Contacts of the helix formed by residues 1165 - 1173 (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 THR1165 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1132E HIS* 3.8 11.2 - - - -
1156E ILE 4.5 2.2 - - - -
1157E GLU* 2.8 33.4 - - - +
1158E GLU 3.9 0.9 - - - +
1159E LEU* 4.2 6.1 - - + -
1164E MSE 1.3 75.1 - - - +
1166E ALA* 1.3 60.6 + - - +
1167E LEU* 3.7 9.1 - - - +
1168E MSE 3.0 44.2 + - + +
1169E ILE* 2.6 38.5 + - - +
1194E TYR* 4.2 16.6 - - + -
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Residues in contact with ALA1166 (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 16.2 - - + -
1132E HIS* 4.3 6.5 - - - -
1135E ALA* 4.3 6.3 - - + +
1156E ILE* 4.1 13.9 + - + +
1165E THR* 1.3 81.5 - - - +
1167E LEU* 1.3 74.9 + - + +
1169E ILE* 2.7 12.5 + - - +
1170E VAL* 3.0 10.3 + - - +
1185E LEU* 3.2 36.6 - - + -
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Residues in contact with LEU1167 (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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1156E ILE 5.7 0.2 - - - +
1157E GLU* 4.9 5.2 - - - +
1165E THR* 3.7 16.6 - - - +
1166E ALA* 1.3 80.8 - - + +
1168E MSE 1.3 60.6 + - + +
1170E VAL* 2.4 38.0 + - + -
1171E ALA* 2.6 17.1 + - + +
1182E ALA* 5.7 9.9 - - + +
1185E LEU* 3.4 17.1 - - + +
1186E VAL* 5.7 5.8 - - + +
1190E ALA* 4.7 17.5 - - + +
1191E LYS 4.4 5.8 - - - +
1192E VAL* 4.4 34.1 - - + +
1210E ALA* 4.6 15.0 - - + -
1225E TYR* 6.5 0.4 - - + -
1226E LEU* 5.3 5.6 - - + -
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Residues in contact with MSE1168 (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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1163E GLY 4.2 7.2 - - - +
1164E MSE 3.9 15.9 - - + -
1165E THR* 3.0 58.6 + - + +
1166E ALA 3.1 0.2 - - - -
1167E LEU* 1.3 84.6 - - + +
1169E ILE* 1.3 61.4 + - - +
1171E ALA* 3.6 2.4 + - - +
1172E HIS* 3.1 20.1 + - - +
1192E VAL 5.7 1.1 - - - +
1194E TYR* 3.5 29.6 - - + +
1195E ASP 5.7 3.1 - - - +
1196E GLY* 6.4 0.4 - - - -
1208E ARG 4.7 7.6 - - - +
1209E THR* 4.2 0.9 - - - +
1210E ALA* 3.8 26.0 - - + +
1213E TYR* 3.4 41.3 - - + +
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Residues in contact with ILE1169 (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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580A GLU* 5.0 4.3 - - - +
1128E ARG* 4.1 26.7 - - - +
1132E HIS* 3.4 44.9 - - + +
1135E ALA* 4.0 10.2 - - + +
1136E ALA* 4.2 16.6 - - - +
1160E ASP* 4.6 6.1 - - - +
1164E MSE 4.3 19.1 - - + +
1165E THR 2.6 26.9 - - - +
1166E ALA 2.7 10.8 + - - +
1168E MSE 1.3 72.8 - - - +
1170E VAL* 1.3 63.4 + - - +
1172E HIS* 3.2 19.1 + - + +
1173E ASN* 3.4 15.6 + - - +
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Residues in contact with VAL1170 (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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1135E ALA* 4.3 15.7 - - + +
1138E ARG* 6.5 0.4 - - + -
1143E MSE 5.1 0.7 - - + -
1166E ALA 3.0 14.7 + - - +
1167E LEU* 2.4 28.0 + - + +
1169E ILE* 1.3 64.2 - - - +
1171E ALA* 1.3 58.6 + - - +
1172E HIS 2.6 15.8 + - - -
1173E ASN* 2.6 28.4 + - - +
1178E GLN* 4.0 38.8 - - + +
1181E SER* 4.0 20.0 - - - +
1182E ALA* 4.5 7.2 - - + -
1185E LEU* 4.0 12.8 - - + -
1222E ILE* 4.5 10.1 - - + -
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Residues in contact with ALA1171 (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* 2.6 16.3 + - + +
1168E MSE 4.1 3.4 - - - +
1170E VAL* 1.3 77.9 - - + +
1172E HIS* 1.3 56.6 + - - +
1210E ALA* 4.0 29.4 - - + +
1213E TYR* 4.2 0.7 - - + +
1214E ALA* 3.6 12.0 - - - +
1219E ASN* 2.8 32.3 + - - +
1222E ILE* 3.9 27.1 - - + -
1226E LEU* 4.8 0.4 - - + -
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Residues in contact with HIS1172 (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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580A GLU* 5.0 6.5 - - - -
582A HIS* 6.1 1.7 + - - -
604A ARG* 3.3 34.4 + - + -
605A SER* 4.6 4.9 - - - -
608A SER* 3.5 28.3 + - - -
610A HIS* 4.3 9.2 + - - -
1164E MSE 5.5 9.2 - - + -
1168E MSE 3.1 14.1 + - - +
1169E ILE* 3.3 17.5 - - + +
1170E VAL 2.6 6.1 + - - -
1171E ALA* 1.3 75.8 - - - +
1173E ASN* 1.3 74.2 + - - +
1213E TYR* 4.1 32.4 + + + +
1216E GLN* 4.6 14.7 + - - -
1219E ASN* 4.2 0.4 - - - -
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Residues in contact with ASN1173 (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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580A GLU* 4.8 4.4 + - - +
604A ARG* 5.1 0.2 - - - -
610A HIS* 3.3 24.5 - - - -
70D HIS* 3.9 9.7 + - - +
1135E ALA 5.5 2.5 - - - +
1136E ALA 4.6 8.4 + - - -
1138E ARG* 3.2 43.7 - - + +
1169E ILE* 3.4 12.0 + - - +
1170E VAL* 2.6 27.5 + - - +
1172E HIS* 1.3 95.6 - - - +
1174E GLU* 1.3 61.5 + - - +
1178E GLN* 2.9 17.5 - - - +
1219E ASN* 3.0 8.8 + - - -
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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