Contacts of the helix formed by residues 1001 - 1017 (chain A) in PDB entry 3KSY
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 MET1001 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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997A MET* 4.1 4.5 - - - -
999A ASN 5.5 0.7 - - - +
1000A SER* 1.3 80.2 - - - +
1002A GLU* 1.3 69.9 + - + +
1003A LYS* 3.4 7.4 - - + +
1004A GLU* 4.0 17.2 + - + +
1005A PHE* 3.0 25.5 + - - +
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Residues in contact with GLU1002 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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829A THR* 4.4 12.0 - - - +
833A LEU* 4.0 16.7 - - - +
997A MET* 3.4 25.4 - - - +
1001A MET* 1.3 75.6 - - + +
1003A LYS* 1.3 65.9 + - - +
1005A PHE* 4.0 1.4 - - - +
1006A THR* 3.0 39.2 + - - +
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Residues in contact with LYS1003 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1001A MET* 3.4 5.4 - - + +
1002A GLU* 1.3 82.3 - - - +
1004A GLU* 1.3 65.7 + - - +
1006A THR* 3.6 4.8 - - - +
1007A ASP* 3.0 56.6 + - - +
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Residues in contact with GLU1004 (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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1000A SER* 4.1 24.6 + - - +
1001A MET* 3.5 21.6 + - + +
1002A GLU 3.4 0.4 - - - -
1003A LYS* 1.3 81.4 - - - +
1005A PHE* 1.3 63.9 + - - +
1007A ASP* 3.2 9.2 + - - +
1008A TYR* 3.1 22.1 + - + +
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Residues in contact with PHE1005 (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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833A LEU* 4.2 25.8 - - + -
837A LYS* 3.8 26.5 - - + -
996A PRO* 3.3 29.4 - - + -
997A MET* 3.7 33.7 - - + -
1000A SER* 4.4 7.6 - - - -
1001A MET 3.0 17.8 + - - +
1002A GLU 4.1 0.9 - - - +
1004A GLU* 1.3 77.7 - - - +
1006A THR* 1.3 64.5 + - - +
1008A TYR* 3.4 25.9 + + - +
1009A LEU* 3.1 53.1 + - + +
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Residues in contact with THR1006 (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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833A LEU* 4.9 9.7 - - - +
881A SER* 6.6 0.2 - - - -
882A PRO* 4.6 6.5 - - + +
1002A GLU* 3.0 34.2 + - - +
1003A LYS* 3.6 5.6 - - - +
1005A PHE* 1.3 76.7 - - - +
1007A ASP* 1.3 69.9 + - - +
1009A LEU* 3.2 14.4 + - + +
1010A PHE* 3.2 21.1 + - + +
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Residues in contact with ASP1007 (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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1003A LYS* 3.0 48.5 + - - +
1004A GLU* 3.5 9.6 - - - +
1006A THR* 1.3 80.7 - - - +
1008A TYR* 1.3 52.6 + - - +
1010A PHE* 3.0 9.3 + - - +
1011A ASN* 2.8 47.0 + - - +
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Residues in contact with TYR1008 (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 GLU* 3.1 38.6 + - + +
1004A GLU* 3.1 11.9 + - + +
1005A PHE* 3.4 27.6 - + + +
1007A ASP* 1.3 79.2 - - - +
1009A LEU* 1.3 72.7 - - + +
1011A ASN* 3.2 11.9 + - + +
1012A LYS* 2.8 60.5 + - + +
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Residues in contact with LEU1009 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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833A LEU* 4.3 6.3 - - + +
836A GLU* 3.4 33.2 - - + +
837A LYS* 4.0 11.9 - - - +
840A VAL* 3.4 27.9 - - + +
882A PRO* 3.6 22.0 - - + +
1005A PHE* 3.1 53.7 + - + +
1006A THR* 3.4 12.1 - - + +
1007A ASP 3.2 0.4 - - - -
1008A TYR* 1.3 84.1 - - + +
1010A PHE* 1.3 58.4 + - - +
1012A LYS* 3.2 5.4 + - - +
1013A SER* 3.0 22.5 + - - -
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Residues in contact with PHE1010 (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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881A SER* 3.7 36.3 - - - -
882A PRO* 3.8 9.4 - - + +
885A ARG* 4.2 18.2 - - - -
1006A THR* 3.2 9.6 + - + +
1007A ASP* 3.0 10.8 + - - +
1009A LEU* 1.3 79.9 - - - +
1011A ASN* 1.3 66.0 + - - +
1013A SER* 3.3 3.0 + - - -
1014A LEU* 3.1 54.1 + - + +
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Residues in contact with ASN1011 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1007A ASP* 2.8 31.9 + - - +
1008A TYR* 3.5 10.8 - - + +
1010A PHE* 1.3 81.3 - - - +
1012A LYS* 1.3 60.6 + - - +
1014A LEU* 3.2 18.9 + - - +
1015A GLU* 3.1 21.5 + - - +
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Residues in contact with LYS1012 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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840A VAL* 3.8 28.0 - - + +
841A GLU* 5.1 4.7 + - + +
843A GLU* 2.9 29.4 + - + -
1008A TYR* 2.8 55.1 + - + +
1009A LEU 3.2 6.0 + - - +
1011A ASN* 1.3 73.4 - - - +
1013A SER* 1.3 60.6 + - - +
1014A LEU 3.3 0.2 - - - -
1015A GLU* 3.1 30.3 + - + +
1016A ILE* 2.9 39.8 + - + +
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Residues in contact with SER1013 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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840A VAL* 4.5 1.1 - - - +
882A PRO* 2.7 35.2 + - - -
885A ARG* 2.8 42.1 + - - +
886A LEU* 3.4 4.9 - - - +
1009A LEU 3.0 11.8 + - - -
1010A PHE* 3.4 9.9 - - - -
1011A ASN 3.2 0.4 - - - -
1012A LYS* 1.3 77.8 - - - +
1014A LEU* 1.3 57.4 + - - +
1015A GLU 3.1 0.2 - - - -
1016A ILE* 3.4 11.5 - - - +
1017A GLU* 3.1 19.9 + - - +
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Residues in contact with LEU1014 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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885A ARG* 3.5 33.2 - - - +
1010A PHE* 3.1 42.3 + - + +
1011A ASN* 3.2 18.6 + - - +
1013A SER* 1.3 75.5 - - - +
1015A GLU* 1.3 59.5 + - - +
1017A GLU 4.0 4.0 - - - -
1018A PRO* 3.6 21.1 - - + +
1019A ARG* 4.7 30.7 - - + +
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Residues in contact with GLU1015 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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843A GLU* 3.6 9.3 - - - +
1011A ASN 3.1 11.0 + - - +
1012A LYS* 3.1 46.0 + - + +
1013A SER 3.1 0.2 - - - -
1014A LEU* 1.3 79.3 - - - +
1016A ILE* 1.3 66.6 + - + +
1017A GLU 3.2 1.9 + - - -
1018A PRO* 3.9 10.1 - - - +
1025A PRO* 4.4 1.4 - - - +
1027A PHE* 3.2 34.0 - - + -
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Residues in contact with ILE1016 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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840A VAL* 3.4 33.2 - - + +
843A GLU* 3.6 32.5 - - + +
848A ARG* 3.7 44.3 + - - +
886A LEU* 3.7 18.8 - - + -
1012A LYS* 2.9 23.5 + - + +
1013A SER* 3.4 10.5 - - - +
1015A GLU* 1.3 77.3 - - + +
1017A GLU* 1.3 67.0 + - - +
1018A PRO* 3.9 3.1 - - - +
1024A LEU* 4.3 9.5 - - - +
1027A PHE* 3.8 18.3 - - + -
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Residues in contact with GLU1017 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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848A ARG* 3.3 12.4 + - - +
885A ARG* 2.8 28.5 + - - +
886A LEU* 3.2 37.0 - - + +
887A ASP 3.4 1.0 + - - -
888A HIS* 3.3 35.7 - - + +
889A THR* 2.7 36.6 + - - -
1013A SER 3.1 12.7 + - - +
1014A LEU* 4.0 2.2 - - - -
1016A ILE* 1.3 86.1 - - - +
1018A PRO* 1.3 71.2 - - - +
1024A LEU* 4.6 5.4 - - + -
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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