Contacts of the helix formed by residues 1011 - 1026 (chain A) in PDB entry 1OFD
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 SER1011 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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227A ASN* 5.2 1.1 - - - -
228A GLY* 6.1 2.5 - - - -
350A ARG* 3.2 12.5 + - - -
502A VAL 3.1 17.0 + - - +
503A THR 4.1 7.6 - - - -
1009A ILE* 3.5 4.5 - - - +
1010A TYR* 1.3 83.1 - - - +
1012A ILE* 1.3 64.3 + - - +
1013A GLU* 3.1 32.0 - - - -
1014A ASP* 3.1 19.2 + - - +
1015A LEU 3.1 16.5 + - - -
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Residues in contact with ILE1012 (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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207A PHE* 3.7 48.9 - - + +
209A THR* 5.4 5.4 - - + -
502A VAL* 3.5 30.1 + - + -
503A THR* 4.3 15.2 - - + +
1011A SER* 1.3 73.0 - - - +
1013A GLU* 1.3 69.7 + - - +
1015A LEU* 3.1 6.6 + - + +
1016A ALA* 2.9 25.3 + - - +
1044A ILE 4.9 0.4 - - - +
1047A GLY* 3.4 33.7 - - - +
1048A VAL* 3.7 3.6 - - - +
1051A ALA* 4.0 8.7 - - + -
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Residues in contact with GLU1013 (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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1A CYS 3.0 23.7 + - - +
30A HIS 4.7 3.6 - - - +
31A ARG* 3.7 41.3 - - + +
207A PHE* 4.3 6.7 - - + -
227A ASN* 2.9 27.7 + - - -
350A ARG* 3.0 20.4 + - - +
1011A SER* 3.1 22.1 + - - +
1012A ILE* 1.3 84.2 - - - +
1014A ASP* 1.3 57.8 + - - +
1016A ALA* 3.3 10.2 + - - +
1017A GLN* 3.0 24.4 + - - +
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Residues in contact with ASP1014 (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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31A ARG* 4.5 6.9 + - - -
350A ARG* 2.9 39.6 + - - -
351A PRO* 5.5 0.3 - - - +
1008A ASP 3.4 23.2 - - - +
1009A ILE* 3.6 6.5 - - - -
1010A TYR* 3.0 17.5 + - - +
1011A SER* 3.1 17.8 + - - +
1012A ILE 3.2 0.8 - - - -
1013A GLU* 1.3 75.6 - - - +
1015A LEU* 1.3 65.2 + - - +
1017A GLN* 3.2 9.9 + - - +
1018A LEU* 3.0 18.9 + - - +
1311A GLN* 5.0 2.8 + - - -
1332A TYR* 3.7 19.5 + - - +
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Residues in contact with LEU1015 (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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502A VAL* 4.0 22.0 - - + -
965A ILE* 3.8 30.3 - - + -
967A MET* 4.8 1.1 - - - -
1009A ILE* 3.7 32.6 - - + +
1011A SER 3.1 8.0 + - - +
1012A ILE* 3.1 16.2 + - + +
1014A ASP* 1.3 74.3 - - - +
1016A ALA* 1.3 59.1 + - - +
1018A LEU* 3.1 1.8 + - + -
1019A ILE* 2.9 47.9 + - + +
1033A VAL* 4.2 9.2 - - + -
1048A VAL* 3.7 33.4 - - + -
1051A ALA* 4.3 1.8 - - + -
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Residues in contact with ALA1016 (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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30A HIS 5.3 5.4 - - - +
207A PHE* 4.8 7.6 - - + -
1012A ILE 2.9 10.0 + - - +
1013A GLU* 3.5 13.9 - - - +
1014A ASP 3.2 0.2 - - - -
1015A LEU* 1.3 76.8 - - - +
1017A GLN* 1.3 57.2 + - - +
1019A ILE* 3.8 1.8 - - - +
1020A TYR* 2.9 29.5 + - - +
1051A ALA* 3.7 37.7 - - + +
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Residues in contact with GLN1017 (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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30A HIS* 4.9 4.0 - - - -
1013A GLU 3.0 14.0 + - - +
1014A ASP* 3.4 12.3 - - - +
1015A LEU 3.1 0.2 - - - -
1016A ALA* 1.3 77.0 - - - +
1018A LEU* 1.3 57.4 + - - +
1020A TYR* 3.3 13.4 + - - +
1021A ASP* 2.7 58.2 + - - +
1278A ARG* 3.6 26.1 + - - +
1279A THR* 3.2 11.7 + - - -
1311A GLN* 3.5 35.5 - - + +
1312A SER* 3.8 12.0 + - - +
1332A TYR* 4.3 11.2 - - + -
1335A LYS* 4.9 0.4 - - - +
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Residues in contact with LEU1018 (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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945A ILE* 4.5 6.3 - - + -
949A ARG* 3.7 28.3 - - - +
965A ILE* 3.7 29.4 - - + -
1006A HIS* 4.5 0.2 - - - +
1008A ASP* 3.5 20.6 - - - +
1009A ILE* 3.7 25.8 - - + -
1014A ASP 3.0 12.3 + - - +
1015A LEU 3.1 6.2 + - - +
1017A GLN* 1.3 75.5 - - - +
1019A ILE* 1.3 63.0 + - - +
1021A ASP* 3.1 14.3 + - + +
1022A LEU* 3.0 34.8 + - + +
1316A PHE* 5.7 3.1 - - + -
1335A LYS* 3.9 11.6 - - + +
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Residues in contact with ILE1019 (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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965A ILE* 3.7 21.3 - - + -
1015A LEU* 2.9 42.4 + - + +
1016A ALA 3.8 4.0 - - - +
1018A LEU* 1.3 74.4 - - - +
1020A TYR* 1.3 58.1 + - - +
1022A LEU* 3.2 3.6 + - - +
1023A HIS* 2.9 51.7 + - + +
1031A VAL* 4.0 16.2 - - + -
1033A VAL* 4.1 2.0 - - + -
1051A ALA* 3.5 23.6 - - + +
1052A ASN* 3.6 14.4 - - + +
1053A ALA* 3.8 23.3 - - + +
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Residues in contact with TYR1020 (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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1016A ALA 2.9 14.8 + - - +
1017A GLN* 3.3 18.2 - - - +
1019A ILE* 1.3 78.1 - - - +
1021A ASP* 1.3 51.6 + - - +
1024A GLN* 2.8 37.8 + - - +
1243A ASN* 2.9 55.0 + - + -
1246A VAL* 2.8 29.3 - - + +
1276A THR 5.0 1.6 + - - -
1278A ARG* 3.2 60.1 + - + +
1279A THR* 3.4 23.8 - - - -
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Residues in contact with ASP1021 (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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1017A GLN* 2.7 31.8 + - - +
1018A LEU* 3.1 14.6 + - + +
1020A TYR* 1.3 72.9 - - - +
1022A LEU* 1.3 59.0 + - - +
1024A GLN* 3.3 2.8 - - - +
1025A ILE* 3.1 27.9 + - - +
1279A THR* 2.6 38.6 + - + +
1282A THR* 4.2 4.2 - - - +
1312A SER* 2.8 24.7 + - - -
1315A ALA* 5.2 0.9 - - + -
1316A PHE* 4.9 12.8 - - + -
1335A LYS* 2.8 25.5 + - - -
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Residues in contact with LEU1022 (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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945A ILE* 3.9 32.3 - - + -
957A LEU* 4.2 22.9 - - + -
963A LEU* 4.1 16.5 - - + +
965A ILE* 3.7 35.9 - - + -
1018A LEU* 3.0 25.3 + - + +
1019A ILE 3.2 5.8 + - - +
1021A ASP* 1.3 74.1 - - - +
1023A HIS* 1.3 59.7 + - - +
1024A GLN 3.1 1.1 - - - -
1025A ILE* 3.4 6.7 + - + +
1026A ASN* 3.0 31.3 + - - +
1031A VAL* 3.9 20.9 - - + -
1316A PHE* 5.0 6.7 - - + -
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Residues in contact with HIS1023 (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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1019A ILE* 2.9 36.4 + - + +
1022A LEU* 1.3 72.7 - - - +
1024A GLN* 1.3 61.2 + - - +
1026A ASN 4.0 4.4 + - - -
1027A PRO* 3.1 19.5 + - + +
1029A ALA 3.6 10.2 + - - -
1031A VAL* 3.6 12.7 - - + +
1052A ASN* 3.3 29.0 + - - -
1054A ASP* 2.8 26.1 + - - -
1240A VAL* 3.5 9.7 - - + +
1241A HIS* 3.5 27.2 + - - +
1243A ASN* 3.4 28.3 - - - +
1283A ARG* 3.0 15.1 + - - +
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Residues in contact with GLN1024 (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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1020A TYR* 2.8 19.7 + - - +
1021A ASP 3.3 8.3 - - - +
1022A LEU 3.1 0.2 - - - -
1023A HIS* 1.3 78.4 - - - +
1025A ILE* 1.3 63.5 + - - +
1027A PRO* 3.9 0.7 - - - +
1243A ASN* 3.1 18.0 + - - +
1246A VAL* 3.6 32.0 - - - +
1248A ASP* 4.1 11.1 + - - +
1278A ARG 3.6 11.5 + - - -
1279A THR* 3.2 42.9 + - + +
1282A THR* 3.9 7.0 - - - -
1283A ARG* 2.9 46.7 + - - +
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Residues in contact with ILE1025 (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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954A PRO* 4.0 28.3 - - + +
957A LEU* 4.2 24.0 - - + -
958A MET* 3.3 20.9 - - - +
963A LEU* 5.0 0.7 - - + -
1021A ASP 3.1 9.4 + - - +
1022A LEU* 3.4 14.4 - - + +
1024A GLN* 1.3 80.7 - - - +
1026A ASN* 1.3 68.2 + - + +
1027A PRO* 3.6 4.2 - - - +
1282A THR* 3.6 23.8 - - + +
1283A ARG* 4.7 2.1 - - - +
1285A SER* 5.1 0.4 - - - -
1286A GLY* 3.6 26.9 - - - +
1316A PHE* 3.7 34.5 - - + -
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Residues in contact with ASN1026 (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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957A LEU 3.1 24.1 + - - +
958A MET* 3.8 28.7 + - - +
960A GLY 3.4 19.0 + - - -
963A LEU* 4.4 2.7 - - + -
1022A LEU 3.0 15.7 + - - +
1023A HIS* 3.5 4.0 - - - +
1025A ILE* 1.3 83.7 - - + +
1027A PRO* 1.3 64.1 - - - +
1028A GLU* 3.5 15.8 + - - +
1029A ALA* 3.1 33.3 + - + +
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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