Contacts of the helix formed by residues 1110 - 1120 (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 THR1110 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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830A TYR* 4.7 1.2 + - - -
831A ARG* 2.9 29.9 + - - +
834A LEU* 3.4 16.3 - - + +
1109A LYS* 1.3 80.7 + - - +
1111A GLY* 1.3 63.8 + - - +
1112A TRP* 3.1 27.1 - - + +
1113A ASP* 3.0 32.5 + - - +
1114A VAL* 3.1 13.5 + - - +
1127A PHE* 4.8 1.0 - - - -
1177A ILE* 4.0 8.9 - - - +
1180A GLU* 3.4 12.1 - - - +
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Residues in contact with GLY1111 (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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1110A THR* 1.3 70.7 - - - +
1112A TRP* 1.3 56.2 + - - +
1114A VAL* 3.2 2.9 + - - +
1115A VAL* 2.9 33.3 + - - +
1177A ILE* 3.6 26.9 - - - +
1180A GLU* 3.2 21.5 + - - -
1181A VAL* 3.7 11.6 - - - +
1184A LEU* 3.9 6.5 - - - -
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Residues in contact with TRP1112 (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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831A ARG* 4.8 3.1 - - - +
837A ARG* 3.8 23.3 - - - -
843A ARG* 3.5 54.3 - - + -
844A ASP* 3.8 10.5 - - - -
846A LEU 4.3 11.6 + - - -
847A ASP* 5.5 3.6 + - - +
848A PHE* 3.6 35.5 - + - -
1110A THR* 3.1 14.1 - - + +
1111A GLY* 1.3 72.5 - - - +
1113A ASP* 1.3 80.3 + - - +
1115A VAL* 3.3 1.7 + - - +
1116A MET* 3.0 41.6 + - + +
1180A GLU* 3.2 11.6 + - - +
1184A LEU* 3.5 16.5 - - + +
1206A ARG* 6.2 2.5 - - - -
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Residues in contact with ASP1113 (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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834A LEU* 5.8 0.2 - - - +
837A ARG* 4.3 6.3 + - - -
843A ARG* 3.2 26.3 + - - +
1080A TRP* 4.2 3.3 - - - -
1107A GLY 3.7 5.1 - - - +
1108A LEU* 4.0 19.4 - - + +
1109A LYS* 2.9 30.7 + - - +
1110A THR* 3.0 24.4 + - - +
1112A TRP* 1.3 93.9 - - - +
1114A VAL* 1.3 57.2 + - - +
1116A MET* 3.4 6.1 + - - +
1117A ALA* 2.9 29.7 + - - +
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Residues in contact with VAL1114 (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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870A PHE* 4.1 13.2 - - + -
1108A LEU* 5.3 2.5 - - + -
1110A THR 3.1 16.3 + - - +
1111A GLY 3.4 8.1 - - - +
1113A ASP* 1.3 77.6 - - + +
1115A VAL* 1.3 52.6 + - - +
1117A ALA* 3.2 7.1 + - - +
1118A ALA* 2.7 33.1 + - - +
1125A TYR* 3.7 34.5 - - + -
1127A PHE* 3.8 29.4 - - + -
1177A ILE* 4.2 7.6 - - + -
1181A VAL* 3.8 19.1 - - + -
1193A LEU* 4.4 9.2 - - + -
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Residues in contact with VAL1115 (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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848A PHE* 3.8 27.6 - - + -
1111A GLY 2.9 19.5 + - - +
1112A TRP 3.8 4.0 - - - +
1113A ASP 3.3 0.2 - - - -
1114A VAL* 1.3 76.0 - - - +
1116A MET* 1.3 57.5 + - - +
1118A ALA* 3.3 6.7 + - - +
1119A LEU* 2.9 33.2 + - + +
1181A VAL* 4.2 22.4 - - + +
1184A LEU* 3.8 25.4 - - + -
1185A LEU* 5.3 2.0 - - + +
1188A LEU* 4.4 8.7 - - + -
1193A LEU* 4.6 7.0 - - + -
1196A ILE* 4.0 17.3 - - + -
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Residues in contact with MET1116 (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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843A ARG* 3.9 21.5 - - + +
846A LEU* 3.8 20.9 - - + +
847A ASP* 5.7 0.9 - - - -
848A PHE* 3.9 16.6 - - + -
1080A TRP* 4.2 2.7 - - + -
1112A TRP* 3.0 49.1 + - + +
1113A ASP 3.6 5.8 - - - +
1115A VAL* 1.3 76.6 - - - +
1117A ALA* 1.3 61.7 + - - +
1119A LEU* 3.3 4.3 + - - +
1120A MET* 3.2 54.9 + - + +
1203A LEU* 3.7 31.4 - - + -
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Residues in contact with ALA1117 (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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1080A TRP* 3.6 28.9 - - + -
1084A VAL* 4.3 0.7 - - - +
1104A ALA* 4.7 6.1 - - + -
1108A LEU* 4.9 5.2 - - + -
1113A ASP 2.9 17.6 + - - +
1114A VAL* 3.6 4.5 - - - +
1116A MET* 1.3 74.8 - - - +
1118A ALA* 1.3 63.5 + - - +
1120A MET* 3.3 4.2 + - - +
1121A GLY 3.3 5.5 + - - -
1122A ALA* 3.0 29.8 + - + +
1125A TYR* 3.9 18.2 - - + -
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Residues in contact with ALA1118 (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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1114A VAL 2.7 19.1 + - - +
1115A VAL* 3.5 9.4 - - - +
1117A ALA* 1.3 73.3 - - - +
1119A LEU* 1.3 63.4 + - - +
1121A GLY* 2.9 9.0 + - - -
1122A ALA 3.3 11.7 - - - +
1125A TYR* 3.3 19.9 - - + +
1193A LEU* 4.3 7.4 - - + -
1196A ILE* 4.3 13.9 - - + -
1197A ILE* 3.2 16.4 - - + +
1198A GLY 2.9 17.8 + - - -
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Residues in contact with LEU1119 (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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848A PHE* 3.8 26.2 - - + -
1115A VAL* 2.9 26.2 + - + +
1116A MET* 3.3 5.8 + - - +
1118A ALA* 1.3 72.4 - - - +
1120A MET* 1.3 57.3 + - - +
1121A GLY 3.2 0.2 - - - -
1188A LEU* 5.1 2.2 - - + -
1196A ILE* 3.5 30.5 - - + +
1198A GLY* 3.1 26.5 - - - -
1199A ARG* 3.4 25.1 - - + +
1200A THR* 3.7 10.1 + - - -
1202A LEU* 4.1 18.2 - - + -
1203A LEU* 3.6 37.5 - - + -
1225A LEU* 4.7 0.3 - - - +
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Residues in contact with MET1120 (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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843A ARG* 4.2 4.7 - - + -
846A LEU* 4.1 14.4 - - + -
1080A TRP* 4.0 4.9 - - + -
1081A GLU* 3.8 46.4 - - + +
1084A VAL* 3.3 24.7 - - + +
1085A THR* 3.8 17.5 - - - +
1088A HIS* 3.8 13.0 - - - +
1116A MET* 3.2 49.3 + - + +
1117A ALA* 3.8 6.3 - - - +
1118A ALA 3.1 0.8 - - - -
1119A LEU* 1.3 76.7 - - - +
1121A GLY* 1.3 56.7 + - - +
1200A THR* 5.3 0.4 - - - +
1203A LEU* 4.4 9.9 - - + -
1222A LEU* 4.5 10.1 - - - +
1225A LEU* 4.0 11.2 - - - +
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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