Contacts of the helix formed by residues 1271 - 1277 (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 GLU1271 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1110E SER* 4.1 15.4 + - - -
1114E GLN* 3.0 36.2 + - + +
1269E GLU 5.3 1.7 - - - +
1270E MET* 1.3 76.4 - - - +
1272E PRO* 1.3 81.5 - - + +
1273E GLY* 3.1 5.8 + - - +
1274E PHE* 3.2 19.2 + - - +
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Residues in contact with PRO1272 (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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1270E MET 3.4 3.8 - - - +
1271E GLU* 1.3 100.1 - - + +
1273E GLY* 1.3 65.7 + - - +
1274E PHE 3.1 0.9 + - - -
1275E ARG* 3.7 12.8 + - - +
1276E GLU* 4.9 2.3 + - - +
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Residues in contact with GLY1273 (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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1271E GLU* 3.1 5.3 + - - +
1272E PRO* 1.3 78.6 - - - +
1274E PHE* 1.3 64.2 + - - +
1276E GLU* 2.9 36.5 + - - +
1277E VAL* 3.5 11.0 - - - +
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Residues in contact with PHE1274 (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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1061E HIS* 3.7 23.8 - + - -
1114E GLN* 5.3 4.3 - - - +
1117E GLY 4.1 14.8 - - - -
1118E GLU* 5.1 0.4 - - + -
1121E ASP* 3.9 11.4 - - + -
1263E ILE* 3.8 28.5 - - + -
1267E LYS* 5.2 4.3 - - + -
1270E MET* 3.6 43.1 - - + -
1271E GLU* 3.2 17.3 + - - +
1272E PRO 3.1 0.4 + - - -
1273E GLY* 1.3 72.8 - - - +
1275E ARG* 1.3 67.2 + - - +
1277E VAL* 2.8 20.9 + - + +
1278E SER* 2.8 43.5 + - - -
1280E TYR* 4.4 4.3 - + + -
1281E TYR* 4.3 15.3 - + + -
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Residues in contact with ARG1275 (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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1268E GLU* 5.0 8.3 + - - -
1272E PRO 3.7 8.9 + - - +
1273E GLY 3.1 1.6 + - - -
1274E PHE* 1.3 78.4 - - - +
1276E GLU* 1.3 60.5 + - + +
1277E VAL 3.7 0.2 + - - -
1278E SER* 4.2 2.1 + - - +
1281E TYR* 3.2 78.5 + - + +
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Residues in contact with GLU1276 (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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1272E PRO 4.9 1.3 - - - +
1273E GLY* 2.9 32.1 - - - +
1274E PHE 2.8 1.8 + - - -
1275E ARG* 1.3 79.0 - - + +
1277E VAL* 1.3 71.7 + - + +
1278E SER 5.4 0.2 - - - -
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Residues in contact with VAL1277 (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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1060E HIS* 3.0 64.0 + - + +
1061E HIS* 4.6 3.4 - - + +
1273E GLY* 3.5 13.0 - - - +
1274E PHE* 2.8 19.3 + - + +
1276E GLU* 1.3 98.5 - - + +
1278E SER* 1.3 67.5 + - - +
1279E PHE 3.9 0.5 + - - -
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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