Contacts of the helix formed by residues 1128 - 1135 (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 GLY1128 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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872A THR 4.1 1.6 - - - -
875A MET* 3.7 22.9 - - - +
1127A PHE* 1.3 71.3 - - - +
1129A SER* 1.3 64.8 + - - -
1130A ILE* 3.2 1.3 - - - +
1131A ALA* 3.0 15.6 + - - +
1132A MET* 3.1 13.9 + - - +
3508A FMN 2.8 32.5 + - - -
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Residues in contact with SER1129 (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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475A MET* 3.1 38.5 - - - +
476A GLY 5.2 0.3 + - - -
797A ASN* 4.9 12.5 + - - -
1064A GLY* 3.7 7.8 + - - -
1128A GLY* 1.3 71.3 - - - +
1130A ILE* 1.3 68.4 + - - +
1132A MET* 3.1 14.4 + - - +
1133A ILE* 3.0 26.5 + - - +
3508A FMN 2.6 34.7 + - - +
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Residues in contact with ILE1130 (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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797A ASN* 5.3 1.8 - - - +
801A MET* 6.3 0.9 - - - -
805A LEU* 4.3 11.4 - - + +
830A TYR* 4.4 4.3 - - + +
1107A GLY* 4.6 1.3 - - - -
1108A LEU 2.7 31.2 - - - +
1109A LYS* 3.4 29.6 - - + +
1127A PHE* 4.4 5.4 - - + -
1128A GLY 3.9 6.1 - - - +
1129A SER* 1.3 78.3 - - - +
1131A ALA* 1.3 57.4 + - - +
1133A ILE* 3.3 13.1 + - + +
1134A ALA* 3.0 26.3 + - - +
1173A PHE* 3.6 33.9 - - + -
3508A FMN 2.9 34.1 - - - +
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Residues in contact with ALA1131 (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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872A THR* 3.7 23.6 - - - +
888A LEU* 3.9 18.7 - - + +
1127A PHE* 3.9 10.8 - - - +
1128A GLY* 3.0 10.5 + - - +
1130A ILE* 1.3 78.6 - - - +
1132A MET* 1.3 62.2 + - - +
1134A ALA* 3.3 18.6 + - - +
1135A GLU* 3.3 17.2 + - - +
1170A VAL* 5.8 0.4 - - - -
1173A PHE* 5.3 1.6 - - - -
1174A PHE* 4.5 16.4 - - + -
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Residues in contact with MET1132 (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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475A MET* 4.9 9.2 - - + +
875A MET* 3.8 18.4 - - + +
880A LEU* 3.9 19.7 - - + -
888A LEU* 5.1 0.2 - - + -
1128A GLY 3.1 10.8 + - - +
1129A SER* 3.1 12.0 + - - +
1131A ALA* 1.3 74.5 - - - +
1133A ILE* 1.3 64.8 + - - +
1135A GLU* 3.1 24.6 + - - +
1136A GLY 3.2 0.9 + - - -
1137A CYS* 3.0 28.0 + - + +
1143A CYS* 5.0 1.6 - - - -
1152A VAL* 3.8 14.1 - - + +
1153A ALA* 4.8 1.3 - - + -
3508A FMN 3.7 38.8 - - + -
3509A F3S 3.6 31.4 - - - -
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Residues in contact with ILE1133 (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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797A ASN* 4.0 20.4 - - - +
801A MET* 4.1 9.6 - - + -
802A SER* 3.5 48.5 - - - +
805A LEU* 3.6 21.8 - - + -
806A HIS* 3.9 9.2 + - - +
1109A LYS* 6.1 0.2 - - - -
1129A SER 3.0 20.2 + - - +
1130A ILE* 3.3 15.7 + - + +
1132A MET* 1.3 77.0 - - - +
1134A ALA* 1.3 56.1 + - - +
1136A GLY* 2.8 21.7 + - - -
1137A CYS* 3.8 23.5 + - - +
1139A MET* 4.1 10.8 - - + -
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Residues in contact with ALA1134 (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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805A LEU* 4.3 8.0 - - + +
806A HIS* 3.2 17.0 + - - +
809A VAL* 3.8 13.1 - - + +
1130A ILE 3.0 12.8 + - - +
1131A ALA* 3.3 12.3 + - - +
1133A ILE* 1.3 75.8 - - - +
1135A GLU* 1.3 57.4 + - - +
1169A GLN* 3.4 13.9 - - - +
1170A VAL* 4.3 14.8 - - + -
1173A PHE* 4.0 33.9 - - + -
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Residues in contact with GLU1135 (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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806A HIS* 3.8 4.7 - - - -
884A ALA* 2.7 47.6 - - - +
887A THR* 3.0 26.1 - - + +
888A LEU* 3.4 20.8 + - - +
1131A ALA 3.3 9.3 + - - +
1132A MET* 3.1 20.4 + - - +
1133A ILE 3.0 0.4 - - - -
1134A ALA* 1.3 76.6 - - - +
1136A GLY* 1.3 55.2 + - - +
1152A VAL* 4.4 4.5 - - + +
1163A PHE* 3.6 12.7 - - + -
1164A LYS 3.1 22.9 - - - +
1165A GLY* 4.0 2.0 - - - -
1169A GLN* 4.3 5.4 - - - -
1170A VAL* 3.8 17.7 - - + -
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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