Contacts of the helix formed by residues 1238 - 1249 (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 PRO1238 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1109R LEU* 3.9 43.3 - - + +
1112R MET* 4.7 18.2 - - + -
1233R LYS* 4.6 0.2 - - - -
1236R ASN 3.5 6.9 - - - +
1237R CYS* 1.3 92.9 - - - +
1239R ASP* 1.3 67.9 + - - +
1240R MET* 2.8 5.9 + - + +
1241R LEU* 3.0 15.4 + - + +
1242R PHE* 3.3 7.8 + - - +
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Residues in contact with ASP1239 (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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1233R LYS* 2.6 35.8 + - - +
1237R CYS 3.4 1.9 + - - +
1238R PRO* 1.3 69.1 - - - +
1240R MET* 1.3 61.5 + - - +
1242R PHE* 3.5 2.3 + - - +
1243R GLU* 3.2 30.6 + - - +
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Residues in contact with MET1240 (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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981K PHE* 3.4 50.5 - - + -
1109R LEU* 4.1 19.5 - - + -
1113R ILE* 3.3 36.8 - - + -
1238R PRO* 2.8 6.3 + - + +
1239R ASP* 1.3 74.0 - - - +
1241R LEU* 1.3 72.2 + - + +
1243R GLU* 2.9 15.1 + - - +
1244R LEU* 3.0 25.0 + - + +
1266R ILE* 3.6 27.4 - - + -
1269R GLU* 6.4 0.7 - - + -
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Residues in contact with LEU1241 (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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1109R LEU* 4.7 4.5 - - + -
1112R MET* 4.1 33.7 - - + -
1113R ILE* 4.1 24.9 - - + -
1116R ALA* 4.8 5.4 - - + -
1202R LEU* 4.2 35.2 - - + +
1205R ILE* 5.1 2.0 - - + -
1206R ALA* 4.3 6.1 - - + -
1237R CYS* 4.2 6.1 - - - -
1238R PRO* 3.0 17.2 + - + +
1240R MET* 1.3 82.4 - - - +
1242R PHE* 1.3 62.8 + - - +
1244R LEU* 3.4 14.7 + - + +
1245R MET* 3.1 42.2 + - + +
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Residues in contact with PHE1242 (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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1203R TRP* 5.6 0.2 - + - -
1230R LEU* 6.5 1.3 - - + -
1231R LEU 3.9 13.0 - - - -
1232R ASP* 4.4 0.4 - - - -
1233R LYS* 3.4 73.8 - - + -
1234R PRO* 4.2 0.7 - - + -
1237R CYS* 3.9 6.0 - - - -
1238R PRO 3.3 2.8 + - - -
1239R ASP 3.9 3.1 - - - +
1240R MET 3.1 1.0 - - - -
1241R LEU* 1.3 76.7 - - - +
1243R GLU* 1.3 69.8 + - - +
1245R MET* 3.1 22.8 + - - +
1246R ARG* 3.0 55.5 + - + +
1249R TRP* 4.2 12.3 - + - -
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Residues in contact with GLU1243 (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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981K PHE* 4.5 17.7 - - + +
982K SER* 5.2 2.7 - - - -
1041K MET* 3.6 16.8 - - + +
1233R LYS* 5.7 1.0 + - - -
1239R ASP* 3.2 20.5 + - - +
1240R MET* 2.9 11.8 + - - +
1242R PHE* 1.3 87.0 - - - +
1244R LEU* 1.3 61.0 + - - +
1246R ARG* 2.6 52.9 + - - +
1247R MET* 3.2 30.5 + - + +
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Residues in contact with LEU1244 (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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981K PHE* 4.0 19.5 - - + -
986K VAL* 4.8 4.3 - - + -
1116R ALA* 5.4 4.5 - - + -
1198R PHE* 5.3 0.2 - - + -
1202R LEU* 4.1 20.2 - - + -
1240R MET* 3.0 27.9 + - + +
1241R LEU* 3.4 17.3 - - + +
1243R GLU* 1.3 74.6 - - - +
1245R MET* 1.3 63.2 + - - +
1247R MET* 3.3 22.0 + - + +
1248R CYS* 3.2 29.7 + - - -
1257R PRO* 5.3 1.1 - - + -
1262R ILE* 4.0 40.6 - - + -
1265R SER* 4.9 1.3 - - - +
1266R ILE* 4.8 7.0 - - + -
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Residues in contact with MET1245 (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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1199R GLY 3.7 15.0 - - - +
1202R LEU* 3.7 20.4 - - + +
1203R TRP* 3.6 45.8 - - - +
1206R ALA* 3.9 15.7 - - + -
1234R PRO* 4.6 1.6 - - + -
1237R CYS* 4.1 8.7 - - - -
1241R LEU* 3.1 26.9 + - + +
1242R PHE* 3.1 20.5 + - + +
1244R LEU* 1.3 74.9 - - - +
1246R ARG* 1.3 62.7 + - - +
1248R CYS* 3.2 7.4 + - - +
1249R TRP* 3.1 51.8 + - + -
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Residues in contact with ARG1246 (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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1041K MET* 3.8 36.1 - - - +
1230R LEU* 5.7 12.1 - - + +
1242R PHE* 3.0 50.9 + - + +
1243R GLU* 2.6 42.9 + - - +
1245R MET* 1.3 76.1 - - - +
1247R MET* 1.3 60.7 + - - +
1249R TRP* 3.2 18.9 + - + +
1250R GLN* 3.3 17.7 + - - +
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Residues in contact with MET1247 (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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981K PHE* 3.6 29.6 - - + -
982K SER 3.7 1.6 - - - -
983K ALA* 3.7 21.5 - - - +
986K VAL* 3.3 28.0 - - + -
987K TYR* 3.6 29.2 - - + +
1041K MET* 3.6 23.1 - - + -
1045K ILE* 4.6 0.2 - - + -
1243R GLU* 3.2 23.1 - - + +
1244R LEU* 3.6 11.0 - - + +
1245R MET 3.2 0.4 - - - -
1246R ARG* 1.3 72.4 - - - +
1248R CYS* 1.3 64.0 + - - +
1249R TRP 3.1 4.7 + - - -
1250R GLN* 3.4 17.3 + - - +
1256R ARG* 3.4 5.9 - - - +
1257R PRO* 3.3 20.4 - - + +
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Residues in contact with CYS1248 (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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1195R VAL* 3.5 42.2 - - - +
1196R TRP* 3.5 15.1 - - - -
1198R PHE* 3.9 21.5 - - - -
1199R GLY* 3.8 14.4 - - - -
1202R LEU* 4.9 1.1 - - - -
1244R LEU* 3.5 15.9 - - - -
1245R MET 3.2 8.2 + - - +
1247R MET* 1.3 78.6 - - - +
1249R TRP* 1.3 58.4 + - - +
1250R GLN 3.5 0.4 - - - -
1256R ARG* 3.4 19.8 + - - -
1257R PRO* 4.2 3.8 - - - -
1262R ILE* 4.1 10.5 - - - -
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Residues in contact with TRP1249 (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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1196R TRP* 3.3 53.9 + + + -
1199R GLY* 3.3 25.8 - - - -
1200R VAL* 3.8 7.2 - - + +
1203R TRP* 4.0 2.7 - + + -
1213R TYR* 5.8 0.7 - - - -
1230R LEU* 3.5 38.1 - - + +
1231R LEU* 3.5 56.5 - - + -
1242R PHE* 4.2 10.1 - + - -
1245R MET* 3.1 45.2 + - + +
1246R ARG* 3.2 12.1 + - + +
1247R MET 3.1 1.4 - - - -
1248R CYS* 1.3 84.7 - - + +
1250R GLN* 1.3 69.0 + - - +
1251R TYR* 3.1 3.1 + - - -
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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