Contacts of the strand formed by residues 1150 - 1154 (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 ASP1150 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1148B ILE* 3.5 5.9 - - - +
1149B THR* 1.3 99.3 + - - +
1151B VAL* 1.3 63.7 - - - +
1152B ILE* 3.8 3.3 - - + +
1178B PRO* 4.5 0.2 - - - -
1179B ARG* 2.6 50.9 + - - +
1181B TRP* 2.8 20.0 + - + +
1198B LEU* 3.7 27.4 - - + +
1199B ASN 5.7 1.4 + - - -
1202B SER* 3.3 5.9 + - - +
1203B SER* 3.5 4.2 + - - +
1204B LEU 2.9 25.5 + - - -
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Residues in contact with VAL1151 (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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1135B VAL* 4.9 3.8 - - + -
1148B ILE* 4.3 13.7 - - + -
1150B ASP* 1.3 76.5 - - - +
1152B ILE* 1.3 63.3 + - - +
1153B ASN 4.9 0.4 - - - +
1178B PRO* 4.3 15.9 - - + -
1179B ARG 2.8 13.2 + - - +
1180B VAL* 3.3 19.0 - - + +
1181B TRP* 2.8 26.7 + - - +
1204B LEU* 3.3 10.1 - - + +
1206B ILE* 3.4 35.2 - - + -
1282B SER* 4.9 3.1 - - - -
1285B LEU* 3.8 24.5 - - + -
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Residues in contact with ILE1152 (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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1150B ASP* 3.8 15.0 - - + +
1151B VAL* 1.3 78.0 - - - +
1153B ASN* 1.3 61.9 + - - +
1154B ILE* 3.6 7.5 + - + +
1181B TRP* 3.6 19.5 - - + +
1183B VAL* 3.8 29.4 - - + -
1194B THR* 4.2 3.1 - - + -
1195B LEU* 6.2 0.2 - - + -
1198B LEU* 3.4 34.5 - - + -
1203B SER* 3.9 13.7 - - - +
1204B LEU 2.9 18.8 + - - +
1205B PHE* 3.4 27.7 - - + +
1206B ILE* 2.8 27.8 + - - -
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Residues in contact with ASN1153 (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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1151B VAL* 4.0 1.6 + - - +
1152B ILE* 1.3 70.5 - - - +
1154B ILE* 1.3 61.3 + - - +
1155B GLY 4.0 4.5 + - - -
1159B SER 3.3 20.5 + - - +
1160B ASP* 4.5 3.1 - - - +
1163B PRO* 5.0 1.7 - - - +
1180B VAL* 5.4 0.2 - - - +
1181B TRP 2.8 10.5 + - - +
1182B PHE* 3.5 34.8 - - + -
1183B VAL 2.8 28.9 + - - +
1206B ILE* 3.5 21.2 + - + +
1208B ALA* 3.8 20.5 - - - +
1245B LEU* 4.3 5.3 - - - +
1279B ILE 4.8 3.8 + - - -
1282B SER* 4.3 18.4 + - - -
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Residues in contact with ILE1154 (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 11.0 - - + +
1153B ASN* 1.3 77.2 - - - +
1155B GLY* 1.3 60.3 + - - +
1183B VAL* 3.4 18.4 - - + +
1191B ILE* 4.8 4.9 - - + -
1205B PHE* 3.8 23.8 - - + -
1206B ILE 2.8 12.3 + - - +
1207B ILE* 3.7 19.0 - - + -
1208B ALA 2.9 28.1 + - - +
1217B THR* 3.6 21.0 - - + +
1220B ASN* 3.5 36.8 - - + +
1221B ALA* 4.1 1.8 - - - +
1224B ALA* 3.9 17.9 - - + -
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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