Contacts of the helix formed by residues 1287 - 1298 (chain B) in PDB entry 1DSZ
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 CYS1287 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1222B ZN 2.4 35.9 - - - -
1270B THR 4.8 2.0 - - - -
1271B CYS* 3.8 13.0 - - - -
1272B ARG 4.9 2.0 - - - -
1277B CYS* 3.9 16.4 - - + -
1279B ILE* 4.4 3.9 - - + +
1283B GLN 4.5 1.2 + - - -
1284B ARG 4.1 4.5 + - - +
1285B ASN 4.6 0.2 - - - -
1286B ARG* 1.3 79.7 - - + +
1288B GLN* 1.3 60.7 + - - +
1289B TYR* 3.7 10.8 - - - -
1290B CYS* 3.4 14.5 - - + +
1291B ARG* 3.1 27.5 + - - +
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Residues in contact with GLN1288 (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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1258B PHE* 3.5 18.8 - - + -
1267B LEU* 5.7 1.2 - - - +
1269B TYR* 3.4 46.4 + - + -
1270B THR 5.9 0.2 + - - -
1284B ARG 5.4 0.4 - - - -
1285B ASN* 4.6 11.0 - - - +
1286B ARG 4.1 0.4 + - - -
1287B CYS* 1.3 69.7 - - - +
1289B TYR* 1.3 66.5 + - - +
1291B ARG* 4.3 2.5 - - - +
1292B TYR* 3.0 22.7 + - - +
1531D C 3.9 10.5 + - - -
1532D T 3.1 28.4 + - - +
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Residues in contact with TYR1289 (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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1269B TYR* 3.5 34.4 - + + +
1270B THR* 3.7 7.4 + - - -
1271B CYS* 3.6 35.2 - - + +
1275B LYS* 3.7 44.2 - - + +
1287B CYS* 3.3 5.9 - - - -
1288B GLN* 1.3 79.4 - - - +
1290B CYS* 1.3 67.4 + - - +
1292B TYR* 3.4 3.1 + + - +
1293B GLN* 3.0 65.0 + - + +
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Residues in contact with CYS1290 (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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1222B ZN 2.3 35.2 - - - -
1275B LYS* 3.5 24.7 - - - -
1276B ASP* 4.3 0.2 - - - -
1277B CYS* 3.4 33.7 - - + +
1279B ILE* 3.7 10.4 - - + +
1287B CYS* 3.4 5.0 - - - -
1288B GLN 3.3 0.4 - - - -
1289B TYR* 1.3 84.1 - - - +
1291B ARG* 1.3 65.8 + - - +
1293B GLN* 3.9 4.7 - - - +
1294B LYS* 3.0 23.7 + - - +
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Residues in contact with ARG1291 (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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1237B ILE* 4.2 6.1 - - + +
1254B GLY* 3.2 22.2 - - - -
1255B CYS* 3.3 22.2 - - - +
1258B PHE* 3.5 46.0 - - + +
1279B ILE* 3.6 22.5 - - + +
1284B ARG* 3.4 36.4 + - - +
1285B ASN* 3.0 21.4 + - - -
1287B CYS 3.1 17.7 + - - +
1288B GLN* 3.7 4.3 - - - +
1289B TYR 3.3 0.2 - - - -
1290B CYS* 1.3 78.0 - - - +
1292B TYR* 1.3 57.1 + - - +
1294B LYS* 3.2 3.5 + - - +
1295B CYS* 2.9 28.7 + - - -
1532D T 4.6 1.8 - - - -
1533D G 2.9 29.5 + - - -
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Residues in contact with TYR1292 (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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1258B PHE* 3.5 15.6 - + + -
1259B PHE* 3.6 32.5 - + - -
1262B THR* 3.6 35.6 - - + +
1263B VAL* 4.4 6.1 - - + +
1267B LEU 5.7 1.8 - - - -
1269B TYR* 4.1 10.5 - + + -
1288B GLN 3.0 16.5 + - - +
1289B TYR* 3.8 3.4 - + - +
1291B ARG* 1.3 78.9 - - - +
1293B GLN* 1.3 76.4 + - - +
1295B CYS* 3.1 5.4 + - - +
1296B LEU* 3.0 42.0 + - + +
1302B ARG* 3.6 29.5 - - - +
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Residues in contact with GLN1293 (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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1289B TYR* 3.0 61.6 + - + +
1290B CYS* 4.1 6.1 - - - +
1292B TYR* 1.3 96.4 - - - +
1294B LYS* 1.3 57.3 + - - +
1296B LEU* 3.4 18.1 + - - +
1297B ALA* 2.9 28.5 + - - +
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Residues in contact with LYS1294 (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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1236B ALA 3.7 14.4 + - - -
1237B ILE* 2.9 35.3 + - + +
1278B LEU* 6.1 1.0 - - - +
1279B ILE* 3.4 34.7 + - + +
1290B CYS 3.0 18.9 + - - +
1291B ARG 3.7 3.8 - - - +
1293B GLN* 1.3 74.3 - - - +
1295B CYS* 1.3 67.6 + - - +
1297B ALA* 4.2 5.8 - - + -
1298B MET* 2.9 48.0 + - + +
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Residues in contact with CYS1295 (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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1237B ILE* 3.7 26.9 - - - +
1255B CYS* 4.4 8.5 - - - -
1258B PHE* 4.3 16.6 - - - -
1259B PHE* 3.7 29.6 - - + -
1291B ARG* 2.9 19.7 + - - -
1292B TYR* 3.3 8.7 - - - +
1294B LYS* 1.3 77.8 - - - +
1296B LEU* 1.3 60.0 + - - +
1298B MET* 3.6 2.1 + - - +
1299B GLY 3.4 3.6 + - - -
1300B MET* 3.0 41.9 + - - +
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Residues in contact with LEU1296 (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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1259B PHE* 3.8 17.9 - - + -
1292B TYR* 3.0 47.5 + - + +
1293B GLN* 3.6 23.6 - - - +
1295B CYS* 1.3 79.3 - - - +
1297B ALA* 1.3 57.0 + - - +
1299B GLY* 3.0 20.1 + - - -
1300B MET 3.7 20.3 + - - +
1302B ARG* 4.2 15.9 - - + -
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Residues in contact with ALA1297 (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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1293B GLN 2.9 18.0 + - - +
1294B LYS* 3.2 8.0 + - + +
1296B LEU* 1.3 76.1 - - - +
1298B MET* 1.3 68.9 + - + +
1299B GLY* 3.2 0.6 + - - -
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Residues in contact with MET1298 (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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1236B ALA* 3.7 34.0 - - + +
1237B ILE* 3.3 29.6 - - + -
1249B VAL* 3.2 16.7 - - + +
1294B LYS* 2.9 34.7 + - + +
1295B CYS 4.2 0.2 - - - +
1297B ALA* 1.3 83.1 - - - +
1299B GLY* 1.3 56.2 + - - +
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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