Contacts of the helix formed by residues 1258 - 1273 (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 HIS1258 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1256G SER* 2.9 14.6 + - - +
1257G ASN* 1.3 86.1 - - + +
1259G GLU* 1.3 65.1 + - - +
1260G GLY 3.3 0.2 - - - -
1261G GLU* 3.5 20.4 - - + +
1262G LEU* 3.1 22.7 + - - +
1283G TYR* 4.0 2.5 - - - -
1458H HIS* 5.4 1.6 - - + -
1460H GLY* 3.4 21.7 + - - -
1461H GLU* 3.4 10.3 - - + -
1464H ASP* 2.9 25.4 + - - -
1658I HIS* 5.0 0.2 - - + -
2403I PO4 3.3 38.2 + - - +
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Residues in contact with GLU1259 (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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1258G HIS* 1.3 70.1 - - - +
1260G GLY* 1.3 58.4 + - - +
1262G LEU* 3.2 7.0 + - - +
1263G VAL* 3.0 28.2 + - - +
1283G TYR* 3.4 29.6 + - + -
1287G SER* 2.6 32.1 + - - +
1289G ALA* 3.8 5.4 + - + +
1290G ILE* 4.3 5.9 - - + +
1459H GLU* 3.9 2.7 - - + +
2407H TRS 2.7 46.5 + - - -
1659I GLU* 4.0 4.3 - - - +
1683I TYR* 3.5 32.2 + - - +
2403I PO4 3.6 6.3 + - - +
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Residues in contact with GLY1260 (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* 1.3 75.8 - - - +
1261G GLU* 1.3 60.3 + - - +
1263G VAL* 3.4 5.7 + - - +
1264G ASP* 3.0 32.4 + - - +
1657I ASN* 3.4 26.2 + - - +
1658I HIS* 3.4 13.4 + - - -
1683I TYR* 4.4 0.2 + - - -
2403I PO4 3.0 15.6 + - - -
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Residues in contact with GLU1261 (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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1255G GLN 4.9 0.2 - - - +
1256G SER* 2.9 25.1 + - - +
1258G HIS* 3.2 25.1 + - + +
1260G GLY* 1.3 75.5 - - - +
1262G LEU* 1.3 64.7 + - - +
1264G ASP* 3.2 9.1 + - + +
1265G TRP* 2.9 62.6 + - + +
1658I HIS* 3.4 11.6 - - + -
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Residues in contact with LEU1262 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1212G LEU* 4.5 14.7 - - + +
1213G ASN 3.9 21.8 - - - +
1214G GLY* 4.0 16.4 - - - -
1256G SER* 4.0 16.6 - - - +
1258G HIS 3.1 12.9 + - - +
1259G GLU* 3.2 5.1 + - - +
1261G GLU* 1.3 74.4 - - - +
1263G VAL* 1.3 57.3 + - - +
1265G TRP* 3.2 17.3 + - + +
1266G ILE* 2.9 38.6 + - + +
1278G ILE* 5.8 5.2 - - + -
1280G PRO* 5.2 2.9 - - + +
1283G TYR* 3.6 32.8 - - + -
1290G ILE* 4.1 16.2 - - + -
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Residues in contact with VAL1263 (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 3.0 16.5 + - - +
1260G GLY* 3.5 10.3 - - - +
1261G GLU 3.2 0.2 - - - -
1262G LEU* 1.3 77.1 - - - +
1264G ASP* 1.3 61.2 + - - +
1266G ILE* 3.2 5.2 + - - +
1267G HIS* 3.0 36.5 + - + +
1289G ALA* 4.0 29.8 - - + +
1290G ILE* 4.2 11.2 - - + -
1293G ALA* 4.2 8.3 - - + -
1615I PRO* 4.8 2.0 - - + -
1616I ASN* 3.7 11.4 - - - +
1657I ASN* 3.4 35.7 - - + +
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Residues in contact with ASP1264 (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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1260G GLY 3.0 18.3 + - - +
1261G GLU* 3.2 11.4 + - + +
1263G VAL* 1.3 76.4 - - - +
1265G TRP* 1.3 69.4 + - + +
1267G HIS* 3.3 9.8 + - - +
1268G GLU* 3.1 19.9 + - - +
1657I ASN* 2.6 37.2 + - - +
1658I HIS* 3.6 15.1 + - - -
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Residues in contact with TRP1265 (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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1210G MET* 3.5 8.5 - - + +
1212G LEU* 3.8 20.9 - - + -
1254G ARG* 3.3 61.8 - - + +
1255G GLN 3.5 26.7 - - - -
1256G SER* 3.7 10.3 - - - -
1261G GLU* 2.9 52.5 + - + +
1262G LEU* 3.2 16.6 + - + +
1264G ASP* 1.3 79.9 - - + +
1266G ILE* 1.3 65.4 + - - +
1268G GLU* 3.2 12.7 + - - +
1269G ALA* 3.0 18.5 + - - +
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Residues in contact with ILE1266 (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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1212G LEU* 3.6 20.9 - - + -
1262G LEU* 2.9 25.2 + - + +
1263G VAL* 3.5 7.6 - - - +
1265G TRP* 1.3 76.9 - - - +
1267G HIS* 1.3 57.5 + - - +
1269G ALA* 3.2 7.0 + - - +
1270G ARG* 3.0 26.7 + - - +
1276G ILE* 4.2 2.7 - - + -
1278G ILE* 4.5 3.6 - - + -
1290G ILE* 3.8 29.2 - - + -
1293G ALA* 3.6 40.8 - - + +
1294G LEU* 3.9 21.3 - - + -
1297G CYS* 3.8 13.5 - - - -
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Residues in contact with HIS1267 (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* 3.0 22.1 + - + +
1264G ASP* 3.3 9.4 + - - +
1266G ILE* 1.3 75.7 - - - +
1268G GLU* 1.3 62.7 + - - +
1270G ARG* 3.4 20.3 + - - +
1271G LEU* 3.6 14.9 + - - +
1293G ALA* 4.4 4.7 - - + -
1296G THR* 4.3 7.9 - - - -
1616I ASN* 2.9 27.0 + - - -
1618I ASN* 3.3 40.4 + - - +
1619I LEU* 3.7 27.1 - - + +
1657I ASN* 3.6 22.3 + - - -
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Residues in contact with GLU1268 (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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1210G MET* 4.4 2.2 - - + -
1254G ARG* 2.6 45.4 + - - -
1264G ASP 3.1 12.4 + - - +
1265G TRP* 3.4 15.2 - - - +
1266G ILE 3.2 0.2 - - - -
1267G HIS* 1.3 72.6 - - - +
1269G ALA* 1.3 61.7 + - - +
1271G LEU* 3.1 3.9 + - - -
1272G ASN* 2.9 50.1 + - - +
1273G HIS* 4.2 8.7 - - + -
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Residues in contact with ALA1269 (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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1210G MET* 3.9 18.6 - - + +
1265G TRP 3.0 12.6 + - - +
1266G ILE* 3.2 8.0 + - - +
1268G GLU* 1.3 71.8 - - - +
1270G ARG* 1.3 67.9 + - - +
1273G HIS* 2.9 42.4 + - + +
1276G ILE* 3.7 30.7 - - + -
1300G LEU* 4.4 4.5 - - + +
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Residues in contact with ARG1270 (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 3.0 12.9 + - - +
1267G HIS* 3.4 14.9 + - - +
1269G ALA* 1.3 76.6 - - - +
1271G LEU* 1.3 82.1 + - + +
1273G HIS 5.1 1.9 - - - +
1296G THR* 2.8 48.0 + - - +
1297G CYS* 3.8 17.9 - - - +
1298G ASP* 5.3 2.8 + - - -
1300G LEU* 4.4 9.2 - - - +
1619I LEU* 3.9 24.0 - - - +
1622I GLN* 3.0 48.8 + - - +
1623I ARG* 5.3 2.4 - - - +
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Residues in contact with LEU1271 (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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1202G ARG* 3.7 19.4 + - - -
1267G HIS 3.8 13.2 - - - +
1268G GLU* 3.1 3.4 + - - +
1269G ALA 3.0 0.6 - - - -
1270G ARG* 1.3 108.5 - - + +
1272G ASN* 1.3 74.2 + - - +
1273G HIS 3.9 0.4 - - - -
1622I GLN* 5.8 0.9 - - - +
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Residues in contact with ASN1272 (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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1202G ARG* 3.9 17.3 + - - +
1207G ALA* 3.5 15.6 - - - +
1208G PRO* 4.1 6.4 - - - +
1268G GLU* 2.9 34.4 + - - +
1271G LEU* 1.3 96.1 - - - +
1273G HIS* 1.3 80.5 + - + +
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Residues in contact with HIS1273 (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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1202G ARG* 3.9 9.3 + - - +
1207G ALA* 4.1 4.7 - - - -
1208G PRO* 3.1 35.2 - - + +
1210G MET* 3.4 47.0 - - + +
1252G ASP* 3.1 27.0 + - + +
1268G GLU* 4.2 12.1 - - - -
1269G ALA* 2.9 29.6 + - + +
1270G ARG 5.1 1.2 - - - +
1271G LEU 5.4 0.2 - - - -
1272G ASN* 1.3 97.9 - - + +
1274G CYS* 1.3 58.2 + - - +
1275G GLY 3.3 5.2 - - - +
1300G LEU* 3.4 17.1 - - + +
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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