Contacts of the helix formed by residues 1258 - 1267 (chain E) in PDB entry 3F5P
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 SER1258 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1195E VAL* 4.6 3.8 - - - -
1256E ARG 3.7 0.6 + - - -
1257E PRO* 1.3 76.2 - - - +
1259E PHE* 1.3 64.1 + - - +
1260E LEU* 3.3 10.4 + - - +
1261E GLU* 2.9 40.8 + - - +
1262E ILE* 3.1 23.4 + - - +
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Residues in contact with PHE1259 (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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1120E ALA* 3.5 25.7 - - + +
1123E MET* 3.4 50.0 - - + -
1124E ALA* 3.8 10.8 - - + -
1127E ASN* 3.6 25.1 - - - -
1194E ASP* 3.8 12.3 - - + -
1195E VAL* 3.7 32.4 - - + +
1198E PHE* 3.6 29.8 - + + -
1258E SER* 1.3 74.0 - - - +
1260E LEU* 1.3 63.2 + - - +
1262E ILE* 3.5 14.5 + - + +
1263E ILE* 3.1 30.0 + - - +
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Residues in contact with LEU1260 (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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1124E ALA* 4.0 22.9 - - + +
1258E SER* 3.2 10.2 + - - +
1259E PHE* 1.3 77.6 - - - +
1261E GLU* 1.3 57.9 + - + +
1263E ILE* 3.1 2.9 + - + -
1264E SER* 2.8 29.8 + - - -
1279E PHE* 4.6 5.8 - - + -
1280E TYR* 3.4 36.0 - - + -
1285E ASN* 3.5 29.6 - - - +
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Residues in contact with GLU1261 (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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1256E ARG 4.7 1.4 - - - +
1257E PRO* 3.8 7.0 - - - +
1258E SER* 2.9 35.1 + - - +
1260E LEU* 1.3 73.4 - - + +
1262E ILE* 1.3 66.1 + - - +
1264E SER* 3.0 18.5 + - - -
1265E SER* 3.0 14.7 + - - -
986F VAL* 3.8 33.8 - - + +
987F TYR* 4.1 21.2 - - - +
989F PRO* 5.7 2.8 - - - +
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Residues in contact with ILE1262 (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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1120E ALA* 4.3 7.6 - - + -
1195E VAL* 4.5 3.1 - - + -
1198E PHE* 3.7 44.9 - - + -
1244E LEU* 4.4 23.8 - - + -
1248E CYS* 4.1 5.8 - - - -
1257E PRO* 3.8 26.2 - - + -
1258E SER 3.1 18.1 + - - +
1259E PHE* 3.6 20.9 - - + +
1261E GLU* 1.3 73.9 - - - +
1263E ILE* 1.3 63.5 + - - +
1265E SER* 2.5 26.3 + - - -
1266E ILE* 3.4 14.0 + - + +
986F VAL* 4.7 3.1 - - - +
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Residues in contact with ILE1263 (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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1117E GLY* 4.2 6.1 - - - +
1120E ALA* 3.7 16.8 - - + +
1121E ASP* 3.3 45.5 - - + +
1124E ALA* 4.3 7.6 - - + -
1259E PHE 3.1 17.0 + - - +
1260E LEU 3.1 6.0 + - - +
1262E ILE* 1.3 76.8 - - - +
1264E SER* 1.3 57.7 + - - +
1266E ILE* 4.2 8.3 - - + -
1267E LYS* 2.8 32.5 + - + +
1270E MET* 5.8 0.7 - - + -
1274E PHE* 3.8 27.8 - - + -
1280E TYR* 3.7 25.1 - - + -
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Residues in contact with SER1264 (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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1260E LEU 2.8 15.1 + - - -
1261E GLU* 3.0 11.6 + - - -
1263E ILE* 1.3 77.7 - - - +
1265E SER* 1.3 57.7 + - - +
1267E LYS* 3.2 37.3 + - - +
1280E TYR* 2.8 26.4 + - - -
985F ASP 5.5 0.4 - - - -
986F VAL 5.7 2.0 - - - -
989F PRO* 5.7 2.2 - - - +
990F ASP* 3.8 18.9 + - - +
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Residues in contact with SER1265 (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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1244E LEU* 4.6 3.6 - - - +
1261E GLU 3.0 9.8 + - - -
1262E ILE* 2.5 23.0 + - - -
1264E SER* 1.3 80.3 - - - +
1266E ILE* 1.3 69.3 + - - +
1267E LYS* 3.5 0.4 - - - -
1268E GLU* 5.2 2.3 + - - +
1269E GLU* 4.8 4.5 - - - +
981F PHE* 3.7 25.8 - - - -
985F ASP* 4.0 10.0 - - - +
986F VAL* 3.8 25.8 - - - +
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Residues in contact with ILE1266 (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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1113E ILE* 3.6 28.2 - - + +
1116E ALA* 4.5 7.9 - - + -
1117E GLY* 3.6 33.9 - - - +
1240E MET* 3.8 29.2 - - + -
1244E LEU* 4.5 6.1 - - + -
1262E ILE* 3.6 17.7 - - + +
1263E ILE* 3.9 7.2 - - + +
1265E SER* 1.3 89.8 + - - +
1267E LYS* 1.3 66.8 + - - +
1268E GLU 3.1 3.4 - - - -
1269E GLU* 2.9 23.6 + - + -
1270E MET* 3.5 11.3 - - - +
981F PHE* 4.5 3.6 - - + -
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Residues in contact with LYS1267 (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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1263E ILE* 2.8 21.8 + - + +
1264E SER* 3.2 35.8 + - - +
1265E SER 3.5 0.4 - - - -
1266E ILE* 1.3 77.2 - - - +
1268E GLU* 1.3 79.7 + - + +
1269E GLU 3.2 1.0 + - - -
1270E MET* 3.3 26.1 + - - +
1274E PHE* 5.2 3.4 - - + -
1280E TYR* 3.6 20.6 + - + +
1281E TYR* 3.6 34.2 + - + +
990F ASP* 3.5 26.7 + - - +
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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