Contacts of the helix formed by residues 1217 - 1221 (chain B) in PDB entry 1CJY
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 ILE1217 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1172B LEU* 3.2 35.4 - - + -
1190B VAL* 5.6 2.2 - - + -
1192B ILE* 4.7 10.3 - - + -
1212B LEU* 3.0 31.4 + - + +
1215B SER* 3.3 17.9 - - - +
1216B GLY* 1.3 74.9 - - - +
1218B LEU* 1.3 57.5 + - - +
1220B CYS* 2.7 30.9 + - - +
1221B ALA* 3.3 5.5 + - - +
1572B ILE* 5.5 2.2 - - + -
1701B THR* 6.1 0.7 - - + -
1705B ILE* 4.2 15.0 - - + -
1708B ILE* 4.1 34.3 - - + -
1709B LYS* 5.5 0.4 - - + -
1712B MET* 4.7 7.2 - - + -
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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
----------------------------------------------------------
1161B ARG* 3.4 12.0 + - - -
1192B ILE* 4.6 12.1 - - + -
1209B MET* 3.6 34.1 - - + +
1212B LEU* 3.0 26.5 + - + +
1213B TYR* 4.1 33.2 - - + +
1217B ILE* 1.3 76.8 - - - +
1219B ASP* 1.3 65.5 + - - +
1220B CYS 3.1 1.0 + - - -
1221B ALA* 3.2 12.4 + - + +
1224B VAL* 4.1 9.6 - - + -
1243B PHE* 5.7 7.9 - - + -
1248B PRO* 5.7 2.0 - - + -
1325B PRO* 3.5 35.5 - - + +
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Residues in contact with ASP1219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1161B ARG* 4.2 5.5 + - - +
1164B HIS* 3.3 28.9 + - - +
1165B ILE* 3.2 16.8 - - - +
1168B SER* 3.5 30.3 + - - +
1213B TYR* 4.2 10.7 - - - +
1216B GLY* 3.4 24.5 - - - +
1217B ILE 3.1 1.0 - - - -
1218B LEU* 1.3 78.2 - - - +
1220B CYS* 1.3 55.5 + - - +
1221B ALA 3.5 0.2 - - - -
1323B GLN 5.8 0.3 - - - +
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Residues in contact with CYS1220 (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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1165B ILE* 3.0 32.1 - - - +
1168B SER* 3.7 21.1 - - - -
1169B MET* 3.6 24.4 - - + +
1172B LEU* 3.7 19.7 - - - -
1188B PRO 4.7 0.2 - - - +
1190B VAL* 3.9 14.3 + - - +
1216B GLY 3.6 16.4 - - - -
1217B ILE 2.7 9.9 + - - +
1219B ASP* 1.3 78.1 - - - +
1221B ALA* 1.3 55.6 + - - +
1222B THR* 3.9 0.7 + - - -
1712B MET* 3.5 19.7 - - + -
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Residues in contact with ALA1221 (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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1161B ARG* 2.7 30.7 + - - -
1165B ILE* 3.3 5.0 - - - +
1190B VAL* 3.6 21.1 - - + +
1192B ILE* 4.0 26.5 - - + -
1217B ILE 3.3 6.0 + - - +
1218B LEU* 3.2 12.3 + - - +
1220B CYS* 1.3 78.8 - - - +
1222B THR* 1.3 61.2 + - - +
1223B TYR 4.1 5.8 - - - +
1325B PRO* 4.0 8.0 - - + +
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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