Contacts of the helix formed by residues 1219 - 1230 (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 ASN1219 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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604A ARG* 5.4 0.4 - - - +
1170E VAL 4.1 0.2 + - - -
1171E ALA* 2.8 29.6 + - - +
1172E HIS 4.2 1.4 - - - -
1173E ASN 3.0 32.3 + - - -
1174E GLU* 3.4 24.1 + - - +
1178E GLN* 5.6 1.0 - - - +
1214E ALA* 3.9 13.9 + - + -
1218E SER* 1.3 77.1 + - - +
1220E MSE 1.3 70.8 + - - +
1221E PRO* 2.6 10.7 - - - +
1222E ILE* 2.6 33.6 + - - +
1223E VAL* 3.7 3.9 + - - +
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Residues in contact with MSE1220 (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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73D ARG* 5.8 1.8 - - - +
1174E GLU* 4.6 0.6 + - - +
1218E SER* 4.2 7.3 - - - +
1219E ASN* 1.3 74.8 - - - +
1221E PRO* 1.3 73.9 - - + +
1222E ILE 2.6 2.6 + - - -
1223E VAL* 2.8 24.1 + - + +
1224E LYS* 2.8 70.1 + - + +
1255E GLU* 4.5 24.7 - - + +
1256E VAL* 3.8 30.1 - - - -
1259E TYR* 3.4 17.5 - - + -
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Residues in contact with PRO1221 (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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1174E GLU* 3.8 20.2 - - + +
1175E GLY 5.0 9.9 - - - +
1179E VAL* 4.0 21.6 - - + +
1219E ASN* 2.6 16.1 - - - +
1220E MSE 1.3 88.3 - - + +
1222E ILE* 1.3 57.8 + - + +
1224E LYS* 3.7 10.1 - - + +
1225E TYR* 3.2 23.0 + - - +
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Residues in contact with ILE1222 (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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1170E VAL* 4.5 9.2 - - + -
1171E ALA* 3.9 15.9 - - + -
1178E GLN* 5.1 2.5 - - + -
1179E VAL* 3.7 32.8 - - + +
1182E ALA* 4.0 18.8 - - + -
1214E ALA* 3.8 13.2 - - + -
1219E ASN* 2.6 37.1 + - - +
1220E MSE 2.6 0.2 + - - -
1221E PRO* 1.3 71.6 - - + +
1223E VAL* 1.3 55.7 + - - +
1224E LYS 2.9 1.8 - - - -
1225E TYR* 2.6 12.7 + - + -
1226E LEU* 2.6 62.5 + - + +
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Residues in contact with VAL1223 (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* 4.0 17.9 - - + -
1214E ALA* 3.3 26.5 - - + -
1215E ALA* 3.5 18.4 - - - +
1218E SER* 6.1 0.2 - - - -
1219E ASN 3.7 0.4 + - - +
1220E MSE 2.8 61.5 + - + +
1222E ILE* 1.3 75.1 - - - +
1224E LYS* 1.3 57.4 + - - +
1226E LEU* 4.5 1.8 - - - +
1227E VAL* 2.8 40.1 + - + +
1256E VAL* 4.4 11.0 - - + -
1259E TYR* 4.0 6.5 - - + -
1260E LEU* 5.6 2.0 - - + -
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Residues in contact with LYS1224 (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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1220E MSE 2.8 47.9 + - + +
1221E PRO* 3.7 8.5 - - + +
1223E VAL* 1.3 77.8 - - - +
1225E TYR* 1.3 59.9 - - - +
1227E VAL* 4.1 0.2 - - - +
1228E GLY* 2.9 29.3 + - - -
1229E GLU 3.9 0.2 + - - -
1259E TYR* 3.4 29.6 + - + +
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Residues in contact with TYR1225 (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* 6.5 0.7 - - + -
1179E VAL* 4.1 14.4 - - + -
1182E ALA* 3.8 30.1 - - + -
1183E LYS* 3.6 33.5 - - + +
1186E VAL* 3.0 26.8 - - + +
1192E VAL* 6.1 0.7 - - + -
1221E PRO 3.2 13.4 + - - +
1222E ILE* 2.6 19.5 + - + +
1224E LYS* 1.3 75.7 - - - +
1226E LEU* 1.3 72.6 + - + +
1229E GLU* 2.4 81.6 + - + +
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Residues in contact with LEU1226 (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* 5.3 7.2 - - + -
1171E ALA* 4.8 1.1 - - + -
1182E ALA* 6.1 0.4 - - + -
1192E VAL* 3.3 31.9 - - + +
1210E ALA* 4.1 10.8 - - + -
1211E LEU* 3.8 26.7 - - + +
1222E ILE* 2.6 45.3 + - + +
1223E VAL* 4.2 4.5 - - - +
1225E TYR* 1.3 95.2 - - + +
1227E VAL* 1.3 62.2 + - + +
1228E GLY 3.1 5.0 + - - -
1229E GLU* 3.8 4.6 - - + +
1230E LYS 3.7 15.1 + - - +
1231E GLY 3.9 9.2 - - - +
1232E SER* 3.9 17.7 - - - +
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Residues in contact with VAL1227 (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* 4.2 31.4 - - + -
1223E VAL* 2.8 28.3 + - + +
1224E LYS 4.1 0.2 - - - +
1226E LEU* 1.3 71.8 - - - +
1228E GLY* 1.3 58.1 + - - +
1230E LYS* 4.9 2.2 + - - -
1231E GLY 4.3 11.7 - - - +
1232E SER* 4.6 1.3 - - - -
1234E LYS* 4.6 18.6 - - + -
1259E TYR* 3.1 38.4 - - + +
1260E LEU* 4.3 15.7 - - + -
1263E GLN* 4.4 18.6 + - + +
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Residues in contact with GLY1228 (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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1224E LYS 2.9 18.7 + - - -
1227E VAL* 1.3 81.1 - - - +
1229E GLU* 1.3 66.6 + - - +
1230E LYS* 4.6 2.3 + - - -
1259E TYR* 4.3 8.1 - - - -
1263E GLN* 5.4 1.8 - - - -
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Residues in contact with GLU1229 (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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1186E VAL* 4.2 10.5 - - - +
1192E VAL* 4.1 17.5 - - + +
1225E TYR* 2.4 77.5 + - + +
1226E LEU* 3.8 9.0 - - + +
1228E GLY* 1.3 76.8 - - - +
1230E LYS* 1.3 106.3 + - - +
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Residues in contact with LYS1230 (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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1192E VAL* 4.7 8.7 - - - +
1226E LEU 3.7 4.0 + - - +
1227E VAL 5.5 1.8 - - - -
1228E GLY 3.5 3.2 + - - -
1229E GLU* 1.3 114.3 + - - +
1231E GLY* 1.3 62.5 + - - +
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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