Contacts of the helix formed by residues 1243 - 1251 (chain B) in PDB entry 1FP7
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 ALA1243 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1143B LEU* 3.7 31.0 - - + -
1146B MET* 3.8 25.8 - - + -
1238B ALA* 3.4 8.7 + - + +
1241B LEU* 3.2 2.8 - - + +
1242B GLU* 1.3 76.2 - - - +
1244B GLN* 1.3 69.1 + - - +
1245B GLY 2.6 5.6 + - - -
1246B SER* 2.8 18.2 + - - -
1247B MET* 3.0 19.7 + - + -
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Residues in contact with GLN1244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1219B LYS* 3.3 33.6 - - + +
1222B PHE* 4.3 4.6 - - + -
1223B SER* 3.2 23.7 - - - +
1238B ALA* 3.6 2.6 + - - +
1239B GLY* 2.9 35.7 - - - +
1242B GLU* 3.4 25.4 - - - +
1243B ALA* 1.3 78.1 - - - +
1245B GLY* 1.3 60.1 + - - +
1247B MET* 3.4 13.9 - - - +
1248B ALA* 2.6 38.5 + - - +
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Residues in contact with GLY1245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1219B LYS* 4.4 10.3 - - - -
1242B GLU 4.6 2.5 + - - -
1243B ALA 2.6 6.1 + - - -
1244B GLN* 1.3 85.4 - - - +
1246B SER* 1.3 66.8 + - - +
1248B ALA* 2.8 12.8 + - - +
1249B LEU* 3.1 9.9 + - - +
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Residues in contact with SER1246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1142B LEU* 3.8 22.2 - - - -
1146B MET* 5.1 6.4 - - - +
1242B GLU 4.7 5.6 + - - -
1243B ALA* 2.8 14.4 + - - -
1245B GLY* 1.3 66.9 - - - -
1247B MET* 1.3 55.3 + - - -
1249B LEU* 2.7 33.4 + - - +
1250B LEU* 2.9 16.5 + - - +
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Residues in contact with MET1247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1139B ALA* 3.2 35.4 - - + +
1142B LEU* 4.5 6.5 - - + +
1143B LEU* 3.9 39.0 - - + +
1205B VAL* 4.1 17.5 - - + -
1222B PHE* 3.6 35.2 - - + -
1225B ILE* 5.4 1.6 - - + -
1238B ALA* 4.5 3.1 - - - -
1243B ALA* 3.0 20.9 + - + +
1244B GLN 3.4 12.6 - - - +
1246B SER* 1.3 78.2 - - - +
1248B ALA* 1.3 63.7 + - - +
1250B LEU* 3.1 25.2 + - - +
1251B MET* 3.4 14.0 + - - +
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Residues in contact with ALA1248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1215B LEU* 3.8 20.6 - - + +
1216B MET* 5.6 0.9 - - + -
1218B LEU* 5.5 0.7 - - - -
1219B LYS* 3.6 33.4 - - + +
1222B PHE* 4.1 9.8 - - - -
1244B GLN 2.6 21.7 + - - +
1245B GLY* 2.8 9.4 + - - +
1247B MET* 1.3 71.7 - - - +
1249B LEU* 1.3 55.1 + - - +
1251B MET* 3.2 8.7 + - - +
1252B LYS* 3.1 20.1 + - - -
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Residues in contact with LEU1249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1215B LEU* 6.3 0.2 - - - -
1245B GLY 3.1 7.2 + - - +
1246B SER* 2.7 19.6 + - - +
1248B ALA* 1.3 67.8 - - - +
1250B LEU* 1.3 66.9 + - + +
1251B MET 2.8 6.8 + - - -
1252B LYS* 2.9 38.9 + - + +
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Residues in contact with LEU1250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1135B ALA* 3.2 36.3 - - - +
1138B TYR* 4.4 27.1 - - + +
1139B ALA* 4.2 4.3 - - + +
1142B LEU* 3.8 18.2 - - + -
1246B SER* 2.9 38.6 - - - +
1247B MET* 3.1 14.3 + - - +
1249B LEU* 1.3 80.1 - - + +
1251B MET* 1.3 58.1 + - - +
1253B ASP 5.1 0.7 + - - -
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Residues in contact with MET1251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1135B ALA* 3.8 8.3 - - - -
1136B VAL* 3.7 43.7 - - + -
1139B ALA* 4.3 6.7 - - + -
1205B VAL 4.5 5.6 - - - +
1209B LEU* 3.4 37.2 - - + -
1215B LEU* 4.8 1.8 - - + -
1218B LEU* 3.7 26.2 - - + -
1222B PHE* 4.3 9.6 - - + -
1247B MET 3.6 11.4 - - - +
1248B ALA 3.3 10.5 - - - +
1249B LEU 2.8 1.2 - - - -
1250B LEU* 1.3 80.8 - - - +
1252B LYS* 1.3 50.8 + - - -
1253B ASP 2.6 18.7 + - - -
1254B ALA* 2.8 18.0 + - + -
1255B ILE* 3.0 12.3 + - - +
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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