Contacts of the helix formed by residues 1005 - 1023 (chain A) in PDB entry 4DQL
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 GLN1005 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1002A ASP* 3.0 8.6 + - - +
1004A SER* 1.3 102.6 + - - +
1006A MET* 1.3 69.2 + - - +
1007A ALA 3.5 0.7 - - - -
1008A PRO* 3.5 4.7 - - - +
1009A ALA* 3.3 21.1 + - - +
1102A NAP 3.7 20.2 + - + +
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Residues in contact with MET1006 (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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902A VAL* 4.6 0.9 - - - -
904A PRO* 3.7 31.0 - - + -
976A VAL* 4.4 0.2 - - + -
999A ILE* 3.8 15.7 - - + -
1000A CYS 3.1 27.6 - - - +
1001A GLY* 4.1 0.4 - - - -
1002A ASP* 2.9 43.4 + - + +
1005A GLN* 1.3 77.7 - - - +
1007A ALA* 1.3 66.8 + - + +
1009A ALA* 2.9 13.9 + - - +
1010A VAL* 3.0 32.2 + - + +
1102A NAP 3.5 40.3 + - + +
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Residues in contact with ALA1007 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
999A ILE* 4.0 18.3 - - + +
1002A ASP 3.0 21.4 + - - +
1003A GLY* 4.0 4.9 - - - -
1006A MET* 1.3 78.2 - - - +
1008A PRO* 1.3 71.8 - - + +
1010A VAL* 3.3 2.0 + - - +
1011A GLU* 3.0 24.4 + - - +
1044A LYS* 5.1 9.9 - - - +
1046A VAL* 3.9 24.7 - - + -
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Residues in contact with PRO1008 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1003A GLY 3.3 24.7 - - - +
1004A SER 3.8 12.6 - - - +
1005A GLN* 3.5 12.6 - - - +
1007A ALA* 1.3 91.4 - - + +
1009A ALA* 1.3 56.3 + - - +
1011A GLU* 3.6 9.7 + - + +
1012A ALA* 3.0 27.5 + - - +
1044A LYS* 6.0 0.7 - - - +
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Residues in contact with ALA1009 (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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977A GLN* 3.6 27.1 - - + +
1005A GLN 3.3 15.5 + - - +
1006A MET 2.9 4.0 + - - +
1008A PRO* 1.3 79.0 - - - +
1010A VAL* 1.3 63.2 + - - +
1012A ALA* 3.3 7.0 + - - +
1013A THR* 3.0 27.5 + - - -
1102A NAP 4.9 2.9 - - - +
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Residues in contact with VAL1010 (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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902A VAL* 3.9 5.8 - - + -
976A VAL* 3.8 22.2 - - + -
977A GLN* 3.8 18.2 - - + +
980A MET* 3.8 22.9 - - + +
997A PHE* 4.0 9.9 - - + -
999A ILE* 3.6 24.2 - - + -
1006A MET* 3.0 37.1 + - - +
1007A ALA 3.7 3.8 - - - +
1009A ALA* 1.3 71.2 - - - +
1011A GLU* 1.3 67.5 + - - +
1013A THR* 3.1 4.0 + - - -
1014A LEU* 2.9 22.4 + - - +
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Residues in contact with GLU1011 (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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999A ILE* 4.3 0.8 - - - +
1007A ALA 3.0 16.0 + - - +
1008A PRO* 3.7 8.3 - - + +
1010A VAL* 1.3 79.9 - - - +
1012A ALA* 1.3 61.1 + - - +
1014A LEU* 3.3 6.3 + - - +
1015A MET* 3.1 35.7 + - + +
1030A ARG* 4.6 12.1 + - - -
1033A LEU* 3.5 22.4 - - + +
1037A GLU* 5.2 0.7 - - - +
1042A TYR* 2.5 35.3 + - - +
1044A LYS* 2.5 27.3 + - - -
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Residues in contact with ALA1012 (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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1008A PRO 3.0 19.0 + - - +
1009A ALA* 3.7 7.6 - - - +
1010A VAL 3.3 0.4 - - - -
1011A GLU* 1.3 75.7 - - - +
1013A THR* 1.3 57.1 + - - +
1015A MET* 3.5 15.4 + - + +
1016A LYS* 2.9 29.0 + - - +
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Residues in contact with THR1013 (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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977A GLN* 3.4 38.9 + - + +
980A MET* 4.0 14.1 - - + -
981A GLU* 3.8 28.3 + - + +
1009A ALA 3.0 14.0 + - - -
1010A VAL* 3.1 7.4 + - - -
1012A ALA* 1.3 73.5 - - - +
1014A LEU* 1.3 66.6 + - - +
1016A LYS* 3.2 7.3 + - - +
1017A SER* 2.9 27.8 + - - +
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Residues in contact with LEU1014 (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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980A MET* 4.3 11.6 - - + +
987A LEU* 5.0 10.3 - - + -
988A ILE* 3.9 10.1 - - + +
991A LEU* 3.6 24.9 - - + -
997A PHE* 3.9 35.7 - - + -
1010A VAL 2.9 14.7 + - - +
1011A GLU* 3.3 6.3 + - - +
1013A THR* 1.3 77.3 - - - +
1015A MET* 1.3 58.2 + - + +
1017A SER* 3.1 8.1 + - - -
1018A TYR* 2.9 27.0 + - - +
1032A TRP* 3.8 18.2 - - + -
1033A LEU* 4.1 9.4 - - + -
1036A LEU* 5.1 0.7 - - + -
1042A TYR* 4.1 19.7 - - + -
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Residues in contact with MET1015 (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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1011A GLU* 3.1 34.6 + - + +
1012A ALA* 3.8 13.0 - - + +
1014A LEU* 1.3 75.5 - - - +
1016A LYS* 1.3 62.4 + - - +
1018A TYR* 3.3 4.5 + - - +
1019A ALA* 3.0 19.9 + - - +
1026A GLU 5.4 0.9 - - - +
1029A ALA* 3.3 28.3 - - + +
1030A ARG* 3.7 45.3 - - - -
1032A TRP* 4.5 3.6 - - + -
1033A LEU* 3.9 21.3 - - + -
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Residues in contact with LYS1016 (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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981A GLU* 4.2 24.0 - - + -
1012A ALA 2.9 18.2 + - - +
1013A THR* 3.2 7.8 + - - +
1015A MET* 1.3 78.1 - - - +
1017A SER* 1.3 56.9 + - - +
1019A ALA* 3.4 5.9 + - + +
1020A ASP* 2.7 67.0 + - - +
1026A GLU* 6.4 1.6 - - - -
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Residues in contact with SER1017 (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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980A MET 4.5 0.5 + - - -
981A GLU* 4.3 9.5 + - - +
984A GLY* 3.9 23.2 - - - -
987A LEU* 6.2 0.4 - - - -
988A ILE* 3.8 18.2 - - - -
1013A THR* 2.9 21.8 + - - +
1014A LEU* 3.4 11.9 - - - -
1016A LYS* 1.3 75.2 - - - +
1018A TYR* 1.3 63.3 + - - +
1020A ASP* 3.3 5.9 + - - +
1021A VAL* 2.9 29.1 + - - +
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Residues in contact with TYR1018 (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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988A ILE* 3.6 14.9 - - + +
992A ASP* 3.9 7.4 - - - -
1014A LEU 2.9 7.6 + - - +
1015A MET 3.6 7.4 - - - +
1016A LYS 3.3 0.2 - - - -
1017A SER* 1.3 75.5 - - - +
1019A ALA* 1.3 57.5 + - - +
1021A VAL 3.8 0.2 - - - -
1022A HIS* 2.9 64.8 + + + +
1024A VAL* 3.9 19.7 - - + +
1028A ASP* 4.6 2.9 - - + -
1029A ALA* 4.0 17.5 - - + -
1032A TRP* 3.3 76.2 - + + +
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Residues in contact with ALA1019 (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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1015A MET 3.0 16.5 + - - +
1016A LYS* 3.4 7.8 + - + +
1018A TYR* 1.3 76.2 - - - +
1020A ASP* 1.3 62.3 + - - +
1023A GLN* 2.9 24.9 + - - -
1024A VAL* 3.1 36.2 + - - +
1025A SER 4.2 11.4 - - - +
1026A GLU* 4.9 7.9 - - + +
1029A ALA* 4.3 2.5 - - + -
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Residues in contact with ASP1020 (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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1016A LYS* 2.7 61.3 + - - +
1017A SER* 3.8 6.0 + - - +
1019A ALA* 1.3 80.8 - - - +
1021A VAL* 1.3 67.5 + - + +
1022A HIS 3.5 0.2 + - - -
1023A GLN* 3.7 13.4 + - - +
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Residues in contact with VAL1021 (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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984A GLY 4.2 7.6 - - - +
985A LYS* 4.0 36.8 - - + +
988A ILE* 3.8 23.3 - - + -
989A GLU* 5.5 4.3 - - + +
992A ASP* 5.3 0.2 - - - +
1017A SER* 2.9 21.8 + - - +
1018A TYR 4.0 2.2 - - - +
1020A ASP* 1.3 78.6 - - + +
1022A HIS* 1.3 73.6 + - + +
1023A GLN* 3.7 6.4 + - - +
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Residues in contact with HIS1022 (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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988A ILE* 3.5 11.8 - - + +
992A ASP* 2.6 32.4 + - - -
1018A TYR* 2.9 50.7 + + + +
1021A VAL* 1.3 87.6 + - + +
1023A GLN* 1.3 73.1 + - - +
1024A VAL* 3.2 21.9 + - + +
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Residues in contact with GLN1023 (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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1019A ALA 2.9 10.3 + - - -
1020A ASP 3.7 11.2 + - - +
1021A VAL 3.5 5.3 - - - +
1022A HIS* 1.3 80.6 - - - +
1024A VAL* 1.3 60.8 + - - +
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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