Contacts of the helix formed by residues 1314 - 1329 (chain B) in PDB entry 1XTB
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 ASN1314 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1080B ARG* 4.2 3.0 - - - +
1305B HIS* 3.8 8.0 + - - -
1306B PHE* 2.8 36.7 + - - +
1309B THR* 3.2 17.2 + - - +
1310B PRO 3.2 7.5 + - - +
1311B LEU* 3.0 16.8 + - - +
1312B GLU 3.6 0.2 - - - -
1313B LYS* 1.3 76.0 - - - +
1315B ALA* 1.3 65.8 + - - +
1316B PRO* 3.0 34.0 - - - +
1317B VAL* 3.0 21.1 + - + +
1318B LEU* 2.9 25.3 + - - +
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Residues in contact with ALA1315 (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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1041B LEU* 3.7 17.2 - - + +
1043B LEU* 4.2 13.0 - - + -
1052B LEU* 4.2 15.2 - - + +
1302B MET* 5.0 0.7 - - - -
1305B HIS* 3.0 20.8 - - + +
1313B LYS 3.4 3.2 + - - -
1314B ASN* 1.3 70.1 - - - +
1316B PRO* 1.3 71.0 - - + +
1318B LEU* 3.2 3.0 + - - +
1319B LEU* 3.0 29.0 + - - +
1492B MET* 4.5 14.6 - - + -
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Residues in contact with PRO1316 (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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1302B MET* 4.4 9.4 - - - -
1305B HIS* 4.0 9.2 - - - +
1306B PHE* 3.5 24.5 - - + -
1314B ASN* 3.0 22.4 - - - +
1315B ALA* 1.3 91.0 - - + +
1317B VAL* 1.3 54.5 + - - -
1319B LEU* 4.4 7.9 - - + -
1320B ALA* 3.0 28.1 + - - +
1492B MET* 3.4 26.9 - - + +
1495B HIS* 3.6 17.3 - - + -
1496B LYS* 3.6 10.1 - - - +
1499B VAL* 4.6 1.8 - - - -
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Residues in contact with VAL1317 (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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1068B LEU* 4.5 5.2 - - + -
1071B ALA* 4.4 11.7 - - + -
1076B VAL* 4.8 3.4 - - + -
1306B PHE* 3.9 17.3 - - + -
1311B LEU* 4.1 33.2 - - + +
1314B ASN* 3.0 37.3 + - + +
1316B PRO* 1.3 74.0 - - - +
1318B LEU* 1.3 61.5 + - - +
1320B ALA* 3.2 5.4 + - - +
1321B MET* 2.9 42.5 + - + +
1499B VAL* 4.2 11.4 - - + -
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Residues in contact with LEU1318 (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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1041B LEU* 4.1 22.0 - - + -
1052B LEU* 4.8 6.7 - - + -
1054B TYR* 3.9 28.7 - - + +
1064B MET* 3.8 26.9 - - + +
1068B LEU* 4.3 12.8 - - + -
1311B LEU 4.2 9.2 - - - +
1312B GLU* 3.8 26.9 - - - +
1313B LYS* 4.3 0.4 - - + -
1314B ASN 2.9 20.4 + - - +
1315B ALA* 3.7 4.3 - - - +
1317B VAL* 1.3 76.9 - - - +
1319B LEU* 1.3 62.5 + - - +
1321B MET* 3.4 4.5 + - + +
1322B LEU* 3.0 33.8 + - + +
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Residues in contact with LEU1319 (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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1052B LEU* 3.8 27.4 - - + -
1315B ALA 3.0 17.8 + - - +
1316B PRO* 3.8 6.5 - - + +
1318B LEU* 1.3 76.6 - - - +
1320B ALA* 1.3 64.1 + - - +
1322B LEU* 3.5 7.5 + - + +
1323B GLY 3.2 15.9 + - - -
1404B ASP* 4.5 9.4 - - - +
1474B ASN* 3.8 26.6 + - - +
1476B ILE* 4.6 3.1 - - + -
1492B MET* 3.7 45.3 - - + -
1493B TYR* 4.2 15.0 - - + -
1496B LYS* 3.7 23.6 + - + -
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Residues in contact with ALA1320 (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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1316B PRO 3.0 20.4 + - - +
1317B VAL 3.4 5.4 - - - +
1319B LEU* 1.3 76.7 - - - +
1321B MET* 1.3 58.4 + - - +
1323B GLY 3.0 1.0 + - - -
1324B ILE* 3.0 16.1 + - - +
1496B LYS* 3.5 20.6 - - - +
1499B VAL* 3.4 30.5 - - + -
1500B GLN* 2.9 29.4 + - + +
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Residues in contact with MET1321 (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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1064B MET* 5.9 2.0 - - + -
1067B LEU* 3.5 49.6 - - + +
1068B LEU* 5.1 3.8 - - + +
1070B LEU* 4.0 26.5 - - + -
1071B ALA* 3.9 25.4 - - + +
1317B VAL* 2.9 26.7 + - + +
1318B LEU* 4.1 4.5 - - - +
1320B ALA* 1.3 70.9 - - - +
1322B LEU* 1.3 66.5 + - - +
1324B ILE* 3.2 19.1 + - + +
1325B TRP* 2.9 23.2 + - - +
1499B VAL* 4.3 8.5 - - - -
1503B VAL* 3.9 19.3 - - + -
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Residues in contact with LEU1322 (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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1052B LEU* 6.2 0.2 - - + -
1054B TYR* 3.6 35.4 - - + -
1057B ASN* 3.7 20.6 - - + +
1059B VAL* 3.9 27.1 - - + -
1064B MET* 4.0 20.9 - - + -
1067B LEU* 4.6 2.5 - - + -
1318B LEU* 3.0 29.3 + - + +
1319B LEU* 3.8 7.6 - - + +
1321B MET* 1.3 77.1 - - - +
1323B GLY* 1.3 62.2 + - - +
1325B TRP* 3.2 8.2 - - + +
1326B TYR* 3.1 37.7 + - + -
1474B ASN* 3.8 14.1 - - - +
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Residues in contact with GLY1323 (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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1319B LEU 3.2 6.8 + - - -
1320B ALA 3.0 8.7 + - - -
1322B LEU* 1.3 77.3 - - - +
1324B ILE* 1.3 52.8 + - - +
1326B TYR* 3.2 7.6 + - - +
1327B ILE* 2.8 43.8 + - - +
1335B GLN* 5.1 8.5 - - - -
1496B LYS* 5.1 4.0 - - - -
1500B GLN* 3.6 14.1 - - - -
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Residues in contact with ILE1324 (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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1003B LEU* 5.4 0.7 - - + -
1009B PHE* 5.2 3.1 - - + -
1012B LEU* 5.2 6.3 - - + -
1067B LEU* 5.3 0.2 - - + -
1070B LEU* 4.6 10.1 - - + -
1320B ALA 3.0 19.4 + - - +
1321B MET* 3.5 30.7 - - + +
1323B GLY* 1.3 75.6 - - - +
1325B TRP* 1.3 59.5 + - - +
1327B ILE* 4.5 1.3 - - - +
1328B ASN* 2.8 47.6 + - + +
1329B CYS* 3.8 0.7 + - - -
1500B GLN* 4.0 19.7 - - + -
1503B VAL* 4.3 19.1 - - + -
1504B TRP* 3.4 39.0 - - + +
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Residues in contact with TRP1325 (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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1012B LEU* 3.6 32.3 - - + -
1015B TRP* 3.9 28.0 - + - -
1016B HIS* 3.7 18.6 - - + -
1023B LEU* 4.2 3.6 - - + -
1058B LEU 2.9 25.5 + - - -
1059B VAL* 3.7 15.4 - - + +
1063B VAL* 3.8 23.8 - - + -
1067B LEU* 4.1 14.1 - - + +
1321B MET 2.9 12.6 + - - +
1322B LEU* 3.2 10.1 - - + +
1323B GLY 3.2 0.2 - - - -
1324B ILE* 1.3 76.4 - - - +
1326B TYR* 1.3 77.6 + + - +
1329B CYS* 3.1 57.9 + - + +
1330B PHE* 3.2 26.0 + + - -
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Residues in contact with TYR1326 (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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1057B ASN* 2.6 32.7 + - - +
1058B LEU* 3.0 29.2 + - + -
1322B LEU* 3.1 31.8 + - + -
1323B GLY* 3.2 6.5 + - - +
1325B TRP* 1.3 93.5 - + - +
1327B ILE* 1.3 59.3 + - + +
1330B PHE* 3.4 13.9 - + - +
1331B GLY 2.9 9.9 + - - -
1332B CYS* 2.8 28.5 + - + -
1400B MET* 3.4 35.0 - - + -
1402B PRO* 3.7 36.1 - - + -
1472B PRO* 3.2 12.8 - - + +
1474B ASN* 6.2 0.9 - - - -
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Residues in contact with ILE1327 (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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399A LYS* 4.3 4.5 - - - +
1323B GLY* 2.8 29.7 + - - +
1324B ILE* 4.0 1.3 - - - +
1326B TYR* 1.3 75.0 - - + +
1328B ASN* 1.3 66.7 + - - +
1331B GLY* 3.2 23.2 - - - -
1332B CYS* 3.9 17.5 - - + +
1334B THR 6.0 0.7 - - - +
1373B GLN* 3.6 25.9 - - + +
1374B THR 3.6 16.6 - - - +
1376B PRO* 3.6 40.2 - - + -
1500B GLN* 4.5 4.5 - - - +
1504B TRP* 3.8 20.4 - - + -
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Residues in contact with ASN1328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1003B LEU* 4.2 5.7 - - - +
1009B PHE* 3.9 27.5 - - + -
1013B GLN* 5.2 4.3 - - - +
1324B ILE* 2.8 32.1 + - + +
1327B ILE* 1.3 75.0 - - - +
1329B CYS* 1.3 60.9 + - - +
1331B GLY* 4.6 0.4 - - - -
1372B HIS* 3.9 10.7 + - - +
1373B GLN* 2.9 42.0 + - - +
1504B TRP* 2.7 28.4 + - - +
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Residues in contact with CYS1329 (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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1009B PHE* 5.1 2.9 - - - -
1012B LEU* 4.0 20.6 - - - -
1013B GLN* 4.3 14.8 - - - -
1016B HIS* 2.9 43.9 + - + +
1324B ILE* 5.1 0.4 - - - -
1325B TRP* 3.1 45.3 + - + +
1328B ASN* 1.3 85.6 - - - +
1330B PHE* 1.3 61.3 + - - +
1331B GLY 3.4 0.9 - - - -
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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