Contacts of the helix formed by residues 1217 - 1223 (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 ASP1217 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1211B LEU 4.6 0.3 - - - +
1212B ALA* 3.5 5.9 - - + -
1213B SER* 2.5 39.7 + - - +
1214B ASP* 2.5 32.5 + - - +
1216B MET* 1.3 71.8 - - - +
1218B LEU* 1.3 65.3 + - - +
1220B GLU* 2.9 27.9 + - - +
1221B ARG* 2.9 31.4 + - - +
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Residues in contact with LEU1218 (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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1208B CYS* 3.3 42.4 - - + +
1209B LEU* 4.0 5.8 - - - -
1212B ALA* 3.3 12.9 - - + +
1214B ASP 2.9 12.3 + - - +
1215B LEU* 4.4 12.8 - - + -
1217B ASP* 1.3 72.3 - - - +
1219B LYS* 1.3 54.9 + - - +
1220B GLU 2.7 15.0 + - - -
1221B ARG* 3.1 12.4 + - - +
1222B PHE* 3.3 45.3 + - + -
1248B ALA* 5.5 0.4 - - - +
1251B MET* 3.7 32.3 - - + -
1255B ILE* 4.1 14.8 - - + -
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Residues in contact with LYS1219 (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 3.9 13.9 + - - +
1216B MET* 3.9 35.1 - - + +
1217B ASP 3.4 0.6 - - - -
1218B LEU* 1.3 77.2 - - - +
1220B GLU* 1.3 61.0 + - - +
1222B PHE* 4.6 4.9 - - - -
1223B SER* 4.0 1.7 + - - -
1244B GLN* 3.3 37.0 - - + +
1245B GLY* 4.6 9.4 - - - -
1248B ALA* 3.6 30.8 - - + +
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Residues in contact with GLU1220 (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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1216B MET 3.7 11.1 + - - +
1217B ASP* 2.9 22.4 + - - +
1218B LEU 2.7 2.6 + - - -
1219B LYS* 1.3 80.6 - - - +
1221B ARG* 1.3 70.3 + - + +
1223B SER* 2.3 30.2 + - - +
1224B ARG* 3.4 36.9 + - - +
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Residues in contact with ARG1221 (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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1208B CYS* 4.1 24.4 - - + +
1211B LEU* 3.1 29.5 + - - +
1212B ALA* 3.9 24.1 - - - +
1217B ASP* 2.9 29.9 + - - +
1218B LEU* 3.8 5.2 - - - +
1220B GLU* 1.3 74.2 - - + +
1222B PHE* 1.3 54.6 + - - +
1224B ARG* 2.4 52.6 + - - +
1225B ILE 3.8 0.8 + - - -
1320B TYR* 3.2 30.5 + - - -
1521B GLY* 3.5 33.2 + - - -
1522B GLY* 4.0 6.7 - - - +
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Residues in contact with PHE1222 (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* 5.2 0.4 - - + -
1205B VAL* 3.9 35.2 - - + -
1208B CYS* 4.1 29.3 - - + -
1218B LEU* 3.3 43.5 + - + +
1219B LYS* 4.3 0.9 - - - +
1221B ARG* 1.3 78.0 - - - +
1223B SER* 1.3 51.2 + - - +
1224B ARG 2.8 7.4 + - - -
1225B ILE* 2.3 44.0 + - + +
1238B ALA* 4.3 1.8 - - - -
1244B GLN* 4.3 11.7 - - + -
1247B MET* 3.6 58.3 - - + -
1248B ALA* 4.1 7.2 - - - -
1251B MET* 4.3 8.1 - - + -
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Residues in contact with SER1223 (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 4.0 0.4 + - - -
1220B GLU* 2.3 32.2 + - - +
1221B ARG 2.5 5.3 + - - -
1222B PHE* 1.3 74.6 - - - +
1224B ARG* 1.3 56.8 + - - +
1237B THR* 3.3 20.3 + - - -
1239B GLY* 3.4 20.2 + - - +
1244B GLN* 3.2 32.7 - - - +
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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