Contacts of the helix formed by residues 982 - 987 (chain R) 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 SER 982 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1243L GLU* 5.2 3.8 - - - -
1247L MET* 3.7 14.3 - - - +
980R SER* 3.9 8.2 + - - -
981R PHE* 1.3 77.1 - - - +
983R ALA* 1.3 57.3 + - - +
984R ALA* 2.9 19.3 - - - +
985R ASP* 2.7 38.0 + - - +
986R VAL* 4.0 0.7 - - - +
1041R MET* 5.8 0.9 - - - -
1044R ARG* 5.0 13.5 - - - -
1070R SER 4.4 3.6 + - - -
1072R GLY 4.9 5.7 + - - -
1075R THR* 5.0 1.4 + - - -
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Residues in contact with ALA 983 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1247L MET* 3.8 14.8 - - - +
982R SER* 1.3 73.1 - - - +
984R ALA* 1.3 61.7 + - - +
985R ASP 3.0 1.0 + - - -
986R VAL 3.2 2.0 + - - -
987R TYR* 3.1 37.1 + - + +
1041R MET* 4.7 12.5 - - + +
1044R ARG* 4.2 21.0 - - + +
1045R ILE* 3.9 29.2 - - + -
1048R LEU* 4.1 5.4 - - + -
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Residues in contact with ALA 984 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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982R SER* 2.8 13.7 + - - +
983R ALA* 1.3 78.4 - - - +
985R ASP* 1.3 55.6 + - - +
987R TYR 4.5 0.4 - - - -
988R VAL* 2.8 31.5 - - + +
1044R ARG* 4.9 2.1 - - - +
1048R LEU* 3.5 18.9 - - + +
1070R SER* 3.2 27.4 - - - +
1075R THR* 3.6 26.7 - - + +
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Residues in contact with ASP 985 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1264L SER* 5.1 1.7 + - - -
1265L SER* 3.5 17.7 + - - +
980R SER 3.5 6.9 - - - +
981R PHE* 3.4 33.7 - - + -
982R SER* 2.7 42.5 + - - +
984R ALA* 1.3 73.9 - - - +
986R VAL* 1.3 56.5 + - - +
988R VAL* 4.4 8.6 - - - +
993R GLU* 5.7 1.1 - - - +
1070R SER 4.0 7.3 - - - +
1071R GLN* 2.7 43.1 + - - +
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Residues in contact with VAL 986 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1244L LEU* 4.7 2.5 - - + -
1247L MET* 3.4 28.9 - - + -
1257L PRO* 3.5 33.0 - - + -
1261L GLU* 3.2 34.5 - - + +
1262L ILE* 4.6 3.4 - - + +
1264L SER* 5.7 1.3 - - - -
1265L SER* 3.7 14.4 - - - +
981R PHE* 3.8 23.6 - - + -
982R SER 4.0 1.1 - - - +
983R ALA 3.2 3.6 + - - +
985R ASP* 1.3 77.2 - - - +
987R TYR* 1.3 73.2 + - + +
988R VAL 3.4 6.6 + - - +
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Residues in contact with TYR 987 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1247L MET* 3.8 19.8 + - + +
1255L MET 2.6 24.5 + - - -
1256L ARG* 3.7 3.8 - - - -
1257L PRO* 3.1 31.0 - - + +
1261L GLU* 4.1 19.3 - - - +
983R ALA* 3.1 30.8 + - + +
986R VAL* 1.3 90.2 - - + +
988R VAL* 1.3 63.5 + - - +
989R PRO* 4.2 2.6 - - - +
1045R ILE* 3.1 47.3 - - + +
1048R LEU* 4.3 20.7 - - + +
1049R ASN* 4.3 18.8 + - - +
1052R SER* 4.0 16.1 + - - -
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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