Contacts of the strand formed by residues 1221 - 1226 (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 ALA1221 (chain B).
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Specific contacts
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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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Residues in contact with THR1222 (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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1157B PHE* 3.7 15.9 - - + -
1158B ARG* 4.7 12.6 - - + +
1161B ARG* 4.4 8.4 - - + +
1165B ILE* 4.6 11.1 - - - +
1188B PRO 4.9 1.6 + - - -
1189B VAL* 3.7 23.9 - - + +
1190B VAL 2.8 10.4 + - - -
1220B CYS 3.9 0.8 + - - -
1221B ALA* 1.3 75.0 - - - +
1223B TYR* 1.3 95.4 + - + +
1325B PRO* 3.5 3.1 - - - +
1326B LEU 2.9 23.1 + - - -
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Residues in contact with TYR1223 (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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1154B GLU* 2.6 31.0 + - + +
1157B PHE* 5.1 1.1 - + - -
1158B ARG* 2.9 37.1 + - + -
1189B VAL* 3.9 11.9 - - + -
1190B VAL 3.2 2.9 + - - +
1191B ALA* 3.3 7.7 - - + -
1192B ILE* 2.7 32.3 + - - +
1221B ALA* 4.1 1.6 - - - +
1222B THR* 1.3 107.6 - - + +
1224B VAL* 1.3 62.3 + - - +
1225B ALA 4.1 0.2 - - - -
1325B PRO* 4.2 1.8 - - - -
1326B LEU* 3.6 27.4 - - + +
1328B LEU* 3.8 14.6 - - + -
1561B ILE* 3.7 29.8 - - + -
1566B ARG* 3.5 21.3 - - + +
1568B VAL* 5.1 0.7 - - + -
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Residues in contact with VAL1224 (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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1192B ILE* 3.3 19.3 - - + +
1205B PHE* 4.2 17.0 - - + -
1209B MET* 4.4 12.1 - - + -
1218B LEU* 4.1 16.4 - - + -
1223B TYR* 1.3 79.0 - - - +
1225B ALA* 1.3 62.1 + - - +
1234B MET* 3.2 33.7 - - + +
1238B TYR* 4.2 14.1 - - + +
1325B PRO* 3.8 19.1 - - + -
1326B LEU 3.2 6.0 + - - +
1327B PRO* 3.4 2.0 - - + +
1328B LEU* 2.8 23.9 + - - +
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Residues in contact with ALA1225 (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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1192B ILE 2.7 14.5 + - - +
1193B LEU* 3.4 17.4 - - + -
1194B GLY 2.9 23.4 + - - +
1205B PHE* 4.9 0.2 - - - -
1224B VAL* 1.3 76.4 - - - +
1226B GLY* 1.3 59.2 + - - +
1234B MET* 4.1 4.1 - - - +
1328B LEU* 3.4 26.2 - - + -
1557B PRO* 3.9 5.9 - - + +
1560B LEU* 4.0 16.6 - - + -
1561B ILE* 4.5 6.3 - - + -
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Residues in contact with GLY1226 (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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1194B GLY 3.3 11.0 - - - -
1225B ALA* 1.3 76.9 - - - +
1227B LEU* 1.3 63.6 + - - +
1230B SER* 4.1 5.6 - - - -
1231B THR* 3.9 6.9 + - - -
1234B MET* 3.6 15.4 - - - -
1328B LEU 3.1 8.9 + - - -
1329B PHE* 3.7 19.8 - - - -
1330B THR 3.9 3.5 + - - -
1557B PRO* 4.0 3.4 - - - -
1560B LEU* 4.0 5.2 - - - +
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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