Contacts of the helix formed by residues 1210 - 1216 (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 ALA1210 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1167E LEU* 4.6 20.6 - - + -
1168E MSE 3.8 27.5 - - + +
1171E ALA* 4.0 12.3 - - + +
1192E VAL* 4.1 17.3 - - + +
1193E ASP* 6.0 0.2 - - - +
1209E THR* 1.3 69.5 - - - +
1211E LEU* 1.3 58.2 + - - +
1213E TYR* 2.6 34.7 + - - +
1214E ALA 3.1 7.9 + - - -
1226E LEU* 4.1 15.9 - - + -
1232E SER* 5.8 0.4 - - - +
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Residues in contact with LEU1211 (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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1209E THR* 2.4 15.5 + - + +
1210E ALA* 1.3 75.2 - - - +
1212E HIS* 1.3 66.9 + - - +
1214E ALA* 3.2 2.4 + - - -
1215E ALA* 2.8 25.4 + - + +
1223E VAL* 4.0 24.7 - - + -
1226E LEU* 3.8 13.0 - - + +
1227E VAL* 4.2 20.4 - - + -
1232E SER* 3.1 32.8 - - - +
1233E ASN 4.7 2.0 - - - +
1234E LYS* 4.0 22.7 - - + +
1244E PRO* 3.6 24.7 - - + -
1260E LEU* 4.7 4.9 - - + -
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Residues in contact with HIS1212 (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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1208E ARG* 3.3 37.7 - - + -
1209E THR* 2.7 40.6 + - + +
1210E ALA 2.7 4.6 + - - -
1211E LEU* 1.3 77.8 - - - +
1213E TYR* 1.3 52.6 - - - +
1215E ALA* 3.0 2.3 - - - +
1216E GLN* 2.6 34.8 + - - +
1236E LYS* 3.7 22.5 + - + -
1238E ASP* 4.0 7.8 + - + -
1242E LYS 3.1 26.2 + - - -
1244E PRO* 3.7 19.6 - - + +
1247E LEU* 3.3 32.0 - - + +
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Residues in contact with TYR1213 (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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607A GLU* 4.9 1.1 - - - -
1162E ASN 5.0 2.1 + - - -
1163E GLY 5.0 2.9 + - - -
1164E MSE 4.2 24.9 - - + +
1168E MSE 3.4 54.3 - - + +
1171E ALA* 4.2 4.3 - - + +
1172E HIS* 4.1 27.6 + + - +
1206E LYS 5.6 1.2 + - - -
1208E ARG* 3.4 53.7 + - + +
1210E ALA 2.6 18.0 + - - +
1212E HIS* 1.3 72.4 - - - +
1214E ALA* 1.3 70.3 + - - +
1216E GLN* 2.9 35.3 + - - +
1217E VAL 4.5 0.3 - - - +
1218E SER 5.1 0.2 - - - +
1247E LEU* 6.3 0.2 - - + -
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Residues in contact with ALA1214 (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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1171E ALA* 3.6 15.2 + - + +
1210E ALA 3.1 6.3 + - - -
1211E LEU* 3.6 8.1 - - - +
1213E TYR* 1.3 78.9 - - - +
1215E ALA* 1.3 71.0 + - - +
1216E GLN 2.7 8.3 - - - +
1217E VAL 3.4 6.4 - - - +
1218E SER 3.6 6.2 - - - +
1219E ASN* 3.9 13.0 - - + -
1222E ILE* 3.8 26.2 - - + -
1223E VAL* 3.3 23.3 - - + -
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Residues in contact with ALA1215 (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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1211E LEU* 2.8 20.1 + - + +
1212E HIS 3.0 8.3 - - - +
1214E ALA* 1.3 73.6 - - - +
1216E GLN* 1.3 64.5 + - - +
1217E VAL 2.8 5.0 + - - -
1218E SER* 3.4 8.4 + - - +
1223E VAL* 3.5 10.1 - - - +
1244E PRO* 3.7 34.5 - - + +
1248E ALA* 4.0 6.3 - - + +
1256E VAL* 3.9 28.5 - - + +
1260E LEU* 4.7 0.4 - - + -
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Residues in contact with GLN1216 (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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605A SER* 3.5 25.9 + - - -
607A GLU* 3.1 32.7 + - - +
1172E HIS* 4.6 8.9 + - - +
1208E ARG* 3.8 9.9 - - - +
1212E HIS 2.6 17.3 + - - +
1213E TYR* 2.9 36.8 - - - +
1214E ALA 2.7 9.4 + - - +
1215E ALA* 1.3 66.6 - - - +
1217E VAL* 1.3 71.8 + - - +
1247E LEU* 3.9 22.9 - - + +
1248E ALA 4.6 2.4 - - - +
1251E GLU* 3.6 32.0 + - + -
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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