Contacts of the strand formed by residues 190 - 199 (chain B) in PDB entry 1TCR
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 TYR 190 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151B GLY 3.3 23.2 + - - -
152B PHE* 3.0 45.2 + - + +
153B PHE* 3.6 30.9 - + - -
155B ASP* 3.6 36.7 + - + -
178B ALA* 3.7 21.3 - - + -
179B TYR 3.2 22.9 - - - -
180B LYS* 3.9 31.9 - - + -
181B GLU* 3.4 4.1 - - - +
189B SER* 1.3 74.2 + - - +
191B CYS* 1.3 62.2 + - - +
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Residues in contact with CYS 191 (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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161A PHE* 4.3 7.2 - - - -
183A TRP* 3.8 28.9 - - + -
149B ALA 3.3 11.2 - - - +
150B ARG* 4.1 6.1 - - + -
152B PHE* 3.8 2.9 - - - -
178B ALA* 3.3 4.9 - - - +
179B TYR* 2.8 57.2 + - - -
181B GLU* 3.8 25.6 - - - +
190B TYR* 1.3 76.8 - - - +
192B LEU* 1.3 64.9 + - - +
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Residues in contact with LEU 192 (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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183A TRP* 5.9 0.4 - - - -
147B CYS 4.0 0.2 - - - +
148B LEU* 3.6 4.4 - - - +
149B ALA* 2.9 35.1 + - + +
152B PHE* 4.1 11.4 - - + -
157B VAL* 4.2 23.1 - - + +
159B LEU* 4.0 33.5 - - + +
174B THR* 4.4 4.5 - - - +
175B ASP* 3.5 38.6 - - + +
177B GLN 4.7 0.2 - - - +
178B ALA* 3.7 26.0 - - + +
191B CYS* 1.3 77.3 - - - +
193B SER* 1.3 66.5 + - - +
214B VAL* 6.0 0.7 - - + -
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Residues in contact with SER 193 (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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163A THR* 3.8 14.2 + - - +
181A ILE* 4.4 24.7 - - - +
183A TRP* 5.0 0.2 - - - -
146B VAL* 5.0 2.0 - - - -
147B CYS 3.1 11.2 - - - -
148B LEU* 4.2 13.0 - - - -
159B LEU* 4.5 2.5 - - - -
174B THR* 3.4 4.3 + - - -
175B ASP* 2.8 51.9 + - - +
192B LEU* 1.3 77.7 - - - +
194B SER* 1.3 66.4 + - - +
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Residues in contact with SER 194 (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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181A ILE* 5.3 0.6 - - - +
145B LEU 3.7 0.2 - - - +
146B VAL* 3.1 7.0 - - - +
147B CYS 2.8 30.0 + - - -
159B LEU* 3.7 15.7 - - - -
161B TRP* 2.7 31.6 + - - -
173B SER 3.5 6.7 - - - -
174B THR* 3.1 25.1 - - - +
193B SER* 1.3 81.4 - - - +
195B ARG* 1.3 68.0 + - - +
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Residues in contact with ARG 195 (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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142A LEU* 3.7 22.9 - - + -
144A THR* 3.5 22.0 + - - -
166A THR* 3.0 43.9 + - - -
168A LEU* 3.5 39.9 - - + +
177A SER* 3.4 19.4 + - - -
178A ASN 3.8 1.2 + - - -
179A GLY* 3.5 15.1 - - - +
181A ILE* 3.8 19.3 - - + +
144B THR* 3.7 18.5 + - + +
145B LEU 3.4 3.1 - - - -
146B VAL* 4.5 2.2 - - + -
161B TRP* 3.9 1.1 + - - -
171B GLY 4.2 1.1 - - - -
172B VAL* 3.2 9.0 - - - +
173B SER 3.0 33.4 + - - +
194B SER* 1.3 82.8 + - - +
196B LEU* 1.3 61.1 + - - +
197B ARG* 4.0 1.0 - - - +
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Residues in contact with LEU 196 (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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143B ALA 3.3 3.3 - - - +
144B THR* 4.3 0.7 - - - -
145B LEU* 2.8 41.5 + - + +
161B TRP* 3.4 49.4 - - + +
163B VAL* 4.2 22.4 - - + -
168B VAL* 3.7 25.6 - - + -
170B SER 4.2 4.0 - - - +
171B GLY 3.6 5.8 - - - +
172B VAL* 4.2 12.8 - - + -
195B ARG* 1.3 74.5 - - - +
197B ARG* 1.3 58.6 + - - +
198B VAL* 4.2 17.3 - - + -
210B PHE* 4.3 13.2 - - + -
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Residues in contact with ARG 197 (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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144A THR* 4.3 8.7 - - - +
145A ASP* 2.7 43.6 + - - -
168A LEU* 3.7 27.1 - - + +
170A MET* 3.5 29.4 - - - +
177A SER* 3.6 16.3 + - - -
136B GLU* 2.6 42.4 + - - +
140B LYS* 4.4 5.1 - - - +
142B LYS* 3.7 33.7 - - + +
143B ALA 3.2 4.5 - - - -
144B THR* 3.0 22.8 + - - +
171B GLY* 3.2 18.8 + - - +
195B ARG* 4.0 1.7 - - - +
196B LEU* 1.3 73.6 - - - +
198B VAL* 1.3 66.6 + - - +
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Residues in contact with VAL 198 (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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170A MET* 4.1 9.3 - - - +
142B LYS* 3.3 7.3 - - - +
143B ALA* 2.7 39.9 + - + +
145B LEU* 4.2 8.7 - - + -
163B VAL* 5.9 1.3 - - + -
196B LEU* 4.2 23.6 - - + +
197B ARG* 1.3 81.2 - - - +
199B SER* 1.3 68.6 + - - +
202B PHE* 4.1 23.8 - - + -
203B TRP* 4.1 22.7 - - + +
210B PHE* 4.4 8.7 - - + -
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Residues in contact with SER 199 (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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170A MET* 4.4 7.9 - - - +
141B GLN 3.7 8.5 - - - -
142B LYS* 4.3 2.2 - - - +
143B ALA 4.5 0.7 - - - -
198B VAL* 1.3 80.3 - - - +
200B ALA* 1.3 66.5 + - - +
201B THR* 4.0 12.5 - - - +
202B PHE* 3.1 23.4 + - - +
203B TRP* 3.1 18.5 + - - +
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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