Contacts of the helix formed by residues 1238 - 1249 (chain F) 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 PRO1238 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1106F PRO* 4.9 8.1 - - + -
1107F PRO 6.0 0.4 - - - +
1109F LEU* 3.9 42.6 - - + +
1112F MET* 5.2 7.4 - - - -
1236F ASN 3.4 9.6 - - - +
1237F CYS* 1.3 97.1 - - - +
1239F ASP* 1.3 66.3 + - - +
1240F MET* 4.5 3.6 - - + +
1241F LEU* 3.1 12.9 + - + +
1242F PHE 3.5 0.5 + - - -
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Residues in contact with ASP1239 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1233F LYS* 2.5 38.5 + - - +
1237F CYS 4.2 1.0 - - - +
1238F PRO* 1.3 69.8 - - - +
1240F MET* 1.3 57.6 + - - +
1242F PHE* 3.0 2.6 + - - -
1243F GLU* 2.8 41.6 + - - +
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Residues in contact with MET1240 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1109F LEU* 4.1 22.9 - - + -
1113F ILE* 3.5 33.7 - - + -
1238F PRO* 3.1 2.2 + - + -
1239F ASP* 1.3 78.7 - - - +
1241F LEU* 1.3 66.1 + - + +
1243F GLU* 3.4 7.6 + - - +
1244F LEU* 3.2 42.6 + - + -
1266F ILE* 4.1 12.8 - - + -
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Residues in contact with LEU1241 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1109F LEU* 4.5 12.6 - - + -
1112F MET* 3.7 42.6 - - + -
1113F ILE* 4.4 22.0 - - + -
1116F ALA* 5.0 3.1 - - + -
1202F LEU* 4.2 31.2 - - + +
1205F ILE* 5.5 0.7 - - + -
1206F ALA* 4.1 3.4 - - + -
1237F CYS* 4.0 5.2 - - - -
1238F PRO* 3.1 11.8 + - + +
1240F MET* 1.3 81.3 - - - +
1242F PHE* 1.3 65.6 + - - +
1244F LEU* 3.5 9.9 + - + +
1245F MET* 3.2 46.7 + - + +
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Residues in contact with PHE1242 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1230F LEU* 5.9 2.5 - - + -
1231F LEU 3.8 15.9 - - - -
1232F ASP* 4.0 1.6 - - - -
1233F LYS* 3.4 66.2 - - + -
1234F PRO* 4.1 2.5 - - + -
1237F CYS* 4.0 9.8 - - - -
1238F PRO 3.5 2.4 + - - +
1239F ASP 3.0 6.5 + - - +
1241F LEU* 1.3 76.5 - - - +
1243F GLU* 1.3 73.6 + - - +
1245F MET* 3.4 19.9 + - + -
1246F ARG* 3.1 50.0 + - + +
1249F TRP* 4.3 11.9 - + - -
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Residues in contact with GLU1243 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1233F LYS* 5.2 1.6 + - - -
1239F ASP* 2.8 32.0 + - - +
1240F MET* 3.5 8.5 - - - +
1241F LEU 3.2 0.2 - - - -
1242F PHE* 1.3 83.6 - - - +
1244F LEU* 1.3 64.8 + - - +
1246F ARG* 2.5 50.4 + - - +
1247F MET* 3.2 32.8 + - + +
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Residues in contact with LEU1244 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1113F ILE* 5.6 0.7 - - + -
1116F ALA* 5.4 5.4 - - + -
1198F PHE* 4.8 1.1 - - + -
1202F LEU* 3.8 20.4 - - + -
1240F MET* 3.2 29.9 + - + +
1241F LEU* 3.5 15.5 - - + +
1243F GLU* 1.3 75.5 - - - +
1245F MET* 1.3 66.2 + - - +
1247F MET* 3.1 25.6 + - + +
1248F CYS* 3.0 28.0 + - - -
1257F PRO* 5.1 1.6 - - + -
1262F ILE* 4.1 39.7 - - + -
1265F SER* 5.4 5.6 - - - +
1266F ILE* 5.1 7.9 - - + -
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Residues in contact with MET1245 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1199F GLY* 3.8 15.3 - - - +
1202F LEU* 3.6 10.1 - - + +
1203F TRP* 3.4 41.1 - - + +
1206F ALA* 4.1 8.1 - - + -
1234F PRO* 4.9 0.9 - - + -
1237F CYS* 4.2 5.4 - - - -
1241F LEU* 3.2 47.0 + - + +
1242F PHE* 3.6 24.5 - - - +
1243F GLU 3.3 0.4 - - - -
1244F LEU* 1.3 76.3 - - - +
1246F ARG* 1.3 55.5 + - - +
1248F CYS* 2.8 29.3 + - - +
1249F TRP* 2.8 39.6 + - + -
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Residues in contact with ARG1246 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1230F LEU* 4.8 18.5 - - + +
1242F PHE* 3.1 46.2 + - + +
1243F GLU* 2.5 42.4 + - - +
1245F MET* 1.3 78.3 - - - +
1247F MET* 1.3 61.3 + - + +
1249F TRP* 3.3 17.6 + - + +
1250F GLN* 3.3 19.4 + - - +
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Residues in contact with MET1247 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1243F GLU* 3.2 33.2 - - + +
1244F LEU* 3.3 21.1 - - - +
1246F ARG* 1.3 73.4 - - + +
1248F CYS* 1.3 58.1 + - - +
1249F TRP 2.9 9.5 + - - -
1250F GLN* 3.0 27.4 + - - +
1255F MET 5.0 0.2 - - - +
1256F ARG* 3.6 1.6 - - - +
1257F PRO* 3.5 30.5 - - + +
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Residues in contact with CYS1248 (chain F).
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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1195F VAL* 3.6 33.4 - - + +
1196F TRP* 3.4 15.6 - - - -
1198F PHE* 3.6 31.4 - - - -
1199F GLY* 3.8 14.6 - - - -
1202F LEU* 5.1 0.4 - - - -
1244F LEU* 3.0 22.2 + - - -
1245F MET 2.8 11.5 + - - +
1247F MET* 1.3 72.2 - - - +
1249F TRP* 1.3 56.4 + - - +
1250F GLN 3.4 0.9 - - - -
1256F ARG* 3.4 18.8 - - - -
1257F PRO* 4.1 3.1 - - - -
1262F ILE* 3.8 11.9 - - - -
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Residues in contact with TRP1249 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1196F TRP* 3.4 55.3 + + + -
1199F GLY* 3.4 24.9 - - - -
1200F VAL* 3.5 13.1 - - + +
1203F TRP* 3.9 13.0 - + + -
1213F TYR* 5.6 1.3 - - - -
1230F LEU* 3.5 39.1 - - + +
1231F LEU* 3.6 52.3 - - + -
1242F PHE* 4.3 9.9 - + - -
1245F MET* 2.8 37.3 + - + +
1246F ARG* 3.3 13.2 + - + +
1247F MET 2.9 1.0 - - - -
1248F CYS* 1.3 85.4 - - - +
1250F GLN* 1.3 67.5 + - - +
1251F TYR* 3.1 4.5 + - - +
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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