Contacts of the helix formed by residues 996 - 1008 (chain A) in PDB entry 4B87
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 996 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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841A TYR* 4.3 1.6 - - - -
846A TYR 3.7 10.3 - - - -
847A THR* 4.8 0.9 - - - -
848A PHE* 3.3 40.9 - - - -
995A SER* 1.3 75.8 - - - +
997A TYR* 1.3 66.3 + - - +
998A LEU* 3.4 8.0 + - - +
999A GLU* 3.0 37.5 + - - +
1000A MET* 2.9 21.9 + - - +
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Residues in contact with TYR 997 (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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841A TYR 3.6 10.9 + - - +
842A CYS* 4.1 4.5 - - - -
843A SER* 3.1 40.6 - - - +
844A PRO* 3.6 37.3 - - + +
846A TYR 3.2 12.5 + - - +
996A SER* 1.3 75.4 - - - +
998A LEU* 1.3 71.4 + - + +
1000A MET* 3.3 5.2 + - - +
1001A LYS* 3.0 45.6 + - + +
1030A TYR* 4.1 21.4 - + - -
1033A GLU* 5.4 1.4 + - - -
1034A TRP* 3.0 42.7 + + - -
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Residues in contact with LEU 998 (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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846A TYR 4.8 0.8 + - - +
847A THR* 5.5 13.0 - - + -
996A SER* 3.3 7.2 + - - +
997A TYR* 1.3 95.7 - - + +
999A GLU* 1.3 57.8 + - + +
1001A LYS* 3.4 12.2 + - + +
1002A ARG* 2.9 30.8 + - - +
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Residues in contact with GLU 999 (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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817A ARG* 2.9 44.9 + - - +
818A ALA* 3.4 32.7 - - + +
848A PHE 5.5 0.3 - - - +
850A SER* 5.3 1.7 - - - -
995A SER* 3.5 4.9 - - - -
996A SER* 3.0 34.4 + - - +
998A LEU* 1.3 76.8 - - + +
1000A MET* 1.3 57.8 + - - +
1002A ARG* 3.5 7.0 + - - +
1003A PHE 3.0 23.2 + - - -
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Residues in contact with MET1000 (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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816A PHE* 5.3 0.9 - - + -
818A ALA* 4.6 0.7 - - - -
837A LEU* 4.0 31.9 - - + -
838A ASP 3.4 23.6 - - - +
839A THR* 3.9 3.8 - - - -
841A TYR 3.7 14.1 - - - +
842A CYS* 3.7 51.1 - - - +
995A SER* 4.0 24.2 - - - +
996A SER 2.9 11.9 + - - +
997A TYR* 3.6 5.2 - - - +
999A GLU* 1.3 76.0 - - - +
1001A LYS* 1.3 60.4 + - - +
1003A PHE* 3.3 5.9 + - - +
1004A VAL* 3.0 34.2 + - - +
1034A TRP* 4.1 6.7 - - + -
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Residues in contact with LYS1001 (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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997A TYR* 3.0 34.6 + - + +
998A LEU* 3.7 13.0 - - + +
1000A MET* 1.3 74.6 - - - +
1002A ARG* 1.3 66.7 + - - +
1004A VAL* 4.2 0.3 - - - +
1005A GLN* 2.9 49.8 + - - +
1034A TRP* 3.5 54.5 - - + +
1037A GLU* 3.0 36.7 + - - -
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Residues in contact with ARG1002 (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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820A PRO* 3.5 35.1 + - - +
823A GLU* 2.7 36.9 + - - +
998A LEU 2.9 18.1 + - - +
999A GLU* 3.8 7.0 - - - +
1001A LYS* 1.3 77.0 - - - +
1003A PHE* 1.3 62.6 + - - +
1005A GLN* 3.2 8.0 + - - +
1006A TRP* 3.0 23.6 + - + +
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Residues in contact with PHE1003 (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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799A MET* 5.2 1.3 - - - -
811A LEU* 3.8 23.6 - - + -
813A THR* 4.4 1.3 - - + -
816A PHE* 3.9 33.9 - + - -
818A ALA* 3.7 13.0 - - + -
819A ASP 5.2 3.1 - - - -
822A MET* 4.3 20.6 - - + -
823A GLU* 4.6 6.3 - - + -
827A LEU* 4.0 17.9 - - + -
835A LEU* 4.3 15.5 - - + -
837A LEU* 4.9 0.2 - - + -
999A GLU 3.0 18.5 + - - +
1000A MET* 3.6 3.4 - - - +
1002A ARG* 1.3 77.9 - - - +
1004A VAL* 1.3 69.0 + - + +
1006A TRP* 3.3 19.1 + + - +
1007A LEU* 2.8 44.5 + - + +
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Residues in contact with VAL1004 (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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835A LEU* 3.8 20.2 - - + -
837A LEU* 3.9 15.7 - - + -
1000A MET 3.0 20.5 + - - +
1003A PHE* 1.3 80.7 - - + +
1005A GLN* 1.3 62.5 + - - +
1007A LEU* 4.3 4.0 - - - +
1008A LYS* 2.8 26.9 + - - -
1009A PRO* 3.4 9.5 - - + +
1012A ILE* 3.5 25.1 - - + -
1031A PHE* 6.0 0.4 - - + +
1034A TRP* 3.8 26.7 - - + -
1040A TYR* 3.6 14.6 + - - +
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Residues in contact with GLN1005 (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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1001A LYS* 2.9 48.3 + - - +
1002A ARG* 3.9 5.8 - - - +
1004A VAL* 1.3 75.8 - - - +
1006A TRP* 1.3 57.3 + - - +
1008A LYS* 3.0 33.1 + - - +
1034A TRP* 2.9 44.3 + - + +
1037A GLU* 3.3 23.9 + - - +
1038A ALA* 3.8 16.9 - - + +
1040A TYR* 4.0 8.4 - - - +
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Residues in contact with TRP1006 (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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822A MET 4.0 6.1 - - - -
823A GLU* 3.3 68.6 + - + +
827A LEU* 3.7 17.5 - - + -
828A ALA* 3.7 32.8 - - + -
1002A ARG* 3.0 17.4 + - + +
1003A PHE* 3.5 13.7 - + - +
1005A GLN* 1.3 77.9 - - - +
1007A LEU* 1.3 98.5 + - + +
1008A LYS* 3.2 12.9 + - - +
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Residues in contact with LEU1007 (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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811A LEU* 4.1 9.2 - - + -
827A LEU* 4.4 17.3 - - + +
830A GLN 5.8 0.2 - - - +
831A LYS* 6.2 0.2 - - - +
832A VAL* 3.9 47.5 + - + +
835A LEU* 4.1 28.3 - - + -
1003A PHE* 2.8 24.5 + - + +
1004A VAL* 3.2 4.7 + - - +
1006A TRP* 1.3 103.4 - - + +
1008A LYS* 1.3 68.1 + - - +
1009A PRO* 3.4 9.3 - - + +
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Residues in contact with LYS1008 (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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831A LYS* 5.5 5.9 - - - +
832A VAL 4.3 2.6 - - - +
1004A VAL 2.8 11.6 + - - -
1005A GLN 3.0 23.7 + - - +
1006A TRP* 3.8 12.3 + - - +
1007A LEU* 1.3 77.9 - - - +
1009A PRO* 1.3 71.3 - - - +
1010A GLN* 4.9 3.6 - - - +
1038A ALA* 5.2 7.8 - - - +
1039A GLY 4.5 5.6 - - - -
1040A TYR* 3.5 45.0 - - + +
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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