Contacts of the strand formed by residues 194 - 199 (chain B) in PDB entry 1TD2
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 PHE 194 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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182B LYS 3.3 21.8 - - - -
183B HIS* 3.4 33.0 - + - -
193B ARG* 1.3 71.4 - - - +
195B GLU* 1.3 65.1 + - - +
196B MET* 3.6 31.0 - - + -
208B SER* 2.8 7.6 - - - -
209B ARG* 2.6 97.6 + - + +
210B PRO 4.5 0.2 - - - +
211B LEU* 3.8 13.3 - - + +
218B GLN* 6.3 0.9 - - - -
222B VAL* 4.9 11.0 - - + -
226B THR* 5.8 0.9 - - - -
248B THR* 6.0 1.6 - - + -
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Residues in contact with GLU 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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183B HIS* 3.4 11.9 + - - -
184B LEU* 3.0 40.9 + - + -
185B ALA 5.4 1.9 - - - +
188B GLY* 3.3 6.2 - - - -
189B TYR* 3.0 19.6 + - - -
190B SER 2.8 37.9 + - - +
193B ARG* 2.9 19.2 + - + +
194B PHE* 1.3 79.7 - - - +
196B MET* 1.3 62.0 + - - +
206B HIS* 2.7 31.2 - - + +
207B ILE 3.4 3.1 - - - +
208B SER* 3.6 20.9 - - - -
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Residues in contact with MET 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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180B LEU* 4.2 7.4 - - + -
181B VAL 3.4 18.6 - - - +
182B LYS* 3.5 20.6 - - - +
184B LEU* 4.3 2.9 - - - -
194B PHE* 3.6 22.2 - - + -
195B GLU* 1.3 73.6 - - - +
197B LEU* 1.3 72.7 + - - +
206B HIS* 3.8 3.1 + - - -
207B ILE* 2.9 34.5 + - + +
226B THR* 3.8 31.9 - - + -
230B LEU* 6.6 0.4 - - + -
244B LEU* 3.7 23.8 - - + -
247B VAL* 4.6 8.5 - - + -
248B THR* 3.7 18.8 - - + +
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Residues in contact with LEU 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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161B VAL* 4.2 13.2 - - + -
164B ALA* 3.8 25.6 - - + -
165B VAL* 3.7 26.7 - - + +
179B VAL 3.5 0.7 - - - +
180B LEU* 3.0 9.9 - - - +
181B VAL* 2.8 46.8 + - + -
184B LEU* 4.0 11.7 - - + -
196B MET* 1.3 79.0 - - - +
198B LEU* 1.3 62.2 + - - +
199B VAL* 4.0 13.0 - - + -
205B TRP 3.5 12.6 - - - +
206B HIS* 3.3 33.7 - - + +
244B LEU* 5.3 1.1 - - - -
287B LEU* 4.4 4.3 - - + -
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Residues in contact with LEU 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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178B ILE* 3.6 26.7 - - + -
179B VAL 3.7 5.6 - - - +
180B LEU* 4.0 18.2 - - + -
197B LEU* 1.3 73.9 - - - +
199B VAL* 1.3 59.1 + - - +
200B THR* 4.4 0.4 + - - -
203B GLU 4.5 0.2 - - - +
204B ALA* 3.5 1.9 - - - -
205B TRP* 2.9 40.8 + - + +
230B LEU* 4.1 26.9 - - + -
234B LEU* 5.4 2.5 - - + -
240B LEU* 3.6 51.9 - - + +
243B ALA* 5.1 1.3 - - + -
244B LEU* 4.3 20.4 - - + +
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Residues in contact with VAL 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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165B VAL* 4.2 20.2 - - + +
168B ALA* 4.0 22.4 - - + -
169B ARG* 3.6 16.8 - - - +
172B ILE* 3.7 10.2 - - + +
178B ILE* 3.5 5.1 - - - +
179B VAL 2.8 41.1 + - - +
181B VAL* 5.3 1.3 - - + -
197B LEU* 4.2 23.3 - - + -
198B LEU* 1.3 77.5 - - - +
200B THR* 1.3 79.0 + - - +
203B GLU 3.8 6.7 - - - +
204B ALA* 4.3 12.1 - - + -
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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