Contacts of the strand formed by residues 175 - 181 (chain B) in PDB entry 1T9G
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 TRP 175 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104B GLY* 3.5 30.1 - - - -
105B GLN* 3.9 12.3 - - + -
108B ILE* 3.5 31.2 - - + -
120B TYR* 3.4 39.3 + + + -
121B LEU* 4.5 2.0 - - + -
123B ARG* 4.3 1.5 - - - +
124B MET* 3.3 22.2 - - - -
130B MET 4.2 0.8 + - - -
131B CYS* 3.3 26.2 - - + +
132B ALA 3.2 21.8 + - - -
173B ALA* 3.5 5.4 - - - +
174B ASN* 1.3 102.1 - - + +
176B TYR* 1.3 76.0 + - - +
177B PHE 4.1 7.9 - - - -
198B ILE* 4.0 13.5 - - + -
199B VAL 3.4 15.5 - - - +
200B GLU* 4.0 6.1 - - - -
201B ALA 4.0 1.1 - - - +
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Residues in contact with TYR 176 (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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132B ALA* 3.4 12.6 - - + -
134B CYS* 3.5 28.7 - - + -
170B GLY* 2.5 37.8 + - - -
173B ALA* 3.9 13.8 + - + -
175B TRP* 1.3 84.2 - - - +
177B PHE* 1.3 63.1 + - - +
178B LEU* 3.7 3.9 + - + +
197B PHE 3.6 0.2 - - - +
198B ILE* 3.5 4.3 - - - -
199B VAL* 2.9 46.2 + - + +
201B ALA* 3.9 26.5 - - + +
206B ILE* 4.2 18.2 - - + -
208B ILE* 3.6 13.9 - - - +
225B ILE* 3.0 19.7 - - + +
227B PHE* 4.4 14.4 - + - -
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Residues in contact with PHE 177 (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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104B GLY 3.7 20.6 - - - +
107B PRO* 3.6 26.2 - - + -
108B ILE* 4.5 3.6 - - + -
132B ALA 2.9 11.7 + - - +
133B TYR* 3.5 39.3 - + - -
134B CYS* 2.7 32.1 + - - +
135B VAL* 4.0 13.5 - - + -
175B TRP* 4.0 5.5 - - + -
176B TYR* 1.3 71.9 - - - +
178B LEU* 1.3 71.3 + - - +
179B LEU* 4.5 7.9 - - + -
196B GLY* 4.1 2.5 - - - -
197B PHE 3.5 3.4 - - - -
198B ILE* 4.8 0.7 - - - +
238B LEU* 3.7 29.2 - - + -
247B VAL* 3.9 21.5 - - + -
248B ALA* 4.3 10.8 - - + -
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Residues in contact with LEU 178 (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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134B CYS* 3.7 16.2 - - + +
149B THR* 4.5 4.3 - - + -
160B ILE* 4.2 20.9 - - + -
164B LYS* 4.5 5.4 - - + -
176B TYR* 3.7 3.3 + - + +
177B PHE* 1.3 78.4 - - - +
179B LEU* 1.3 86.5 + - - +
180B ALA* 3.9 15.0 - - + +
196B GLY* 3.3 3.8 - - - -
197B PHE* 2.8 41.7 + - + +
199B VAL* 4.0 20.0 - - + -
227B PHE* 3.3 48.2 - - + -
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Residues in contact with LEU 179 (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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134B CYS 3.4 5.5 + - - -
135B VAL* 3.8 31.2 - - + -
144B VAL* 3.9 13.9 - - + -
147B ILE* 3.2 34.2 - - + +
164B LYS* 3.4 15.6 + - - -
177B PHE* 4.5 7.4 - - + -
178B LEU* 1.3 79.9 - - - +
180B ALA* 1.3 59.1 + - - +
194B PHE* 3.7 25.6 - - + -
195B THR 3.5 20.0 - - - +
196B GLY* 4.1 3.4 - - - +
244B GLY* 3.9 20.2 - - - +
245B PHE* 5.4 3.1 - - + -
248B ALA* 4.5 11.2 - - + -
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Residues in contact with ALA 180 (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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147B ILE* 4.3 0.7 - - - -
149B THR* 3.3 21.3 - - + +
150B LYS 4.0 2.5 - - - +
151B ALA* 3.3 27.3 - - + +
160B ILE* 4.3 2.0 - - + -
178B LEU* 3.9 16.2 - - + +
179B LEU* 1.3 75.5 - - - +
181B ARG* 1.3 61.6 + - - +
182B SER* 3.3 1.4 + - - -
194B PHE* 3.5 7.1 - - - -
195B THR 3.0 32.8 + - - +
197B PHE* 4.4 1.8 - - + -
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Residues in contact with ARG 181 (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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145B ALA 4.0 8.7 + - - -
147B ILE* 4.0 16.1 + - - +
148B LYS* 4.9 6.1 - - - +
149B THR 2.6 16.5 + - - +
150B LYS* 3.5 4.9 - - - +
151B ALA 3.0 20.2 + - - -
180B ALA* 1.3 69.4 - - - +
182B SER* 1.3 59.2 + - - +
183B ASP 3.2 19.5 + - - +
184B PRO* 4.7 4.7 + - - -
185B ASP 3.0 26.1 + - - -
186B PRO* 3.3 18.1 + - - +
188B ALA* 3.4 18.2 + - - +
193B ALA* 3.5 13.3 - - - +
194B PHE* 3.4 46.0 - - + -
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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