Contacts of the helix formed by residues 1139 - 1147 (chain E) in PDB entry 2FO1
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 ASP1139 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57D ILE 4.6 2.1 - - - +
58D GLY* 4.6 10.9 - - - -
59D ASP 5.2 1.0 + - - -
1102E VAL 5.3 1.7 - - - +
1105E ARG* 3.6 45.3 - - + +
1107E ARG* 4.3 12.0 + - - -
1134E ALA* 3.3 11.9 + - - +
1137E ASN* 3.0 6.3 + - - +
1138E ARG* 1.3 70.5 - - - +
1140E PHE* 1.3 68.9 + - - +
1141E GLY* 3.7 3.8 + - - -
1142E MSE 2.8 43.4 + - + +
1143E MSE 3.4 8.7 + - - +
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Residues in contact with PHE1140 (chain E).
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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1138E ARG 3.5 6.9 + - - -
1139E ASP* 1.3 72.7 + - - +
1141E GLY* 1.3 71.8 + - - +
1143E MSE 2.8 26.4 + - + +
1144E VAL* 3.0 34.1 + - + -
1177E ASP* 3.1 52.9 - - + +
1180E ALA* 3.6 30.3 - - + -
1181E SER* 4.2 15.3 - - - -
1184E LEU* 5.3 8.7 - - + -
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Residues in contact with GLY1141 (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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1107E ARG* 3.4 26.9 - - - +
1139E ASP* 3.4 3.4 + - - -
1140E PHE* 1.3 79.9 - - - +
1142E MSE 1.3 65.6 + - - +
1143E MSE 2.6 2.9 + - - -
1144E VAL* 2.7 28.0 + - - -
1145E TYR* 2.7 12.3 + - - +
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Residues in contact with MSE1142 (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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1102E VAL* 3.4 47.8 - - + -
1105E ARG* 4.0 7.9 - - - -
1107E ARG* 3.4 40.1 - - + +
1110E VAL* 3.2 39.0 - - + -
1134E ALA* 4.3 6.1 - - + -
1139E ASP* 2.8 37.7 + - + +
1141E GLY* 1.3 72.8 - - - +
1143E MSE 1.3 58.8 + - - +
1145E TYR* 3.9 3.2 - - - +
1146E MSE 3.2 25.9 + - - +
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Residues in contact with MSE1143 (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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1131E LEU* 3.3 33.9 - - + -
1134E ALA* 3.2 18.2 - - + +
1135E ALA* 2.9 47.1 - - + +
1138E ARG* 4.4 3.8 - - - -
1139E ASP 4.2 13.0 - - - +
1140E PHE* 2.8 26.1 + - + +
1141E GLY 2.6 3.6 + - - -
1142E MSE 1.3 74.3 - - - +
1144E VAL* 1.3 60.1 + - - +
1145E TYR 2.7 6.6 + - - -
1146E MSE 2.8 14.6 + - - +
1147E LEU* 2.7 24.5 + - + +
1170E VAL* 5.1 2.7 - - + -
1181E SER* 2.9 32.8 - - - +
1184E LEU* 5.7 3.4 - - + -
1185E LEU* 5.0 8.7 - - - -
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Residues in contact with VAL1144 (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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1107E ARG* 5.2 1.3 - - - +
1140E PHE* 3.0 30.6 + - + -
1141E GLY* 2.7 44.8 + - - +
1143E MSE 1.3 73.7 - - + +
1145E TYR* 1.3 58.8 + - + +
1147E LEU* 3.9 13.9 + - - +
1148E ASN* 3.3 13.5 + - - -
1184E LEU* 4.1 24.2 - - + -
1188E LYS* 5.2 2.9 - - - -
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Residues in contact with TYR1145 (chain E).
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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52D GLU* 5.2 7.7 + - + +
54D GLU* 6.6 0.7 - - + -
1107E ARG* 4.4 23.8 - - + +
1110E VAL* 5.3 3.1 - - + -
1111E ALA* 3.2 46.1 + - + +
1114E MSE 3.2 29.3 - - + +
1141E GLY 2.7 13.8 + - - +
1142E MSE 3.9 5.6 - - - +
1143E MSE 2.7 0.6 + - - -
1144E VAL* 1.3 80.5 - - + +
1146E MSE 1.3 64.9 + - + +
1148E ASN* 2.7 29.8 + - - +
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Residues in contact with MSE1146 (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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1098E LEU* 3.4 22.2 - - + -
1102E VAL* 3.3 30.1 - - + -
1110E VAL* 4.0 6.3 - - + -
1114E MSE 3.2 27.1 - - + +
1120E PRO* 4.0 10.5 - - + -
1130E ALA* 3.8 30.7 - - + +
1131E LEU* 5.0 4.7 - - + -
1134E ALA* 5.2 1.8 - - - -
1142E MSE 3.2 28.7 + - - +
1143E MSE 2.8 14.4 + - - +
1145E TYR* 1.3 69.7 - - + +
1147E LEU* 1.3 52.1 + - + +
1148E ASN 2.7 18.8 + - - -
1149E SER* 3.3 19.8 + - - -
1152E LEU* 3.8 15.4 - - + +
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Residues in contact with LEU1147 (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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1131E LEU* 3.9 10.1 - - + -
1143E MSE 2.7 56.7 + - + +
1144E VAL 3.7 6.3 - - - +
1145E TYR 3.1 1.8 + - - -
1146E MSE 1.3 69.1 - - - +
1148E ASN* 1.3 61.1 + - - +
1149E SER 3.7 0.7 - - - -
1152E LEU* 3.3 29.8 - - + -
1153E LYS* 3.9 12.8 - - + +
1156E ILE* 4.1 20.0 - - + -
1184E LEU* 3.7 14.8 - - + -
1185E LEU* 4.9 2.2 - - + -
1188E LYS* 2.9 56.0 + - + +
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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