Contacts of the helix formed by residues 1086 - 1093 (chain E) in PDB entry 3F5P
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 ASP1086 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1084E ARG 4.3 0.2 - - - +
1085E GLY* 1.3 73.7 - - - -
1087E LEU* 1.3 63.1 + - - +
1088E LYS* 2.6 35.9 + - - +
1089E SER* 2.7 32.5 + - - -
1090E TYR* 3.0 21.6 + - - +
1139E ARG* 3.7 20.4 - - - +
1141E CYS 3.2 11.7 - - - +
1142E MET* 4.0 8.7 - - - +
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Residues in contact with LEU1087 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1085E GLY 4.0 0.6 + - - -
1086E ASP* 1.3 72.5 - - - +
1088E LYS* 1.3 59.4 + - - +
1090E TYR* 3.9 8.7 - - + -
1091E LEU* 2.9 49.9 + - + +
1115E MET* 4.2 10.1 - - - -
1119E ILE* 3.9 23.1 - - + -
1138E ALA* 3.1 25.7 + - + +
1141E CYS* 2.7 34.4 + - + +
1143E VAL* 3.9 24.7 - - + -
1149E VAL* 4.0 14.8 - - + -
1201E VAL* 5.5 1.1 - - + -
1205E ILE* 4.4 12.3 - - + -
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Residues in contact with LYS1088 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1086E ASP* 2.6 15.2 + - - +
1087E LEU* 1.3 74.6 - - - +
1089E SER* 1.3 63.7 + - - +
1091E LEU* 3.2 9.4 + - - +
1092E ARG* 3.1 33.2 + - + +
1138E ALA* 3.5 8.2 + - + -
1139E ARG* 3.6 34.9 - - + +
1178E TRP* 5.1 10.5 - - - -
1204E GLU* 4.4 16.5 + - - +
1209E ALA* 3.6 24.7 + - + +
1210E GLU 5.7 2.6 + - - -
1211E GLN* 6.0 2.0 - - - +
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Residues in contact with SER1089 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1085E GLY* 5.6 0.3 - - - -
1086E ASP* 2.7 41.3 + - - -
1088E LYS* 1.3 74.9 - - - +
1090E TYR* 1.3 64.7 + - - +
1092E ARG* 2.9 11.1 + - - +
1093E SER* 2.9 23.0 + - - -
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Residues in contact with TYR1090 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5E 741 5.9 1.3 - - - -
1084E ARG* 4.2 27.0 + - + +
1086E ASP 3.0 18.3 + - - +
1087E LEU* 3.9 18.6 - - + +
1089E SER* 1.3 76.6 + - - +
1091E LEU* 1.3 68.0 + - + +
1093E SER* 2.7 28.2 + - - -
1094E LEU* 3.5 34.2 + - + +
1111E LYS* 6.0 1.4 - - - +
1115E MET* 4.4 21.2 - - + +
1143E VAL* 4.2 17.3 - - + -
1147E PHE* 3.6 34.6 - + - -
1004S GLU* 3.5 22.5 + - - -
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Residues in contact with LEU1091 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1087E LEU* 2.9 47.6 + - + +
1088E LYS 3.4 5.4 - - - +
1090E TYR* 1.3 90.4 - - + +
1092E ARG* 1.3 60.9 + - - +
1094E LEU* 3.4 17.2 + - + +
1095E ARG* 4.0 0.2 - - - +
1107E PRO* 4.9 0.4 - - + -
1115E MET* 4.8 3.8 - - + -
1138E ALA* 4.3 10.1 - - + -
1204E GLU 3.9 8.1 - - - +
1205E ILE* 3.8 50.9 - - + +
1208E LEU* 3.4 33.3 - - + +
1209E ALA* 3.9 12.6 - - + +
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Residues in contact with ARG1092 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1088E LYS* 3.1 24.9 + - - +
1089E SER* 2.9 13.5 + - - +
1091E LEU* 1.3 74.0 - - - +
1093E SER* 1.3 60.2 + - - +
1094E LEU 3.0 5.6 - - - -
1095E ARG* 2.5 70.4 + - - +
1208E LEU 4.1 0.7 - - - +
1209E ALA* 3.3 27.1 + - + -
1210E GLU* 4.8 5.3 - - - +
1211E GLN 5.8 0.2 - - - +
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Residues in contact with SER1093 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1089E SER 2.9 11.5 + - - -
1090E TYR* 2.7 30.8 + - - -
1092E ARG* 1.3 76.4 - - - +
1094E LEU* 1.3 64.3 + - - +
1095E ARG 3.2 7.2 + - - +
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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