Contacts of the strand formed by residues 180 - 183 (chain B) in PDB entry 1TX6
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 MET 180 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98B THR 3.2 28.0 - - - +
99B LEU 3.5 21.8 - - - +
100B ASP* 3.7 10.3 - - + +
101B ASN 5.9 0.2 - - - +
165B ASP* 5.1 4.0 - - - +
168B CYS* 5.0 0.3 - - - -
175B GLN 3.6 15.0 - - - +
176B ILE* 4.0 14.9 - - + +
177B THR* 3.2 40.8 + - + +
178B GLY* 3.2 3.9 - - - +
179B ASN* 1.3 84.3 - - + +
181B ILE* 1.3 68.9 + - - +
215B TRP* 3.7 21.1 - - - +
227B VAL* 3.8 17.9 - - + -
228B TYR 3.3 6.7 - - - +
229B THR* 5.5 1.3 - - - -
230B LYS* 4.3 0.4 - - - +
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Residues in contact with ILE 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B ALA* 6.3 1.3 - - + -
162B VAL* 5.1 18.2 - - + -
163B LEU 5.8 0.9 - - - +
168B CYS* 4.1 5.8 - - - -
180B MET* 1.3 77.7 - - - +
182B CYS* 1.3 61.6 + - - +
183B VAL* 4.1 16.2 - - + -
199B VAL* 6.0 0.4 - - + -
210B GLN* 3.5 33.4 - - + +
211B GLY* 4.4 2.5 - - - -
227B VAL* 4.5 0.9 - - - -
228B TYR* 2.7 53.1 + - + +
230B LYS* 3.5 39.7 - - + +
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Residues in contact with CYS 182 (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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162B VAL* 4.0 3.6 - - - +
163B LEU* 3.0 36.0 + - + +
168B CYS* 2.0 59.4 - - + +
172B TYR* 4.1 15.5 - - - -
181B ILE* 1.3 71.9 - - - +
183B VAL* 1.3 67.9 + - - +
225B PRO* 4.0 24.5 - - + -
226B GLY 3.1 6.3 - - - +
227B VAL* 4.1 9.2 - - - -
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Residues in contact with VAL 183 (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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136B CYS* 5.0 0.4 - - + -
138B ILE* 4.0 20.0 - - + +
160B ALA* 4.2 9.6 - - + +
161B PRO 3.6 16.8 - - - +
162B VAL* 4.4 10.3 - - + -
163B LEU* 3.5 5.8 - - - -
181B ILE* 4.1 20.9 - - + -
182B CYS* 1.3 80.6 - - - +
184B GLY* 1.3 60.5 + - - +
189B ASP* 4.3 1.6 - - - +
199B VAL* 4.3 17.5 - - + -
225B PRO* 4.5 0.9 - - - -
226B GLY 3.0 24.8 + - - -
228B TYR* 3.5 36.4 + - + -
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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