Contacts of the helix formed by residues 1274 - 1287 (chain B) in PDB entry 1B08
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 ALA1274 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1273B SER* 1.3 71.8 - - - +
1275B ALA* 1.3 61.7 + - - +
1277B ASN* 3.3 1.3 + - - +
1278B ALA* 2.9 31.0 + - - +
1314B TYR* 3.7 27.6 - - + +
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Residues in contact with ALA1275 (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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1240B VAL* 3.8 16.6 - - + +
1273B SER* 3.4 8.2 + - - +
1274B ALA* 1.3 78.0 - - - +
1276B GLU* 1.3 62.6 + - + +
1278B ALA* 3.4 5.5 + - - +
1279B ALA* 3.1 22.9 + - - +
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Residues in contact with GLU1276 (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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1240B VAL* 4.2 24.9 - - + +
1243B LYS* 2.9 41.6 + - + +
1245B PHE* 3.6 12.0 - - + -
1271B PRO* 3.6 7.9 - - + +
1272B ARG* 2.9 31.0 + - - +
1273B SER* 3.0 21.2 + - - +
1275B ALA* 1.3 76.9 - - + +
1277B ASN* 1.3 61.6 + - - +
1279B ALA 3.3 1.4 + - - -
1280B LEU* 3.0 19.6 + - - +
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Residues in contact with ASN1277 (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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1271B PRO* 3.9 11.3 - - + +
1273B SER 2.8 19.6 + - - +
1274B ALA 3.3 2.9 + - - +
1276B GLU* 1.3 71.9 - - - +
1278B ALA* 1.3 57.4 + - - +
1280B LEU* 3.2 4.4 + - - +
1281B GLN* 2.8 32.2 + - - +
1314B TYR* 3.7 21.9 + - + +
1316B ASN* 3.8 6.8 - - - +
1334B ILE* 3.6 11.9 - - - +
1338B GLY* 2.9 29.9 + - - -
1340B TRP* 2.6 35.1 + - - -
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Residues in contact with ALA1278 (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 ALA 2.9 21.3 + - - +
1275B ALA* 3.7 6.1 - - - +
1276B GLU 3.3 0.2 - - - -
1277B ASN* 1.3 72.3 - - - +
1279B ALA* 1.3 62.1 + - - +
1281B GLN* 3.4 18.3 + - - +
1282B GLN* 3.1 35.0 + - - +
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Residues in contact with ALA1279 (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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1238B GLN* 3.5 35.1 - - + +
1239B SER 5.0 1.3 - - - +
1240B VAL* 3.6 35.0 - - + -
1245B PHE* 4.4 2.9 - - + -
1275B ALA 3.1 10.6 + - - +
1276B GLU 3.3 3.6 + - - +
1278B ALA* 1.3 74.5 - - - +
1280B LEU* 1.3 65.4 + - - +
1282B GLN* 3.3 18.5 + - - +
1283B LEU* 3.7 2.8 + - - +
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Residues in contact with LEU1280 (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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1245B PHE* 4.1 17.6 - - + -
1269B ALA* 3.7 11.4 - - + -
1271B PRO* 3.5 18.2 - - + -
1276B GLU 3.0 14.3 + - - +
1277B ASN 3.6 7.2 - - - +
1279B ALA* 1.3 73.3 - - - +
1281B GLN* 1.3 63.1 + - - +
1283B LEU* 3.1 19.1 + - + +
1284B VAL* 3.2 21.4 + - + +
1291B ALA* 4.9 0.9 - - + -
1293B LEU* 3.4 33.2 - - + -
1334B ILE* 4.0 12.1 - - + -
1352B VAL* 3.8 36.8 - - + -
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Residues in contact with GLN1281 (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 ASN* 2.8 18.3 + - - +
1278B ALA* 3.4 18.9 + - - +
1280B LEU* 1.3 76.2 - - - +
1282B GLN* 1.3 57.6 + - - +
1284B VAL* 3.2 9.6 + - - +
1285B VAL* 2.9 36.8 + - + +
1334B ILE* 4.4 5.1 - - + +
1335B PHE 4.6 0.7 - - - +
1336B THR 3.5 20.6 - - - +
1337B ASN* 3.5 11.6 + - - +
1338B GLY* 3.9 29.7 - - - +
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Residues in contact with GLN1282 (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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1238B GLN* 3.9 25.7 + - - +
1278B ALA* 3.1 24.7 + - - +
1279B ALA* 3.7 12.2 - - - +
1280B LEU 3.3 0.4 - - - -
1281B GLN* 1.3 75.4 - - + +
1283B LEU* 1.3 60.5 + - - +
1285B VAL* 4.1 10.5 - - + +
1286B ALA* 3.1 24.1 + - - +
2263C GLN* 4.9 17.6 + - - +
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Residues in contact with LEU1283 (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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1235B PRO 4.3 8.7 - - - +
1236B ASN 3.8 31.6 - - - +
1237B GLY 4.2 9.9 - - - +
1238B GLN* 4.3 12.3 - - + +
1245B PHE* 4.0 21.8 - - + +
1247B THR* 4.1 19.5 - - + +
1279B ALA 3.7 3.9 + - - +
1280B LEU* 3.1 14.1 + - + +
1282B GLN* 1.3 75.4 - - - +
1284B VAL* 1.3 66.6 + - + +
1286B ALA* 3.3 6.0 + - + +
1287B LYS* 3.0 31.7 + - + +
1350B LEU* 5.1 2.2 - - + -
1352B VAL* 3.9 28.0 - - + -
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Residues in contact with VAL1284 (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 LEU* 3.2 17.4 + - + +
1281B GLN* 3.5 10.5 - - - +
1283B LEU* 1.3 75.4 - - + +
1285B VAL* 1.3 50.2 + - - +
1287B LYS 3.6 0.2 - - - -
1288B ASN* 2.6 34.8 + - - -
1289B GLU 3.3 25.1 + - - +
1291B ALA* 3.8 28.3 - - + -
1334B ILE* 4.1 16.6 - - + +
1335B PHE 3.8 30.5 - - - +
1336B THR* 3.9 8.9 - - + +
1350B LEU* 4.6 7.4 - - + -
1352B VAL* 5.1 0.2 - - + -
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Residues in contact with VAL1285 (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 GLN* 2.9 34.3 + - + +
1282B GLN* 4.1 10.1 - - + +
1284B VAL* 1.3 71.4 - - - +
1286B ALA* 1.3 65.8 + - - +
1288B ASN* 3.2 18.0 + - - +
1336B THR* 3.3 37.2 - - - +
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Residues in contact with ALA1286 (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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1235B PRO 5.7 1.6 - - - +
1282B GLN 3.1 19.7 + - - +
1283B LEU* 3.5 8.3 - - + +
1285B VAL* 1.3 80.6 - - + +
1287B LYS* 1.3 74.6 + - + +
1288B ASN* 4.8 1.4 - - - +
2250C PHE* 6.1 0.9 - - - -
2252C LYS* 4.8 12.1 + - - -
2260C LEU* 5.7 9.6 - - + -
2263C GLN* 6.0 1.8 - - - +
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Residues in contact with LYS1287 (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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1235B PRO* 3.5 27.3 + - - +
1236B ASN* 2.9 29.2 + - - -
1247B THR* 4.1 15.7 - - + -
1249B GLY* 5.1 9.2 - - - +
1283B LEU* 3.0 17.9 + - + +
1284B VAL 4.2 0.2 - - - +
1286B ALA* 1.3 87.0 - - + +
1288B ASN* 1.3 69.8 + - - +
1289B GLU* 3.4 4.8 + - + +
1350B LEU* 4.0 33.9 - - + -
2250C PHE* 4.3 15.3 - - - -
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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