Contacts of the helix formed by residues 1177 - 1189 (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 ASP1177 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59D ASP* 4.4 6.4 - - - +
62D ALA* 3.8 15.3 - - + +
1138E ARG 5.4 2.9 - - - +
1140E PHE* 3.1 45.2 + - + +
1175E GLY* 4.7 0.2 - - - -
1176E ARG* 1.3 111.1 + - - +
1178E GLN* 1.3 58.9 + - - +
1180E ALA* 2.6 13.2 + - - +
1181E SER* 2.5 33.7 + - - -
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Residues in contact with GLN1178 (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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1138E ARG* 3.1 45.5 - - - +
1170E VAL* 4.0 24.6 - - + +
1173E ASN* 2.9 26.0 + - - +
1174E GLU* 2.6 27.7 + - - +
1175E GLY* 3.7 16.7 - - - +
1177E ASP* 1.3 75.9 - - - +
1179E VAL* 1.3 55.6 + - - +
1180E ALA 2.4 13.5 + - - -
1181E SER* 2.6 25.2 + - - -
1182E ALA* 2.8 11.3 + - - +
1219E ASN* 5.0 1.1 - - - +
1222E ILE* 5.1 5.4 - - + -
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Residues in contact with VAL1179 (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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1175E GLY 5.0 2.2 - - - +
1176E ARG* 3.5 22.2 - - - +
1178E GLN* 1.3 75.0 - - - +
1180E ALA* 1.3 59.7 + - + +
1182E ALA* 3.9 4.7 - - - +
1183E LYS* 3.6 25.6 + - + +
1221E PRO* 4.0 31.4 - - + +
1222E ILE* 3.7 15.8 - - + +
1225E TYR* 4.1 18.0 - - + -
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Residues in contact with ALA1180 (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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1140E PHE* 3.6 21.5 - - + -
1176E ARG 4.7 3.6 - - - +
1177E ASP* 2.6 17.7 + - - +
1178E GLN 2.4 4.8 + - - -
1179E VAL* 1.3 74.8 - - + +
1181E SER* 1.3 60.1 + - - +
1182E ALA 2.7 5.6 - - - -
1183E LYS* 2.9 11.8 + - + +
1184E LEU* 2.7 25.5 + - - +
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Residues in contact with SER1181 (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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1140E PHE* 4.2 16.7 - - - -
1143E MSE 2.9 41.0 - - - +
1170E VAL* 4.0 10.7 - - - +
1177E ASP 2.5 16.5 + - - -
1178E GLN* 2.6 20.8 + - - -
1180E ALA* 1.3 71.3 - - - +
1182E ALA* 1.3 57.7 + - - +
1184E LEU* 3.1 22.1 - - - +
1185E LEU* 3.3 16.2 + - - +
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Residues in contact with ALA1182 (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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1167E LEU* 5.7 10.0 - - + +
1170E VAL* 4.5 8.9 - - + +
1178E GLN 2.8 12.7 + - - +
1179E VAL 3.9 4.7 - - - +
1180E ALA 2.7 0.6 - - - -
1181E SER* 1.3 74.3 - - - +
1183E LYS* 1.3 56.5 + - - +
1184E LEU 2.5 15.5 + - - -
1185E LEU* 2.7 23.4 + - - +
1186E VAL* 2.9 14.5 + - - +
1222E ILE* 4.0 12.1 - - + -
1225E TYR* 3.8 23.3 - - + -
1226E LEU* 6.1 0.7 - - + -
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Residues in contact with LYS1183 (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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1179E VAL* 3.6 18.4 + - - +
1180E ALA* 2.9 12.6 + - + +
1182E ALA* 1.3 76.8 - - - +
1184E LEU* 1.3 60.1 + - - +
1186E VAL* 3.0 22.6 - - - +
1187E GLU* 3.1 16.5 + - - +
1225E TYR* 3.6 30.0 + - + +
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Residues in contact with LEU1184 (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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1140E PHE* 5.3 9.2 - - + -
1143E MSE 5.7 3.1 - - + -
1144E VAL* 4.1 31.4 - - + +
1147E LEU* 3.7 22.7 - - + -
1180E ALA 2.7 11.5 + - - +
1181E SER* 3.1 17.9 - - - +
1182E ALA 2.5 4.4 + - - -
1183E LYS* 1.3 72.8 - - - +
1185E LEU* 1.3 56.2 + - + +
1187E GLU* 2.8 14.3 + - + +
1188E LYS* 2.5 67.3 + - + +
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Residues in contact with LEU1185 (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* 3.4 38.6 - - + -
1143E MSE 5.0 5.2 - - - -
1147E LEU* 4.9 1.6 - - + -
1156E ILE* 4.1 10.5 - - + +
1166E ALA* 3.2 27.4 - - + -
1167E LEU* 3.4 29.2 - - + +
1170E VAL* 4.0 11.4 - - + -
1181E SER* 3.5 15.7 - - - +
1182E ALA* 2.7 10.5 + - - +
1184E LEU* 1.3 86.6 - - + +
1186E VAL* 1.3 56.7 + - - +
1188E LYS* 3.1 4.1 + - - +
1189E GLY 2.9 26.2 + - - -
1190E ALA* 3.2 15.2 + - + +
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Residues in contact with VAL1186 (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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1167E LEU* 5.7 6.4 - - + +
1182E ALA 2.9 19.1 + - - +
1183E LYS* 3.0 15.9 - - - +
1185E LEU* 1.3 75.0 - - - +
1187E GLU* 1.3 62.0 + - - +
1189E GLY* 3.8 5.7 + - - -
1190E ALA* 3.5 23.4 + - - +
1192E VAL* 4.4 16.2 - - + -
1225E TYR* 3.0 30.3 - - + +
1229E GLU* 4.2 10.1 - - - +
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Residues in contact with GLU1187 (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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1183E LYS 3.1 15.6 + - - +
1184E LEU* 2.8 16.7 + - + +
1186E VAL* 1.3 79.2 - - - +
1188E LYS* 1.3 75.6 + - + +
1189E GLY* 3.2 1.6 + - - -
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Residues in contact with LYS1188 (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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1144E VAL* 5.2 3.8 - - - -
1147E LEU* 2.9 47.4 + - + +
1148E ASN* 4.2 10.7 + - - +
1153E LYS* 4.4 31.2 + - + +
1156E ILE* 4.5 10.1 - - + -
1184E LEU* 2.5 46.8 + - + +
1185E LEU* 3.1 13.0 + - - +
1187E GLU* 1.3 80.4 - - + +
1189E GLY* 1.3 58.1 + - - +
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Residues in contact with GLY1189 (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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1153E LYS* 5.1 2.5 - - - +
1156E ILE* 4.0 15.8 - - - +
1157E GLU* 4.6 3.3 - - - +
1185E LEU 2.9 10.5 + - - -
1186E VAL 4.2 2.7 - - - -
1187E GLU 3.2 4.4 + - - -
1188E LYS* 1.3 76.2 - - - +
1190E ALA* 1.3 58.8 + - - +
1191E LYS 4.4 0.2 + - - -
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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