Contacts of the helix formed by residues 1214 - 1232 (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 THR1214 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A HIS* 4.0 16.8 - - + -
1156B ILE* 4.0 14.8 - - + -
1209B SER* 4.3 1.3 + - - -
1211B THR* 3.5 3.5 + - - +
1212B PHE 3.8 0.6 - - - -
1213B THR* 1.3 77.1 + - - +
1215B GLN* 1.3 64.8 + - - +
1216B GLU* 3.5 22.7 - - - +
1217B THR* 3.3 7.2 + - - +
1218B ILE* 3.0 24.7 + - - +
1518B LYS* 5.4 8.3 + - - +
2001B S6P 2.7 41.4 + - - +
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Residues in contact with GLN1215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423A ILE* 3.7 32.5 - - + +
427A ASN* 4.6 6.5 - - - +
1213B THR 3.1 6.8 + - - -
1214B THR* 1.3 73.6 - - - +
1216B GLU* 1.3 67.5 + - - +
1218B ILE* 4.2 3.1 - - - +
1219B THR* 2.7 42.9 + - - +
1521B ALA* 5.7 3.2 - - - +
1522B LYS* 3.5 20.3 + - - +
1525B GLU* 3.0 35.2 + - - +
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Residues in contact with GLU1216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384A THR* 3.5 14.5 - - - +
387A GLN* 4.5 5.4 - - - +
388A HIS* 2.6 40.2 + - - -
423A ILE* 5.6 2.5 - - + -
427A ASN* 4.9 8.7 + - - +
1156B ILE* 4.1 11.9 - - + -
1184B SER 4.0 15.0 - - - +
1186B ILE* 3.5 41.0 - - + +
1214B THR* 3.4 7.6 - - - +
1215B GLN* 1.3 79.0 + - + +
1217B THR* 1.3 58.0 + - - +
1219B THR* 3.8 1.2 - - - -
1220B ASN* 2.9 36.5 + - - -
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Residues in contact with THR1217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1154B ILE* 3.6 31.3 - - - +
1155B GLY* 3.5 16.3 - - - -
1156B ILE* 3.6 16.8 + - - +
1184B SER 5.7 0.7 - - - -
1207B ILE* 4.0 16.6 - - + -
1208B ALA 3.7 14.1 + - - +
1209B SER* 4.1 9.4 - - - -
1214B THR* 3.3 12.8 + - - +
1216B GLU* 1.3 78.6 - - - +
1218B ILE* 1.3 59.6 + - + +
1220B ASN* 3.3 3.0 + - - +
1221B ALA* 2.8 31.4 + - - +
2001B S6P 4.3 3.8 + - - -
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Residues in contact with ILE1218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1207B ILE* 5.0 2.0 - - + -
1209B SER* 5.0 0.2 - - - +
1212B PHE* 3.1 56.8 - - + +
1213B THR* 3.8 11.2 - - - +
1214B THR 3.0 19.0 + - - +
1215B GLN* 4.2 3.4 - - - +
1217B THR* 1.3 83.2 - - + +
1219B THR* 1.3 58.3 + - - +
1221B ALA* 3.3 4.5 + - + +
1222B LYS* 2.9 53.8 + - + +
1255B PHE* 5.3 7.0 - - + -
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Residues in contact with THR1219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416A ARG* 3.6 9.0 + - - +
419A LEU* 3.5 26.4 - - + +
420A HIS* 3.4 22.7 - - + +
423A ILE* 4.1 4.3 - - - +
1186B ILE* 3.8 11.2 - - + -
1215B GLN* 2.7 34.7 + - - +
1216B GLU 3.8 2.5 - - - -
1218B ILE* 1.3 75.6 - - - +
1220B ASN* 1.3 64.8 + - - +
1222B LYS* 3.3 12.8 + - - +
1223B THR* 3.0 26.9 + - - -
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Residues in contact with ASN1220 (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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420A HIS* 3.1 26.2 + - - -
1154B ILE* 3.5 21.0 - - + +
1183B VAL* 4.0 11.3 - - + +
1184B SER* 3.5 16.8 + - - +
1185B ASN 3.1 27.6 + - - +
1186B ILE* 4.2 0.8 - - - +
1191B ILE* 3.3 26.9 - - + +
1216B GLU 2.9 22.8 + - - +
1217B THR* 4.7 0.4 - - - +
1219B THR* 1.3 75.4 - - - +
1221B ALA* 1.3 63.0 + - - +
1223B THR* 3.2 1.4 + - - -
1224B ALA* 2.9 20.4 + - - +
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Residues in contact with ALA1221 (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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1154B ILE* 4.1 5.3 - - - +
1207B ILE* 3.6 39.5 - - + -
1212B PHE* 6.0 0.2 - - + -
1217B THR 2.8 18.4 + - - +
1218B ILE* 3.5 8.3 - - + +
1220B ASN* 1.3 76.9 - - - +
1222B LYS* 1.3 57.6 + - - +
1224B ALA* 3.1 4.3 + - - +
1225B LYS* 2.9 29.1 + - - +
1242B PHE* 4.3 1.2 - - - -
1255B PHE* 3.7 19.7 - - + -
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Residues in contact with LYS1222 (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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416A ARG* 3.3 19.3 - - - +
1218B ILE* 2.9 41.2 + - + +
1219B THR* 3.8 10.5 + - - +
1221B ALA* 1.3 75.7 - - - +
1223B THR* 1.3 57.2 + - - +
1225B LYS* 3.4 9.2 + - - +
1226B ASP* 3.0 35.9 + - - +
1255B PHE* 3.8 21.8 - - + -
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Residues in contact with THR1223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415A ILE* 4.3 11.7 - - + -
416A ARG* 2.7 32.5 + - + +
420A HIS* 2.9 22.5 + - - -
1191B ILE* 3.8 25.8 - - + -
1195B LEU* 4.6 7.6 - - + -
1219B THR 3.0 8.5 + - - -
1220B ASN 3.2 7.6 + - - -
1222B LYS* 1.3 76.0 - - - +
1224B ALA* 1.3 57.4 + - - +
1226B ASP* 3.5 3.0 + - - +
1227B TRP* 3.0 27.1 + - + +
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Residues in contact with ALA1224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1154B ILE* 3.9 13.7 - - + -
1191B ILE* 4.0 9.6 - - + -
1195B LEU* 4.5 3.4 - - + -
1205B PHE* 3.8 29.2 - - + -
1220B ASN 2.9 12.7 + - - +
1221B ALA 3.5 7.6 - - - +
1223B THR* 1.3 72.7 - - - +
1225B LYS* 1.3 61.0 + - - +
1227B TRP* 3.2 11.3 + - - +
1228B PHE* 2.8 30.0 + - - +
1242B PHE* 3.9 6.5 - - + -
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Residues in contact with LYS1225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1221B ALA 2.9 16.3 + - - +
1222B LYS* 3.7 9.3 - - - +
1224B ALA* 1.3 77.0 - - - +
1226B ASP* 1.3 61.0 + - - +
1228B PHE* 3.2 1.2 + - - +
1229B LEU* 2.8 48.8 + - + +
1238B VAL* 4.3 23.8 - - + -
1242B PHE* 3.5 17.9 - - + -
1255B PHE* 2.7 57.8 + - + +
1256B GLY* 5.7 0.2 - - - -
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Residues in contact with ASP1226 (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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416A ARG* 3.6 25.7 + - - +
1222B LYS* 3.0 24.3 + - - +
1223B THR* 3.8 4.9 - - - +
1225B LYS* 1.3 82.5 - - - +
1227B TRP* 1.3 64.1 + - - +
1229B LEU* 3.3 8.2 + - - +
1230B LEU* 2.9 33.6 + - + +
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Residues in contact with TRP1227 (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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1195B LEU* 3.6 53.7 + - + +
1198B LEU* 3.6 33.0 - - + -
1199B ASN 4.1 0.2 - - - -
1200B PRO* 3.5 43.5 - - + +
1203B SER* 4.5 0.2 - - - -
1205B PHE* 3.6 26.9 - + - -
1223B THR* 3.0 15.6 + - + +
1224B ALA 3.4 9.9 - - - +
1226B ASP* 1.3 76.3 - - - +
1228B PHE* 1.3 78.8 + - + +
1230B LEU* 3.0 29.4 - - + +
1231B SER* 3.9 3.8 + - - -
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Residues in contact with PHE1228 (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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1143B TYR* 3.7 20.9 - + - -
1200B PRO* 3.5 28.9 - - + +
1205B PHE* 5.0 3.1 - + + -
1224B ALA 2.8 17.0 + - - +
1225B LYS 3.5 3.6 - - - +
1227B TRP* 1.3 85.5 - + + +
1229B LEU* 1.3 74.2 + - + +
1230B LEU 3.0 5.8 + - - -
1231B SER* 3.1 7.3 + - - -
1232B ALA* 3.1 23.2 + - + +
1237B THR* 3.4 23.1 - - - -
1238B VAL* 4.0 16.8 - - + -
1241B HIS* 3.2 43.1 - + + -
1242B PHE* 3.8 22.7 - + + -
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Residues in contact with LEU1229 (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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1225B LYS* 2.8 42.4 + - + +
1226B ASP* 4.0 8.3 - - - +
1228B PHE* 1.3 76.4 - - + +
1230B LEU* 1.3 65.2 + - - +
1231B SER 3.1 0.4 - - - -
1232B ALA* 4.1 0.2 - - - -
1233B LYS* 3.0 37.3 + - - +
1234B ASP 3.4 31.4 - - - +
1235B PRO* 4.2 8.3 - - + -
1237B THR* 4.1 7.2 - - - +
1238B VAL* 3.9 21.1 - - + -
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Residues in contact with LEU1230 (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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1226B ASP* 2.9 20.7 + - + +
1227B TRP* 3.0 26.9 - - + +
1228B PHE 3.0 0.4 - - - -
1229B LEU* 1.3 79.1 - - - +
1231B SER* 1.3 60.2 + - - +
1233B LYS* 4.2 13.7 - - - -
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Residues in contact with SER1231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1143B TYR* 3.9 9.9 + - - -
1200B PRO* 3.9 25.4 - - - +
1227B TRP 4.8 2.0 + - - -
1228B PHE 3.1 7.4 + - - -
1230B LEU* 1.3 82.3 - - - +
1232B ALA* 1.3 68.6 + - - +
1233B LYS* 3.9 7.7 - - - +
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Residues in contact with ALA1232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1143B TYR* 3.7 27.8 + - + -
1228B PHE* 3.1 31.1 + - + +
1229B LEU* 4.1 2.5 - - + -
1231B SER* 1.3 81.2 - - - +
1233B LYS* 1.3 73.9 + - - +
1234B ASP 3.7 2.0 + - - -
1237B THR* 3.5 25.6 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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