Contacts of the helix formed by residues 1268 - 1285 (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 THR1268 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1265B LEU 4.6 5.6 + - - -
1266B LEU 2.6 11.0 + - - -
1267B LEU* 1.3 74.5 - - - +
1269B PRO* 1.3 74.1 - - - +
1270B GLN* 3.3 15.5 - - + +
1271B LYS* 2.9 33.2 - - + +
1272B VAL* 2.8 24.5 + - - +
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Residues in contact with PRO1269 (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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1267B LEU 4.8 1.1 - - - +
1268B THR* 1.3 90.9 - - + +
1270B GLN* 1.3 61.6 + - - +
1272B VAL* 3.6 1.3 + - + -
1273B LYS* 3.1 28.5 + - - +
1472B LEU* 3.9 18.9 - - + +
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Residues in contact with GLN1270 (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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1268B THR* 3.2 9.7 - - + +
1269B PRO* 1.3 79.7 - - - +
1271B LYS* 1.3 63.9 + - - +
1273B LYS* 3.3 9.1 + - + +
1274B ARG* 3.0 61.9 + - + +
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Residues in contact with LYS1271 (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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1266B LEU* 3.1 42.1 + - - +
1267B LEU* 5.1 0.7 - - - -
1268B THR* 2.9 14.9 - - + +
1270B GLN* 1.3 79.4 - - - +
1272B VAL* 1.3 68.8 + - - +
1273B LYS 3.0 1.1 - - - -
1274B ARG* 3.0 19.2 + - + +
1275B TYR* 2.9 57.1 + - + +
1301B GLU* 3.0 36.5 + - - +
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Residues in contact with VAL1272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1267B LEU* 4.1 26.0 - - + -
1268B THR 2.8 28.2 + - - +
1269B PRO* 4.9 0.7 - - + -
1271B LYS* 1.3 71.2 - - - +
1273B LYS* 1.3 56.9 + - - +
1275B TYR* 3.3 12.3 + - + +
1276B VAL* 2.9 37.8 + - + +
1294B ILE* 5.5 5.6 - - + -
1469B ILE* 4.4 32.8 - - + -
1472B LEU* 3.9 25.4 - - + -
1473B VAL* 4.5 5.8 - - + -
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Residues in contact with LYS1273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1269B PRO* 3.1 23.0 + - - +
1270B GLN* 3.4 9.0 - - + +
1271B LYS 3.0 0.4 - - - -
1272B VAL* 1.3 74.6 - - - +
1274B ARG* 1.3 60.5 + - + +
1276B VAL* 3.1 9.4 + - + +
1277B GLU* 2.8 29.8 + - + +
1472B LEU* 3.9 31.4 - - + +
1476B SER* 5.9 2.7 - - - +
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Residues in contact with ARG1274 (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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1270B GLN* 3.0 46.1 + - + +
1271B LYS* 3.0 20.4 + - + +
1273B LYS* 1.3 75.0 - - - +
1275B TYR* 1.3 67.9 + - + +
1277B GLU* 3.1 7.6 + - - +
1278B SER* 2.9 25.9 + - - -
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Residues in contact with TYR1275 (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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1267B LEU* 4.3 16.6 - - + -
1271B LYS* 2.9 41.7 + - + +
1272B VAL* 3.3 14.6 - - + +
1273B LYS 3.2 0.2 - - - -
1274B ARG* 1.3 79.2 - - + +
1276B VAL* 1.3 58.0 + - + +
1278B SER* 3.4 0.8 + - - -
1279B LEU* 2.9 28.3 + - + +
1294B ILE* 3.9 28.9 - - + -
1297B MET* 3.1 41.1 - - + +
1298B LEU* 3.6 39.3 - - - +
1301B GLU* 2.4 29.0 + - + +
1308B MET* 6.0 1.1 - - + -
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Residues in contact with VAL1276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1272B VAL* 2.9 24.8 + - + +
1273B LYS* 3.5 11.0 - - + +
1275B TYR* 1.3 74.8 - - + +
1277B GLU* 1.3 69.1 + - - +
1279B LEU* 3.2 2.4 + - - +
1280B TRP* 3.1 26.7 + - + -
1294B ILE* 5.0 2.7 - - + -
1472B LEU* 5.3 2.5 - - + +
1473B VAL* 4.1 24.7 - - + +
1476B SER* 3.3 36.6 - - - +
1478B LEU* 3.8 27.5 - - + +
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Residues in contact with GLU1277 (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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1273B LYS* 2.8 17.8 + - + +
1274B ARG* 3.5 11.2 - - - +
1276B VAL* 1.3 74.6 - - - +
1278B SER* 1.3 62.8 + - - +
1280B TRP* 3.1 23.5 + - - +
1281B LYS* 3.8 2.8 + - - +
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Residues in contact with SER1278 (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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1274B ARG 2.9 16.5 + - - -
1275B TYR* 3.6 5.2 - - - -
1277B GLU* 1.3 77.6 - - - +
1279B LEU* 1.3 62.4 + - - +
1281B LYS* 3.2 22.3 + - - +
1282B LYS* 4.2 1.0 + - - +
1297B MET* 4.5 15.0 - - - +
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Residues in contact with LEU1279 (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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1275B TYR 2.9 13.3 + - - +
1276B VAL 3.2 0.4 + - - +
1278B SER* 1.3 73.4 - - - +
1280B TRP* 1.3 61.9 + - - +
1281B LYS 3.1 2.7 - - - -
1282B LYS* 2.9 30.8 + - + +
1283B LYS* 3.0 12.3 + - - +
1289B VAL* 4.0 5.0 - - + +
1293B ASP* 3.8 34.1 - - + +
1294B ILE* 3.7 29.2 - - + +
1297B MET* 3.2 35.0 - - + -
1387B HIS* 5.7 3.4 - - - +
1478B LEU* 3.8 26.5 - - + +
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Residues in contact with TRP1280 (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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1276B VAL* 3.1 34.0 + - + +
1277B GLU* 3.1 15.0 + - - +
1279B LEU* 1.3 73.6 - - - +
1281B LYS* 1.3 58.3 + - - +
1283B LYS* 3.9 30.5 - - + +
1284B SER* 2.7 51.0 + - - -
1476B SER* 3.0 31.4 + - - -
1477B ALA* 3.6 24.7 - - + -
1478B LEU* 3.9 18.3 - - + +
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Residues in contact with LYS1281 (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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1277B GLU 3.8 3.2 + - - +
1278B SER* 3.2 15.5 + - - +
1280B TRP* 1.3 80.1 - - - +
1282B LYS* 1.3 59.8 + - - +
1284B SER* 3.8 5.9 - - - -
1285B SER* 3.5 18.4 + - - -
1382B GLU* 3.1 40.0 + - - -
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Residues in contact with LYS1282 (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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1278B SER 4.2 0.6 + - - +
1279B LEU* 2.9 21.4 + - + +
1281B LYS* 1.3 79.6 - - - +
1283B LYS* 1.3 64.9 + - - +
1285B SER* 2.7 25.7 + - - -
1287B GLN* 3.5 34.6 + - + +
1288B PRO 3.6 19.2 + - - -
1289B VAL* 4.1 9.2 - - + -
1293B ASP* 2.6 30.9 + - - +
1384B ASN* 2.8 33.0 + - - +
1385B PRO* 6.2 0.4 - - + -
1388B PHE* 3.5 18.4 - - - +
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Residues in contact with LYS1283 (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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1279B LEU 3.0 9.8 + - - +
1280B TRP* 3.2 33.4 + - + +
1282B LYS* 1.3 76.8 - - - +
1284B SER* 1.3 63.5 + - - +
1286B GLY* 3.0 15.6 + - - -
1287B GLN 3.6 13.8 - - - +
1289B VAL* 3.9 14.5 - - + +
1477B ALA 2.9 16.2 + - - -
1478B LEU* 2.6 39.5 + - + +
1479B PHE* 4.1 4.4 - - - +
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Residues in contact with SER1284 (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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1280B TRP* 2.7 36.9 + - - -
1281B LYS* 3.8 7.2 - - - -
1283B LYS* 1.3 74.2 - - - +
1285B SER* 1.3 59.2 + - - +
1286B GLY 3.3 0.4 + - - -
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Residues in contact with SER1285 (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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1281B LYS 3.5 9.5 + - - -
1282B LYS* 2.7 21.2 + - - -
1283B LYS 3.1 0.4 - - - -
1284B SER* 1.3 78.8 - - - +
1286B GLY* 1.3 57.4 + - - +
1287B GLN* 3.4 20.5 + - - -
1381B TYR* 2.9 34.7 + - - -
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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