Contacts of the helix formed by residues 1262 - 1267 (chain A) in PDB entry 2CKJ
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 GLU1262 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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881A ARG* 5.6 0.7 - - - -
913A ARG* 3.3 13.8 - - + -
914A GLY* 2.3 47.5 + - - +
915A PHE* 4.2 7.8 + - - +
1006A PHE* 3.7 27.3 - - + -
1080A ALA* 3.5 26.0 - - - +
1081A SER* 2.6 30.9 + - - +
1261A GLY* 1.3 77.1 - - - -
1263A PRO* 1.3 80.0 - - + +
1264A PRO* 3.0 5.2 - - - -
1265A LEU* 2.9 21.4 + - - +
1266A PHE 4.5 0.3 + - - -
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Residues in contact with PRO1263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1004A THR* 4.5 13.5 + - + +
1006A PHE* 3.6 41.2 - - + -
1008A ILE* 4.5 5.6 - - + -
1081A SER* 4.6 3.4 - - - +
1155A SER* 3.5 25.4 - - - +
1181A MET* 3.8 17.9 - - + -
1259A ALA 4.9 1.6 - - - +
1260A VAL* 4.2 7.9 - - - +
1261A GLY 3.8 0.9 - - - +
1262A GLU* 1.3 96.3 - - + +
1264A PRO* 1.4 70.1 - - + +
1265A LEU 3.0 1.0 + - - -
1266A PHE* 3.5 15.4 + - - +
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Residues in contact with PRO1264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1004A THR* 5.6 0.2 - - + -
1179A ILE* 5.9 1.7 - - + +
1181A MET* 3.9 26.7 - - + -
1195A GLN 4.9 0.2 - - - +
1196A VAL* 4.4 29.6 - - + +
1199A ALA* 3.9 16.4 - - + -
1200A PHE* 4.5 8.0 - - + -
1260A VAL* 3.6 18.4 - - + +
1262A GLU 3.0 5.2 - - - -
1263A PRO* 1.4 98.6 - - + +
1265A LEU* 1.3 63.2 + - - +
1266A PHE 3.3 0.2 - - - -
1267A LEU* 3.1 28.3 + - + +
1268A ALA 4.5 0.5 + - - -
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Residues in contact with LEU1265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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840A ARG* 4.1 14.8 - - - +
912A PHE* 5.3 0.2 - - + -
913A ARG* 3.6 44.9 - - + +
914A GLY* 5.5 1.3 - - - -
918A PRO* 4.2 22.4 - - + -
1199A ALA* 3.6 27.3 - - + +
1200A PHE* 4.7 0.7 - - - -
1202A GLN* 4.0 17.9 - - + +
1203A GLY* 3.7 22.8 - - - +
1206A LEU* 4.7 7.9 - - + -
1207A PHE* 4.8 2.1 - - + -
1262A GLU 2.9 14.2 + - - +
1264A PRO* 1.3 79.9 - - - +
1266A PHE* 1.3 68.7 + - - +
1267A LEU 3.3 0.3 + - - -
1268A ALA* 3.5 8.1 + - - +
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Residues in contact with PHE1266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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888A ASN* 4.1 4.5 - - - -
918A PRO* 4.3 16.6 - - + +
921A MET* 2.9 61.2 - - + -
922A LEU* 4.4 9.2 - - + -
925A GLU* 4.1 15.7 - - + -
1002A ILE* 4.5 3.6 - - + -
1003A PRO 3.9 12.8 - - - -
1004A THR* 3.5 22.7 - - - +
1006A PHE* 6.4 1.6 - - + -
1207A PHE* 3.7 14.7 - + - -
1262A GLU 4.5 0.2 + - - -
1263A PRO 3.5 9.9 + - - +
1264A PRO 3.3 1.0 - - - -
1265A LEU* 1.3 85.8 - - - +
1267A LEU* 1.3 53.2 + - + +
1268A ALA 2.6 13.9 + - - -
1269A ALA* 2.9 38.0 + - + +
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Residues in contact with LEU1267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1002A ILE* 4.2 14.1 - - + +
1003A PRO 4.5 2.2 - - - +
1004A THR* 3.4 33.7 - - + -
1157A GLY 4.2 3.1 - - - +
1158A VAL 3.6 24.9 - - - +
1159A ALA* 3.7 20.0 - - + +
1179A ILE* 3.7 27.8 - - + -
1181A MET* 4.5 12.1 - - - -
1200A PHE* 3.7 10.6 - - + -
1263A PRO 4.7 0.2 + - - -
1264A PRO* 3.1 18.7 + - + +
1266A PHE* 1.3 75.2 - - + +
1268A ALA* 1.3 53.5 + - - +
1269A ALA* 3.2 3.3 - - - +
1270A SER* 2.6 33.5 + - - -
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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