Contacts of the helix formed by residues 1040 - 1051 (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 GLY1040 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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498A ARG* 4.2 7.4 - - - -
1039A ILE* 1.3 78.3 - - - +
1041A ILE* 1.3 64.5 + - - +
1042A GLY 3.2 3.3 + - - -
1043A THR* 3.4 12.8 + - - -
1044A ILE* 3.1 31.2 + - - +
1086A GLU* 3.0 10.7 + - - -
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Residues in contact with ILE1041 (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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501A GLN* 4.1 7.9 - - - +
1035A LEU* 3.8 29.4 - - + -
1036A VAL 3.5 26.9 - - - +
1037A ALA* 4.0 4.5 - - - -
1038A GLU* 3.0 24.3 + - - +
1039A ILE 3.4 0.4 + - - -
1040A GLY* 1.3 77.5 - - - +
1042A GLY* 1.3 55.4 + - - +
1044A ILE* 3.6 10.4 - - + +
1045A ALA* 2.7 33.4 + - - +
1058A ILE* 4.0 19.5 - - + -
1083A GLY* 3.9 15.3 - - - +
1086A GLU* 3.7 12.3 - - - +
1087A VAL* 3.7 19.7 - - + -
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Residues in contact with GLY1042 (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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1041A ILE* 1.3 73.8 - - - +
1043A THR* 1.3 60.6 + - - +
1045A ALA* 3.2 4.2 + - - +
1046A ALA 3.0 19.1 + - - -
1086A GLU* 2.8 37.9 + - - -
1087A VAL* 4.2 7.0 - - - -
1090A VAL* 3.3 27.5 - - - +
1091A LEU* 5.5 0.2 - - - +
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Residues in contact with THR1043 (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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209A THR* 3.2 38.4 - - + +
503A THR* 5.9 1.6 - - + -
1040A GLY* 3.6 14.5 - - - +
1042A GLY* 1.3 69.5 - - - +
1044A ILE* 1.3 68.7 + - + +
1046A ALA* 3.2 4.7 + - - +
1047A GLY 3.2 17.3 + - - -
1086A GLU* 4.5 1.0 + - - -
1090A VAL* 4.1 10.2 - - - +
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Residues in contact with ILE1044 (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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498A ARG* 5.4 4.3 - - - +
499A PHE 5.8 0.2 - - - +
501A GLN* 3.6 44.6 - - + +
502A VAL* 4.0 16.1 - - + +
503A THR* 3.7 30.6 - - + +
1012A ILE* 4.9 2.1 - - - +
1035A LEU* 4.1 23.8 - - + -
1038A GLU* 4.6 5.8 - - - +
1040A GLY* 3.1 20.1 + - - +
1041A ILE* 3.6 6.7 - - - +
1043A THR* 1.3 80.0 - - + +
1045A ALA* 1.3 57.2 + - - +
1047A GLY* 3.2 4.7 + - - -
1048A VAL* 3.0 25.3 + - + +
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Residues in contact with ALA1045 (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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1035A LEU* 4.5 7.9 - - + -
1041A ILE 2.7 21.7 + - - +
1042A GLY 3.2 4.9 + - - +
1044A ILE* 1.3 71.4 - - - +
1046A ALA* 1.3 60.1 + - - +
1048A VAL* 3.2 11.0 + - - +
1049A ALA* 2.9 27.2 + - - +
1056A ILE* 3.6 15.0 - - + +
1087A VAL* 3.5 33.4 - - + -
1091A LEU* 3.8 4.2 - - + +
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Residues in contact with ALA1046 (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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209A THR 3.3 24.9 - - - +
1042A GLY 3.0 11.4 + - - +
1043A THR 3.2 5.6 + - - +
1045A ALA* 1.3 73.2 - - - +
1047A GLY* 1.3 64.6 + - - +
1049A ALA* 3.3 3.3 + - - +
1050A LYS* 3.0 28.5 + - - +
1090A VAL* 4.2 13.9 - - + -
1091A LEU* 3.9 7.5 - - + +
1094A ASN* 4.2 4.7 - - - +
1096A LEU* 3.6 20.9 - - + +
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Residues in contact with GLY1047 (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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207A PHE* 4.6 1.8 - - - -
209A THR* 4.2 16.6 - - - -
1012A ILE* 3.4 23.1 - - - +
1043A THR 3.2 10.1 + - - -
1044A ILE 3.2 4.4 + - - -
1046A ALA* 1.3 78.5 - - - +
1048A VAL* 1.3 56.5 + - - +
1050A LYS* 3.0 9.9 + - - +
1051A ALA* 2.9 28.1 + - - +
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Residues in contact with VAL1048 (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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502A VAL* 4.2 19.3 - - + -
1012A ILE* 4.1 0.4 - - - -
1015A LEU* 3.7 18.6 - - + -
1033A VAL* 3.6 23.1 - - + -
1035A LEU* 4.6 4.3 - - + -
1044A ILE* 3.0 24.0 + - + +
1045A ALA* 3.2 9.4 + - - +
1047A GLY* 1.3 74.4 - - - +
1049A ALA* 1.3 61.5 + - - +
1051A ALA* 3.1 20.9 + - - +
1053A ALA* 3.4 32.7 + - + -
1056A ILE* 3.8 18.6 - - + -
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Residues in contact with ALA1049 (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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1045A ALA 2.9 13.6 + - - +
1046A ALA 3.6 8.5 - - - +
1048A VAL* 1.3 77.2 - - - +
1050A LYS* 1.3 59.6 + - - +
1052A ASN* 3.2 15.4 + - - -
1053A ALA 4.4 1.3 + - - +
1056A ILE* 4.5 0.4 - - - +
1091A LEU* 3.8 19.1 - - + -
1096A LEU* 4.2 13.9 - - + -
1099A ARG* 4.2 22.6 + - + +
1100A VAL* 4.1 24.7 - - + -
1241A HIS* 5.9 0.2 - - - -
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Residues in contact with LYS1050 (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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33A GLY* 4.4 0.9 - - - -
34A CYS 3.1 25.8 + - - +
42A ASP* 2.7 36.0 + - - -
207A PHE* 3.9 18.1 - - + -
208A SER 3.0 19.1 + - - +
210A ASN 2.8 34.1 + - - +
211A THR* 4.8 1.8 - - - +
1046A ALA 3.0 19.0 + - - +
1047A GLY 3.0 8.3 + - - +
1049A ALA* 1.3 75.0 - - - +
1051A ALA* 1.3 56.8 + - - +
1052A ASN* 3.2 5.6 + - - +
1096A LEU* 4.1 20.6 - - + -
1099A ARG* 4.5 11.4 + - - +
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Residues in contact with ALA1051 (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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207A PHE* 4.6 2.2 - - + -
1012A ILE* 4.0 15.0 - - + -
1015A LEU* 4.3 1.1 - - + -
1016A ALA* 3.7 38.2 - - + +
1019A ILE* 3.5 21.0 - - + +
1047A GLY 2.9 11.6 + - - +
1048A VAL* 3.3 13.5 - - - +
1049A ALA 3.1 0.4 - - - -
1050A LYS* 1.3 76.8 - - - +
1052A ASN* 1.3 67.8 + - - +
1053A ALA 3.4 1.1 - - - -
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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