Contacts of the helix formed by residues 1238 - 1249 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1106H PRO* 4.6 9.4 - - + -
1107H PRO 5.9 0.4 - - - +
1109H LEU* 4.0 39.3 - - + +
1112H MET* 5.1 8.1 - - - -
1236H ASN 3.6 8.5 - - - +
1237H CYS* 1.3 104.3 - - - +
1239H ASP* 1.3 67.4 + - - +
1240H MET* 4.5 4.0 - - + +
1241H LEU* 3.3 12.1 + - + +
1242H PHE* 3.4 2.1 + - - +
1036R ASN* 3.8 19.9 - - + +
1037R GLU* 4.6 15.3 - - + +
1038R ALA* 4.9 0.4 - - + -
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Residues in contact with ASP1239 (chain H).
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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1233H LYS* 3.2 32.3 + - - +
1237H CYS 4.3 2.1 - - - +
1238H PRO* 1.3 70.4 - - - +
1240H MET* 1.3 67.1 + - - +
1242H PHE* 3.1 2.3 + - - +
1243H GLU* 2.8 35.3 + - + +
1037R GLU* 2.9 28.8 + - - +
1038R ALA* 5.1 4.7 + - - +
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Residues in contact with MET1240 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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981C PHE* 3.5 54.9 - - + +
1109H LEU* 4.0 24.0 - - + -
1113H ILE* 3.9 31.2 - - + -
1238H PRO* 3.3 2.4 - - + +
1239H ASP* 1.3 80.5 - - - +
1241H LEU* 1.3 69.6 + - - +
1243H GLU* 3.3 4.4 + - - +
1244H LEU* 3.2 38.9 + - + -
1266H ILE* 4.1 6.7 - - + -
1037R GLU* 5.4 0.4 + - - -
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Residues in contact with LEU1241 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1109H LEU* 4.6 7.9 - - + -
1112H MET* 3.5 43.7 - - + -
1113H ILE* 3.7 30.1 - - + -
1116H ALA* 5.0 0.7 - - + -
1202H LEU* 4.3 26.2 - - + +
1205H ILE* 5.2 0.9 - - + -
1206H ALA* 4.1 4.7 - - + -
1237H CYS* 4.3 4.5 - - - -
1238H PRO* 3.3 12.9 + - + +
1239H ASP 3.2 0.8 - - - -
1240H MET* 1.3 87.1 - - + +
1242H PHE* 1.3 62.0 + - - +
1244H LEU* 3.3 9.6 + - + +
1245H MET* 3.2 44.5 + - + +
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Residues in contact with PHE1242 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1203H TRP* 5.2 0.2 - + - -
1230H LEU* 6.0 2.0 - - + -
1231H LEU 3.9 16.4 - - - -
1232H ASP 4.1 1.8 - - - -
1233H LYS* 3.4 64.8 - - + -
1234H PRO* 4.1 2.2 - - + -
1237H CYS* 4.1 5.1 - - - -
1238H PRO 3.4 8.7 + - - +
1239H ASP 3.1 6.5 + - - +
1241H LEU* 1.3 76.0 - - - +
1243H GLU* 1.3 72.6 + - - +
1245H MET* 3.5 20.8 + - + -
1246H ARG* 3.1 48.9 + - + +
1249H TRP* 4.3 13.5 - + - -
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Residues in contact with GLU1243 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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981C PHE* 4.1 22.4 - - + +
982C SER* 5.4 2.3 - - - -
1041C MET* 3.1 21.5 - - - +
1233H LYS* 5.7 1.2 + - - -
1239H ASP* 2.8 27.9 + - + +
1240H MET* 3.6 5.8 - - - +
1242H PHE* 1.3 85.6 - - - +
1244H LEU* 1.3 57.0 + - - +
1246H ARG* 2.9 47.4 + - - +
1247H MET* 3.1 30.2 + - + +
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Residues in contact with LEU1244 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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981C PHE* 3.9 21.5 - - + -
986C VAL* 4.9 4.3 - - + -
1113H ILE* 5.3 1.8 - - + -
1116H ALA* 5.5 1.6 - - + -
1198H PHE* 5.0 0.9 - - + -
1202H LEU* 4.1 19.1 - - + -
1240H MET* 3.2 23.9 + - + +
1241H LEU* 3.3 16.6 - - + +
1243H GLU* 1.3 78.7 - - - +
1245H MET* 1.3 62.0 + - - +
1247H MET* 3.3 18.4 + - + +
1248H CYS* 3.1 25.1 + - - -
1257H PRO* 5.3 0.9 - - + -
1262H ILE* 4.1 38.8 - - + -
1265H SER* 5.0 2.0 - - - +
1266H ILE* 4.7 10.5 - - + -
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Residues in contact with MET1245 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1199H GLY* 3.9 10.8 - - - +
1202H LEU* 3.5 34.3 - - + +
1203H TRP* 3.5 22.4 - - + +
1206H ALA* 3.8 15.7 - - + -
1234H PRO* 4.9 0.7 - - + -
1237H CYS* 4.2 7.0 - - - -
1241H LEU* 3.2 29.3 + - + +
1242H PHE* 3.8 24.0 - - - +
1243H GLU 3.3 0.2 - - - -
1244H LEU* 1.3 75.7 - - - +
1246H ARG* 1.3 59.7 + - - +
1248H CYS* 2.9 23.5 + - - -
1249H TRP* 2.9 46.0 + - + -
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Residues in contact with ARG1246 (chain H).
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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1041C MET* 3.6 43.0 - - + +
1230H LEU* 4.7 20.2 - - + +
1242H PHE* 3.1 45.6 + - + +
1243H GLU* 2.9 41.1 + - - +
1245H MET* 1.3 76.0 - - - +
1247H MET* 1.3 60.7 + - - +
1249H TRP* 3.3 17.1 + - + +
1250H GLN* 3.2 18.0 + - - +
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Residues in contact with MET1247 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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981C PHE* 4.0 12.1 - - + -
982C SER 3.6 10.1 - - - +
983C ALA* 3.6 25.4 - - - +
986C VAL* 3.0 31.6 - - + -
987C TYR* 3.5 29.3 + - + +
1041C MET* 3.8 18.2 - - + -
1045C ILE* 4.3 1.3 - - + -
1243H GLU* 3.1 26.2 + - + +
1244H LEU* 3.5 13.2 - - - +
1246H ARG* 1.3 73.8 - - - +
1248H CYS* 1.3 60.3 + - - +
1249H TRP 3.0 5.8 + - - -
1250H GLN* 3.3 22.5 + - - +
1256H ARG* 3.7 1.4 - - - +
1257H PRO* 3.4 20.6 - - + +
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Residues in contact with CYS1248 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1195H VAL* 3.7 35.0 - - - +
1196H TRP* 3.4 16.5 - - - -
1198H PHE* 3.7 26.9 - - - -
1199H GLY* 3.8 15.3 - - - -
1202H LEU* 4.9 0.4 - - - -
1244H LEU* 3.1 22.5 + - - +
1245H MET 2.9 9.0 + - - +
1247H MET* 1.3 76.2 - - - +
1249H TRP* 1.3 64.7 + - - +
1250H GLN 3.5 0.7 - - - -
1256H ARG* 3.7 12.6 - - - -
1257H PRO* 4.2 2.5 - - - -
1262H ILE* 4.0 10.3 - - - -
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Residues in contact with TRP1249 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1196H TRP* 3.4 53.3 + + + -
1199H GLY 3.3 23.6 - - - -
1200H VAL* 3.5 13.9 - - + +
1203H TRP* 3.9 13.7 - + - -
1213H TYR* 5.6 1.3 - - - -
1230H LEU* 3.5 40.9 - - + +
1231H LEU* 3.7 50.0 - - + -
1242H PHE* 4.3 11.0 - + - -
1245H MET* 2.9 35.6 + - + +
1246H ARG* 3.3 12.1 + - + +
1247H MET 3.0 0.6 - - - -
1248H CYS* 1.3 87.9 - - - +
1250H GLN* 1.3 66.3 + - - +
1251H TYR* 3.3 2.8 + - - -
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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