Contacts of the helix formed by residues 1282 - 1294 (chain J) in PDB entry 6C6U
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 TYR1282 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1258J ARG* 6.4 0.2 - - - -
1262J ARG* 3.0 25.4 + - + +
1263J LYS 4.5 0.4 - - - +
1264J ALA* 4.3 14.4 - - + -
1280J VAL 3.8 0.6 + - - -
1281J GLU* 1.3 73.1 - - - +
1283J SER* 1.3 62.5 + - - +
1285J VAL* 3.3 11.8 - - + +
1286J LYS* 2.9 72.4 + - + +
1302J TYR* 3.2 50.5 + + - -
1304J ARG* 3.2 37.2 + - - +
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Residues in contact with SER1283 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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891J ASP* 3.7 31.0 + - - +
892J PHE* 3.8 30.6 + - - -
1258J ARG* 6.2 1.8 - - - -
1262J ARG* 6.2 0.8 - - - +
1281J GLU* 3.4 3.0 - - - +
1282J TYR* 1.3 84.8 - - - +
1284J ARG* 1.3 57.3 + - - +
1286J LYS* 3.8 8.4 - - - +
1287J ILE* 2.9 33.0 + - - +
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Residues in contact with ARG1284 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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892J PHE* 5.2 6.6 - - + -
1274J PHE* 4.4 13.7 - - + -
1280J VAL* 4.2 17.5 - - + -
1281J GLU* 3.3 31.2 + - + +
1282J TYR 3.2 0.2 - - - -
1283J SER* 1.3 78.5 - - - +
1285J VAL* 1.3 57.5 + - - +
1287J ILE* 3.3 25.0 - - - +
1288J ALA* 2.9 47.3 + - - +
1291J GLU* 5.6 2.4 + - - -
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Residues in contact with VAL1285 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1264J ALA* 4.9 2.7 - - + -
1266J ILE* 3.8 23.6 - - + -
1274J PHE* 3.9 20.4 - - + -
1280J VAL* 4.0 15.9 - - + -
1281J GLU 3.4 4.9 + - - +
1282J TYR* 3.3 22.9 + - + +
1284J ARG* 1.3 78.6 - - - +
1286J LYS* 1.3 60.8 + - - +
1288J ALA* 4.0 4.7 - - + -
1289J ASN* 2.9 29.8 + - - +
1300J ALA* 4.6 17.7 - - + +
1302J TYR* 4.4 23.8 - - + -
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Residues in contact with LYS1286 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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888J CYS 4.4 5.1 + - - -
889J ASP* 3.5 33.2 + - - +
890J THR 5.3 1.6 + - - -
891J ASP* 3.4 24.6 + - - +
1258J ARG* 5.8 3.0 - - - +
1282J TYR* 2.9 63.4 + - + +
1283J SER* 3.8 6.7 - - - +
1284J ARG 3.2 0.2 - - - -
1285J VAL* 1.3 75.8 - - - +
1287J ILE* 1.3 60.7 + - + +
1289J ASN* 2.8 20.8 - - - +
1290J ARG* 2.9 24.2 + - + +
1302J TYR* 5.8 4.3 - - + -
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Residues in contact with ILE1287 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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891J ASP* 3.3 36.6 - - + +
892J PHE* 6.3 4.3 - - + -
1283J SER* 2.9 25.5 + - - +
1284J ARG* 3.3 30.7 - - - +
1286J LYS* 1.3 74.3 - - + +
1288J ALA* 1.3 64.4 + - - +
1290J ARG* 3.6 24.4 + - - +
1291J GLU* 3.0 37.3 + - - +
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Residues in contact with ALA1288 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1272J SER* 4.8 6.1 - - - +
1274J PHE* 4.2 15.5 - - + -
1284J ARG* 2.9 36.9 + - - +
1285J VAL* 3.6 9.4 - - + +
1286J LYS 3.2 0.2 - - - -
1287J ILE* 1.3 79.0 - - - +
1289J ASN* 1.3 59.1 + - - +
1291J GLU* 3.3 14.8 - - - +
1292J LEU* 2.9 31.4 + - + +
1300J ALA* 6.2 0.4 - - + -
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Residues in contact with ASN1289 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1285J VAL 2.9 20.1 + - - +
1286J LYS* 2.8 26.3 - - - +
1288J ALA* 1.3 74.2 - - - +
1290J ARG* 1.3 59.1 + - - +
1292J LEU* 3.8 8.1 - - - -
1293J GLU* 2.9 32.2 + - + +
1299J GLY* 4.0 3.6 - - - -
1300J ALA* 2.5 48.2 + - + +
1301J THR* 4.7 1.6 - - - +
1302J TYR* 4.4 17.6 - - - -
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Residues in contact with ARG1290 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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891J ASP* 4.0 17.5 + - - -
1286J LYS* 2.9 24.8 + - + +
1287J ILE* 3.6 27.3 + - - +
1288J ALA 3.2 0.2 - - - -
1289J ASN* 1.3 78.9 + - - +
1291J GLU* 1.3 60.2 + - - +
1293J GLU* 4.6 3.7 - - - +
1294J ALA* 3.3 28.5 + - + +
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Residues in contact with GLU1291 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1284J ARG* 5.6 1.9 + - - -
1287J ILE* 3.0 22.6 + - - +
1288J ALA* 3.3 18.7 - - - +
1290J ARG* 1.3 78.9 - - - +
1292J LEU* 1.3 67.4 + - + +
1294J ALA* 4.2 6.5 + - - +
1295J ASN* 4.1 17.0 + - - -
1297J LYS* 5.4 2.6 + - - +
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Residues in contact with LEU1292 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1271J SER* 4.2 15.7 - - - +
1272J SER* 3.7 36.6 - - - +
1288J ALA* 2.9 21.2 + - + +
1289J ASN* 4.1 2.9 - - - +
1290J ARG 3.4 0.2 - - - -
1291J GLU* 1.3 82.2 - - + +
1293J GLU* 1.3 62.5 + - - +
1294J ALA 3.3 0.9 + - - -
1295J ASN 3.5 9.2 + - - +
1297J LYS* 3.4 49.6 - - + +
1298J VAL 4.2 4.9 - - - +
1299J GLY* 4.0 28.0 - - - -
1300J ALA* 4.4 1.8 - - + +
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Residues in contact with GLU1293 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1289J ASN* 2.9 20.9 + - + +
1290J ARG* 4.6 3.7 - - - +
1292J LEU* 1.3 75.3 - - - +
1294J ALA* 1.3 63.4 + - - +
1295J ASN 3.0 14.0 - - - +
1297J LYS 4.7 10.6 - - - +
1299J GLY* 4.8 13.7 - - - +
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Residues in contact with ALA1294 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1290J ARG* 3.3 20.5 + - + +
1291J GLU* 4.5 6.7 - - - +
1292J LEU 3.3 1.2 - - - -
1293J GLU* 1.3 81.6 + - - +
1295J ASN* 1.3 65.2 + - - +
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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