Contacts of the strand formed by residues 236 - 243 (chain A) in PDB entry 2HT8
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 ASP 236 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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232A CYS* 4.1 0.9 - - - -
233A ILE 3.0 22.9 + - - +
234A GLN 3.1 10.1 + - - +
235A GLY* 1.3 75.8 - - - +
237A CYS* 1.3 60.5 + - - +
238A TYR* 2.9 24.5 + - + +
256A LYS* 3.4 33.7 + - + -
257A ALA 3.1 6.2 - - - +
258A ASN* 2.7 28.0 + - - -
263A ILE* 3.1 18.1 - - - +
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Residues in contact with CYS 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A CYS* 3.8 7.2 - - - -
185A ASP* 3.9 17.3 - - - -
190A MET* 3.6 32.8 - - + -
207A TYR* 6.1 0.4 - - - -
231A THR 2.9 5.6 - - - +
232A CYS* 2.0 46.0 - - - -
235A GLY 4.0 2.0 + - - -
236A ASP* 1.3 74.0 - - - +
238A TYR* 1.3 62.0 + - - +
239A TRP* 3.7 5.7 - - - -
256A LYS* 3.5 1.3 - - - -
257A ALA 2.9 32.8 + - - +
258A ASN* 6.4 0.2 - - - -
259A GLN 6.3 1.6 - - - -
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Residues in contact with TYR 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226A GLN* 4.6 0.5 + - - -
230A CYS* 3.3 2.3 - - - +
231A THR* 2.6 41.4 + - - +
233A ILE* 4.4 23.1 + - + +
236A ASP* 2.9 29.3 + - + +
237A CYS* 1.3 76.3 - - - +
239A TRP* 1.3 67.2 + - - +
254A ILE* 4.8 7.9 - - + -
255A TYR 3.2 7.9 - - - +
256A LYS* 3.9 33.3 - - + -
280A CYS* 5.9 0.3 - - - -
287A VAL* 4.2 25.2 - - + +
305A ILE* 4.4 17.5 - - + -
306A SER 3.8 18.8 - - - -
308A PRO* 3.1 32.6 + - + +
310A LEU* 5.0 3.6 - - + -
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Residues in contact with TRP 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A THR* 4.4 8.5 - - + -
190A MET* 3.5 31.2 - - + -
192A VAL* 4.2 17.3 - - + +
205A ILE* 4.3 23.6 - - + -
215A VAL* 5.3 1.3 - - + -
225A THR* 3.7 11.7 - - - -
226A GLN* 3.2 17.0 - - - +
230A CYS* 3.7 12.1 - - + -
237A CYS 3.7 12.6 - - - -
238A TYR* 1.3 80.6 - - - +
240A VAL* 1.3 68.7 + - - +
241A MET* 3.5 37.4 - - + +
254A ILE* 3.5 5.1 - - - +
255A TYR* 2.8 62.5 + + + +
256A LYS 4.8 0.2 - - - -
257A ALA* 3.8 20.6 - - + -
262A ILE* 4.7 8.1 - - + -
280A CYS* 5.7 0.9 - - - -
305A ILE* 6.0 0.4 - - - -
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Residues in contact with VAL 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225A THR* 3.0 20.1 + - - -
226A GLN* 2.9 26.0 + - - +
239A TRP* 1.3 79.9 - - - +
241A MET* 1.3 75.2 + - - +
242A THR* 5.3 1.1 - - - +
252A TYR* 5.0 0.7 - - + -
253A ARG 3.1 15.9 - - - +
254A ILE* 4.4 3.6 - - + -
268A ILE* 4.3 12.1 - - + -
275A ILE* 4.7 7.4 - - + -
278A CYS* 4.1 22.2 - - - -
289A CYS* 4.6 4.5 - - - -
303A LEU* 4.0 13.5 - - + -
305A ILE* 4.0 24.2 - - + -
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Residues in contact with MET 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192A VAL* 4.7 3.1 - - + -
194A VAL* 4.1 8.7 - - + -
203A ALA* 3.5 32.8 - - + -
215A VAL* 4.6 6.5 - - + -
218A TRP* 3.8 13.7 - - + -
223A LEU* 3.8 21.3 - - + -
224A ARG 3.6 8.5 - - - +
225A THR* 3.9 11.2 - - - +
239A TRP* 3.5 23.1 - - + +
240A VAL* 1.3 83.3 - - - +
242A THR* 1.3 64.2 + - - +
252A TYR* 3.4 3.6 - - - -
253A ARG 3.0 28.9 + - - +
255A TYR* 3.1 37.2 - - + -
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Residues in contact with THR 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218A TRP* 3.9 2.5 - - - -
222A ILE 3.4 4.2 - - - +
223A LEU* 4.0 0.7 - - - +
224A ARG* 3.0 57.2 + - - +
225A THR* 5.0 0.2 - - - +
240A VAL* 5.3 0.9 - - - +
241A MET* 1.3 76.0 + - - +
243A ASP* 1.3 62.3 + - - +
250A ALA* 4.2 11.9 - - + -
251A GLN 3.5 4.5 - - - +
252A TYR* 3.9 16.0 - - + +
274A HIS* 5.2 0.2 - - - +
275A ILE* 2.5 33.9 + - - +
276A GLU* 3.8 17.0 - - - +
277A GLU 5.1 0.5 + - - -
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Residues in contact with ASP 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217A SER* 2.8 20.0 + - - -
218A TRP* 3.0 34.8 + - + -
219A ALA* 2.7 33.0 + - + +
221A ASP 2.9 33.5 + - - +
222A ILE 4.1 0.2 - - - -
223A LEU* 4.3 6.1 - - + +
242A THR* 1.3 76.2 - - - +
244A GLY* 1.3 58.7 + - - +
251A GLN* 2.9 38.5 + - - +
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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