Contacts of the helix formed by residues 1187 - 1196 (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 ASP1187 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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341A ASP* 3.5 8.5 - - - +
342A GLN* 2.6 34.4 + - + +
411A THR* 4.5 7.6 + - - -
420A HIS* 5.1 0.4 - - - -
421A HIS* 5.0 2.3 + - - -
424A LEU* 3.9 30.4 - - + +
1185B ASN* 3.1 24.9 + - + +
1186B ILE* 1.3 76.9 - - - +
1188B GLY* 1.3 57.7 + - - +
1189B THR* 2.7 33.6 + - - -
1190B HIS* 2.9 19.6 + - - +
1191B ILE* 4.3 0.9 + - - +
1220B ASN* 5.5 0.2 - - - +
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Residues in contact with GLY1188 (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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411A THR* 5.6 0.8 + - - -
413A HIS* 4.4 8.7 - - - -
415A ILE* 3.7 16.1 - - - +
420A HIS* 3.6 24.5 - - - +
421A HIS* 5.0 1.8 + - - +
1186B ILE 2.8 10.0 + - - -
1187B ASP* 1.3 71.6 + - - +
1189B THR* 1.3 62.2 + - - +
1190B HIS 3.2 0.4 - - - -
1191B ILE* 3.5 4.3 + - - +
1192B ALA* 3.0 28.0 + - - +
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Residues in contact with THR1189 (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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341A ASP* 5.5 1.0 + - - -
342A GLN* 4.0 13.9 - - + -
343A TYR* 3.5 46.9 - - + +
411A THR* 4.4 7.2 + - - -
412A GLN* 4.9 1.2 + - - +
413A HIS* 3.3 24.0 + - + +
1187B ASP* 2.7 27.4 + - - -
1188B GLY* 1.3 74.2 - - - +
1190B HIS* 1.3 64.7 + - - +
1193B LYS* 3.0 27.2 + - + +
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Residues in contact with HIS1190 (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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342A GLN* 3.8 31.5 + - + +
385A ASN* 5.2 0.2 - - - -
1182B PHE 3.3 20.6 + - - -
1183B VAL* 4.3 4.4 - - + +
1184B SER* 3.1 31.8 + - - -
1185B ASN* 3.1 31.7 + - - +
1187B ASP 2.9 12.8 + - - +
1189B THR* 1.3 82.1 - - - +
1191B ILE* 1.3 59.0 - - - +
1193B LYS* 4.5 1.9 - - - +
1194B THR* 2.8 29.4 + - - -
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Residues in contact with ILE1191 (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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415A ILE* 3.6 27.1 - - + -
420A HIS* 4.1 4.0 - - + -
1154B ILE* 4.8 4.5 - - + -
1183B VAL* 3.9 17.2 - - + +
1187B ASP 4.3 0.2 + - - -
1188B GLY 3.5 4.0 + - - +
1190B HIS* 1.3 76.8 - - - +
1192B ALA* 1.3 63.6 + - - +
1194B THR* 4.4 2.0 - - - -
1195B LEU* 2.9 44.6 + - + +
1205B PHE* 5.9 0.4 - - + -
1220B ASN* 3.3 51.1 + - + +
1223B THR* 3.8 18.2 - - + -
1224B ALA* 3.8 15.7 - - + +
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Residues in contact with ALA1192 (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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413A HIS* 3.9 29.2 - - + +
415A ILE* 4.2 15.7 - - + -
1188B GLY 3.0 20.3 + - - +
1189B THR 3.8 2.2 - - - +
1191B ILE* 1.3 81.1 - - - +
1193B LYS* 1.3 62.2 + - - +
1195B LEU* 4.0 5.4 - - - +
1196B ALA* 3.2 24.4 + - - +
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Residues in contact with LYS1193 (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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171A LYS* 4.3 14.5 + - - +
172A PRO* 4.2 20.0 - - - +
343A TYR* 2.7 40.3 + - + +
413A HIS* 3.8 17.9 + - + +
1181B TRP* 5.3 0.9 - - - -
1189B THR* 3.0 24.3 + - + +
1190B HIS* 4.6 2.2 - - - +
1192B ALA* 1.3 75.1 - - - +
1194B THR* 1.3 60.6 + - - +
1196B ALA* 3.8 9.5 + - + +
1197B CYS* 3.5 22.9 - - - -
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Residues in contact with THR1194 (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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1152B ILE* 4.2 3.8 - - + -
1181B TRP* 3.9 40.2 - - + +
1182B PHE 5.1 1.4 + - - -
1183B VAL* 3.6 25.3 - - + +
1190B HIS* 2.8 26.3 + - - -
1191B ILE 3.4 4.0 + - - -
1192B ALA 3.2 0.6 - - - -
1193B LYS* 1.3 76.5 - - - +
1195B LEU* 1.3 68.8 + - + +
1196B ALA 3.1 1.3 - - - -
1197B CYS* 3.0 16.5 + - - +
1198B LEU* 3.4 22.7 - - + +
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Residues in contact with LEU1195 (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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1152B ILE* 6.2 0.2 - - + -
1191B ILE* 2.9 44.9 + - + +
1192B ALA* 4.1 4.9 - - - +
1194B THR* 1.3 77.8 - - + +
1196B ALA* 1.3 62.6 + - - +
1197B CYS 3.2 0.9 + - - -
1198B LEU* 3.2 18.1 + - + +
1205B PHE* 3.7 36.8 - - + -
1223B THR* 4.5 8.1 - - + +
1224B ALA* 4.5 4.7 - - + -
1227B TRP* 3.6 64.2 + - + +
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Residues in contact with ALA1196 (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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1192B ALA 3.2 17.8 + - - +
1193B LYS* 3.9 13.5 - - + +
1194B THR 3.1 1.0 - - - -
1195B LEU* 1.3 76.2 - - - +
1197B CYS* 1.3 63.2 + - - +
1198B LEU 3.4 2.1 + - - +
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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