Contacts of the helix formed by residues 1287 - 1296 (chain G) in PDB entry 2BT4
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 SER1287 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1259G GLU* 2.6 23.8 + - - -
1283G TYR* 2.9 23.6 + - - +
1285G HIS 4.0 0.4 - - - -
1286G THR* 1.3 73.7 + - - +
1288G VAL* 1.3 61.7 + - - +
1289G ALA 3.6 0.2 + - - -
1290G ILE* 3.0 41.6 + - - +
1291G LEU* 3.3 16.5 + - - +
1321G TYR* 3.9 11.3 - - - +
1322G VAL* 5.0 2.1 - - - +
2407H TRS 3.4 7.9 - - - -
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Residues in contact with VAL1288 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1286G THR 3.4 2.2 + - - -
1287G SER* 1.3 74.4 - - - +
1289G ALA* 1.3 57.0 + - - +
1291G LEU* 3.1 7.8 + - + +
1292G ASP* 2.8 30.1 + - - +
1321G TYR* 3.9 31.9 - - + -
1682I ALA* 3.4 23.3 - - + +
1685I HIS* 4.4 5.6 - - + -
1686I THR* 3.6 26.9 - - + +
1716I PHE* 3.8 20.6 - - + -
1717I ARG* 3.8 22.9 - - - +
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Residues in contact with ALA1289 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1259G GLU* 3.8 8.7 + - - +
1263G VAL* 4.0 9.3 - - + +
1287G SER* 3.1 1.2 - - - +
1288G VAL* 1.3 79.4 - - - +
1290G ILE* 1.3 57.6 + - - +
1293G ALA* 3.0 23.7 + - - +
1615I PRO* 3.9 19.5 - - + -
1616I ASN* 3.2 12.1 + - - +
1682I ALA* 3.4 11.2 - - + +
1683I TYR* 3.7 33.1 - - + +
1686I THR* 5.7 0.6 - - - +
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Residues in contact with ILE1290 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1259G GLU* 4.3 7.0 - - + +
1262G LEU* 4.1 27.6 - - + -
1263G VAL* 4.2 15.3 - - + -
1266G ILE* 3.8 17.3 - - + -
1278G ILE* 4.0 13.9 - - + -
1280G PRO* 5.0 3.6 - - + -
1283G TYR* 3.8 21.1 - - + -
1287G SER* 3.0 32.1 + - - +
1289G ALA* 1.3 72.2 - - - +
1291G LEU* 1.3 66.2 + - - +
1293G ALA* 3.2 6.6 + - - +
1294G LEU* 3.0 24.3 + - + +
1322G VAL* 3.9 21.5 - - + -
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Residues in contact with LEU1291 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1287G SER 3.3 11.0 + - - +
1288G VAL* 3.1 8.9 + - - +
1290G ILE* 1.3 78.9 - - - +
1292G ASP* 1.3 58.7 + - - +
1294G LEU* 3.1 9.3 + - - +
1295G ASN* 2.8 39.4 + - - +
1321G TYR* 3.4 37.0 - - + +
1322G VAL* 4.7 3.9 - - - +
1324G GLN* 3.8 22.9 - - + +
1325G ARG* 3.6 29.8 - - + +
1716I PHE* 4.0 19.1 - - + -
1717I ARG* 4.3 7.0 - - - +
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Residues in contact with ASP1292 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1288G VAL 2.8 20.3 + - - +
1289G ALA 4.3 0.2 - - - -
1291G LEU* 1.3 73.2 - - - +
1293G ALA* 1.3 61.9 + - - +
1295G ASN* 3.3 21.8 + - - +
1296G THR* 3.3 14.7 + - - +
1616I ASN* 3.2 23.6 + - + +
1682I ALA* 3.2 11.1 + - - +
1717I ARG* 2.7 32.9 + - - -
1760I CA2 2.5 42.0 + - + +
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Residues in contact with ALA1293 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1263G VAL* 4.2 11.9 - - + -
1266G ILE* 3.6 34.3 - - + +
1267G HIS* 4.3 2.7 - - - +
1289G ALA 3.0 12.8 + - - +
1290G ILE* 3.6 8.7 - - - +
1291G LEU 3.2 0.4 - - - -
1292G ASP* 1.3 73.9 - - - +
1294G LEU* 1.3 64.0 + - - +
1296G THR* 2.7 25.4 + - - -
1297G CYS* 3.8 1.7 - - - -
1616I ASN* 3.2 21.5 - - - +
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Residues in contact with LEU1294 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1266G ILE* 3.9 20.4 - - + -
1276G ILE* 4.0 28.3 - - + -
1278G ILE* 4.6 7.4 - - + -
1290G ILE* 3.0 30.1 + - + +
1291G LEU* 3.6 6.1 - - - +
1293G ALA* 1.3 74.4 - - - +
1295G ASN* 1.3 54.1 + - - +
1297G CYS* 2.8 33.4 + - - +
1302G VAL* 4.2 23.3 - - + -
1322G VAL* 3.6 33.9 - - + +
1325G ARG* 3.4 28.9 + - + -
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Residues in contact with ASN1295 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1291G LEU* 2.8 31.6 + - - +
1292G ASP* 3.3 15.5 + - - +
1293G ALA 3.2 0.2 - - - -
1294G LEU* 1.3 77.6 - - - +
1296G THR* 1.3 57.8 + - - +
1297G CYS 3.1 2.0 + - - -
1298G ASP* 4.1 3.1 + - - +
1324G GLN 5.4 0.5 - - - +
1325G ARG* 3.4 31.5 + - - +
1623I ARG* 3.0 36.0 + - - +
1717I ARG* 4.2 14.1 - - - +
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Residues in contact with THR1296 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1267G HIS* 4.3 3.5 - - - -
1270G ARG* 2.8 42.3 + - - +
1292G ASP 3.4 15.7 - - - +
1293G ALA* 2.7 19.8 + - - +
1294G LEU 3.1 1.4 + - - -
1295G ASN* 1.3 74.7 - - - +
1297G CYS* 1.3 56.1 + - - +
1298G ASP* 3.1 18.3 + - - +
1616I ASN* 4.6 6.3 - - + +
1619I LEU* 3.6 21.6 - - + +
1623I ARG* 3.6 21.7 - - - +
1760I CA2 4.4 16.2 - - + -
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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