Contacts of the helix formed by residues 1279 - 1292 (chain B) in PDB entry 1AIS
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 GLU1279 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1268B GLN* 4.1 11.2 + - + +
1269B ARG* 3.7 50.7 + - - +
1272B ALA* 4.0 11.2 - - + +
1278B THR* 1.3 72.3 - - - +
1280B VAL* 1.3 60.2 + - + +
1282B VAL* 3.3 5.4 + - - +
1283B ARG* 2.8 49.7 + - - +
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Residues in contact with VAL1280 (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 THR* 3.2 10.2 - - - +
1279B GLU* 1.3 80.4 - - + +
1281B THR* 1.3 57.4 + - - +
1283B ARG* 3.2 22.8 + - + +
1284B ASN* 2.8 51.6 + - - +
1401C A 5.1 7.2 - - - +
1430E A 6.2 3.1 - - + +
1431E A 6.2 1.8 - - - +
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Residues in contact with THR1281 (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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1249B GLY* 4.0 19.7 - - - -
1277B VAL* 4.0 14.6 - - + -
1278B THR* 3.1 13.5 + - - -
1280B VAL* 1.3 78.0 - - - +
1282B VAL* 1.3 60.8 + - - +
1284B ASN* 3.3 9.8 + - - +
1285B ARG* 3.0 27.2 + - + +
1429E T 3.4 35.1 + - - +
1430E A 2.5 29.6 + - - +
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Residues in contact with VAL1282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1249B GLY 5.0 3.4 - - - -
1252B ALA* 3.9 13.7 - - + +
1253B ALA* 4.2 15.9 - - - +
1256B TYR* 4.5 13.2 - - + -
1268B GLN* 4.4 25.1 - - + +
1271B VAL* 5.2 1.3 - - + -
1272B ALA* 3.9 18.6 - - + +
1277B VAL* 3.6 19.3 - - + -
1278B THR 3.2 15.0 + - - +
1279B GLU* 3.3 8.0 + - - +
1281B THR* 1.3 72.6 - - - +
1283B ARG* 1.3 61.0 + - - +
1285B ARG* 4.1 3.3 - - - +
1286B TYR* 2.9 37.8 + - + +
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Residues in contact with ARG1283 (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 GLN* 3.1 33.1 + - - +
1279B GLU* 2.8 32.3 + - - +
1280B VAL* 3.5 28.6 - - - +
1282B VAL* 1.3 77.3 - - - +
1284B ASN* 1.3 60.0 + - - +
1286B TYR* 3.5 9.6 - - + -
1287B LYS* 3.0 62.2 + - + +
1401C A 3.1 46.1 + - - -
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Residues in contact with ASN1284 (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 VAL* 2.8 38.5 + - - +
1281B THR* 3.6 9.1 + - - +
1282B VAL 3.2 0.2 - - - -
1283B ARG* 1.3 82.5 - - - +
1285B ARG* 1.3 81.5 + - - +
1287B LYS* 4.1 4.5 - - - +
1288B GLU* 3.3 23.0 + - - +
1429E T 5.5 10.1 + - - +
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Residues in contact with ARG1285 (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 LYS* 3.4 37.8 - - - +
1249B GLY* 3.2 35.0 - - - +
1250B LEU* 3.8 20.0 - - + -
1253B ALA* 3.5 9.6 - - + -
1281B THR* 3.0 20.0 + - + +
1282B VAL 4.1 0.2 - - - +
1284B ASN* 1.3 92.7 + - - +
1286B TYR* 1.3 58.4 + - - +
1288B GLU* 3.4 27.5 + - - +
1289B LEU* 3.0 33.8 + - + +
1428E G 4.6 3.8 + - - +
1429E T 2.9 30.8 + - - -
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Residues in contact with TYR1286 (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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1253B ALA* 3.3 19.2 - - + +
1256B TYR* 3.9 26.0 + + + -
1257B ILE* 3.8 16.3 - - + +
1260B LEU* 5.2 4.9 - - + -
1268B GLN* 3.6 24.5 - - - -
1282B VAL* 2.9 14.7 + - + +
1283B ARG* 3.5 20.9 - - + -
1285B ARG* 1.3 78.0 - - - +
1287B LYS* 1.3 84.6 + - + +
1290B VAL* 3.0 51.4 + - + +
1297B VAL* 5.4 8.7 - - + +
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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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1283B ARG* 3.0 44.8 + - + +
1284B ASN* 4.1 4.7 - - - +
1286B TYR* 1.3 97.8 + - + +
1288B GLU* 1.3 65.1 + - - +
1290B VAL* 3.6 4.5 + - - +
1291B GLU* 3.1 26.8 + - - +
1401C A 5.8 1.8 - - - -
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Residues in contact with GLU1288 (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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1241B LEU* 3.5 28.4 - - + +
1245B LYS* 4.0 15.9 + - - +
1250B LEU* 5.3 1.2 - - - +
1284B ASN 3.3 16.2 + - - +
1285B ARG* 3.5 23.8 + - - +
1287B LYS* 1.3 77.4 - - - +
1289B LEU* 1.3 63.9 + - - +
1291B GLU* 3.2 9.8 - - - +
1292B LYS* 2.9 67.1 + - + +
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Residues in contact with LEU1289 (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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1232B ILE* 4.1 12.8 - - + -
1233B LEU* 5.5 1.6 - - + -
1236B ALA* 3.8 28.9 - - + -
1241B LEU* 4.6 11.7 - - + -
1250B LEU* 4.2 22.4 - - + +
1253B ALA* 3.8 26.9 - - + -
1254B ALA* 4.0 8.5 - - + +
1257B ILE* 3.7 18.4 - - + -
1285B ARG* 3.0 20.8 + - - +
1288B GLU* 1.3 81.3 - - - +
1290B VAL* 1.3 63.3 + - - +
1292B LYS* 5.1 1.3 - - - -
1293B LEU* 3.0 40.8 + - + +
1295B ILE* 4.0 3.7 - - + +
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Residues in contact with VAL1290 (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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1257B ILE* 3.8 16.2 - - + -
1286B TYR* 3.0 46.0 + - + +
1287B LYS* 4.0 4.7 - - - +
1288B GLU 3.3 0.2 - - - -
1289B LEU* 1.3 76.1 - - - +
1291B GLU* 1.3 58.0 + - - +
1294B LYS* 2.9 24.8 + - - -
1295B ILE* 3.0 40.4 + - + +
1297B VAL* 4.6 17.0 - - + -
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Residues in contact with GLU1291 (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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1287B LYS 3.1 20.4 + - - +
1288B GLU* 3.2 11.0 - - - +
1290B VAL* 1.3 79.3 - - - +
1292B LYS* 1.3 103.0 + - - +
1294B LYS* 3.2 33.9 + - - +
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Residues in contact with LYS1292 (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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1239B ARG* 5.3 4.3 - - - +
1241B LEU* 3.6 36.6 - - + +
1288B GLU* 2.9 46.8 + - + +
1291B GLU* 1.3 97.2 + - - +
1293B LEU* 1.3 63.8 + - - +
1294B LYS* 5.2 2.2 - - - +
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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