
860A GLY* 4.8 3.1 - - - -
861A PRO* 3.7 21.8 - - - -
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Residues in contact with LEU 806 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
804A LEU 3.6 2.3 + - - -
805A SER* 1.3 70.2 - - - +
807A LYS* 1.3 66.1 + - - +
809A VAL* 3.2 11.1 + - + +
810A SER* 2.9 20.3 + - - -
848A LYS* 3.9 23.0 - - + +
849A ILE* 5.5 3.4 - - + +
852A LEU* 5.5 6.7 - - + -
858A VAL* 3.6 44.0 - - + +
860A GLY 5.5 0.8 - - - +
861A PRO 5.1 6.2 + - - +
862A ASP 6.1 0.9 - - - +
863A GLY* 6.2 0.9 - - - -
869A ILE* 5.3 8.5 - - + +
872A ASN* 3.2 41.3 - - + +
873A LEU* 6.0 1.6 - - + -
876A ILE* 4.5 15.3 - - + -
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Residues in contact with LYS 807 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
805A SER* 4.3 7.2 - - - +
806A LEU* 1.3 77.5 - - - +
808A PHE* 1.3 56.9 + - - +
810A SER* 3.3 2.6 + - - -
811A ASP* 2.9 53.3 + - - +
861A PRO 5.6 3.9 + - - +
862A ASP* 6.1 4.5 - - + +
868A LYS* 6.1 3.4 - - + -
872A ASN* 3.5 30.8 - - - +
875A ASP* 4.8 10.1 + - - -
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Residues in contact with PHE 808 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
753A MET* 4.4 3.8 - - + -
754A GLU* 3.2 56.1 - - - +
757A PHE* 3.4 50.5 - + + -
758A SER* 5.5 2.9 - - - -
770A ILE* 6.3 1.6 - - + -
804A LEU* 3.7 30.3 - - + -
805A SER* 3.1 8.9 + - - +
807A LYS* 1.3 75.9 - - - +
809A VAL* 1.3 64.2 + - - +
810A SER 3.0 4.9 + - - -
811A ASP* 3.1 7.1 + - + +
812A LEU* 3.0 55.3 + - + +
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Residues in contact with VAL 809 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
804A LEU* 3.6 23.3 - - + +
805A SER 3.1 14.8 + - - +
806A LEU* 3.2 14.1 + - + +
808A PHE* 1.3 76.0 - - - +
810A SER* 1.3 59.4 + - - +
812A LEU* 3.7 8.3 - - + -
813A LEU* 3.3 24.1 + - + +
841A ALA 4.5 5.6 - - - +
844A VAL* 3.5 23.3 - - + -
845A THR* 3.5 40.6 - - - +
848A LYS* 4.8 3.4 - - + -
876A ILE* 4.1 6.9 - - + +
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Residues in contact with SER 810 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
806A LEU 2.9 11.9 + - - -
807A LYS* 3.3 10.3 + - - +
808A PHE 3.0 0.2 - - - -
809A VAL* 1.3 76.2 - - - +
811A ASP* 1.3 72.7 + - - +
813A LEU* 3.1 4.5 + - - +
814A THR* 2.9 26.7 + - - -
872A ASN* 3.6 14.8 + - - -
875A ASP* 3.2 30.2 + - - +
876A ILE* 3.7 21.7 - - - +
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Residues in contact with ASP 811 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
757A PHE* 5.1 12.8 - - + -
807A LYS* 2.9 49.5 + - - +
808A PHE* 3.1 8.1 + - + +
810A SER* 1.3 82.8 + - - +
812A LEU* 1.3 51.7 + - - +
814A THR* 3.2 8.6 + - - -
815A ALA* 2.6 36.3 + - - +
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Residues in contact with LEU 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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757A PHE* 4.1 23.3 - - + -
804A LEU* 5.1 4.5 - - + -
808A PHE* 3.0 54.2 + - + +
809A VAL* 3.7 17.0 - - + +
811A ASP* 1.3 74.4 - - - +
813A LEU* 1.3 61.5 + - + +
815A ALA* 3.4 8.0 - - - +
816A LEU* 2.6 67.9 + - + +
831A LEU* 5.4 2.0 - - + -
837A PHE* 4.3 15.7 - - + -
841A ALA* 4.1 17.3 - - + +
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Residues in contact with LEU 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 VAL* 3.3 17.2 + - + +
810A SER* 3.1 4.1 + - - +
812A LEU* 1.3 80.5 - - + +
814A THR* 1.3 59.7 + - - +
816A LEU* 4.0 7.0 - - + -
817A PHE* 3.1 36.6 + - + -
841A ALA* 3.5 37.5 - - + +
842A VAL* 4.2 11.9 - - + -
845A THR* 3.5 31.0 - - - -
876A ILE* 5.2 9.6 - - + -
879A VAL* 3.0 24.6 - - + +
880A LEU* 4.8 13.9 - - + -
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Residues in contact with THR 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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810A SER* 2.9 20.8 + - - -
811A ASP* 3.4 10.8 - - - -
813A LEU* 1.3 75.3 - - - +
815A ALA* 1.3 59.1 + - - +
818A ARG* 3.4 19.7 + - + +
819A ASP* 3.0 24.1 + - + +
875A ASP* 4.0 8.3 + - - +
876A ILE* 5.3 0.3 - - - -
878A ARG* 5.1 4.1 + - - +
879A VAL* 3.1 29.5 - - + +
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Residues in contact with ALA 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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757A PHE* 4.4 16.6 - - + -
811A ASP 2.6 20.3 + - - +
812A LEU* 3.1 10.7 + - - +
814A THR* 1.3 74.6 - - - +
816A LEU* 1.3 61.5 + - + +
819A ASP* 2.9 42.7 - - + +
828A LEU* 3.4 7.0 - - - +
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Residues in contact with LEU 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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767A PHE* 6.0 0.4 - - + -
812A LEU* 2.6 50.9 + - + +
813A LEU* 4.0 13.9 - - + -
815A ALA* 1.3 75.0 - - + +
817A PHE* 1.3 72.0 + - + +
819A ASP 3.9 0.2 - - - +
827A SER 5.6 0.2 - - - -
828A LEU* 3.1 45.6 - - + +
831A LEU* 3.6 31.4 - - + -
832A ARG* 5.5 3.3 - - + +
837A PHE* 4.3 1.1 - - + -
838A MET* 3.3 35.4 - - + -
841A ALA* 4.3 4.5 - - + -
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Residues in contact with PHE 817 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
813A LEU* 3.1 40.8 + - + +
816A LEU* 1.3 86.5 - - + +
818A ARG* 1.3 65.6 + - - +
819A ASP 3.6 1.7 + - - +
820A SER* 4.7 5.0 + - - -
828A LEU* 5.1 0.5 - - - +
838A MET* 4.8 12.6 - - - -
842A VAL* 3.7 31.4 - - + -
879A VAL* 4.0 12.8 - - + +
880A LEU* 5.7 2.7 - - + -
882A TRP* 3.2 40.0 - + + -
883A ARG* 3.4 56.5 - - + -
903A ILE* 4.0 10.3 - - + -
907A CYS* 4.6 4.5 - - - -
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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