Contacts of the strand formed by residues 243 - 250 (chain A) in PDB entry 1W21
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 VAL 243 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239A CYS* 3.2 1.0 - - - -
240A HIS* 2.8 40.5 + - - +
241A LYS 4.4 5.4 - - - +
242A GLY* 1.3 78.2 - - - +
244A CYS* 1.3 63.7 + - - +
245A PRO* 3.6 6.8 - - + +
263A TYR* 4.0 34.1 - - + -
264A PHE 3.2 6.7 - - - +
265A LYS* 4.7 13.5 - - + -
270A GLN* 5.1 3.6 - - + -
314A PRO* 3.6 25.6 - - - +
317A MET* 4.2 13.0 - - - -
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Residues in contact with CYS 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A CYS* 3.9 5.4 - - - -
192A ASP* 4.0 13.0 - - - -
197A MET* 3.8 26.7 - - + -
214A TYR* 6.3 1.1 - - - -
238A VAL 3.4 5.2 - - - +
239A CYS* 2.0 47.6 - - - -
242A GLY 4.3 5.2 - - - -
243A VAL* 1.3 75.1 - - - +
245A PRO* 1.3 66.9 - - - +
246A VAL* 4.1 0.5 - - - +
264A PHE* 2.7 42.1 + - + +
265A LYS* 5.9 0.2 - - - -
266A GLU 6.1 0.7 - - - -
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Residues in contact with PRO 245 (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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233A GLN* 4.2 2.8 + - - -
237A CYS* 3.5 15.8 - - - +
238A VAL 3.1 18.9 + - - +
243A VAL* 3.6 7.9 - - + +
244A CYS* 1.3 87.5 - - - +
246A VAL* 1.3 64.5 + - - +
247A VAL* 5.9 0.2 - - - -
261A ILE* 4.3 3.1 - - + -
262A ILE 3.4 5.6 - - - +
263A TYR* 3.8 30.7 - - + -
287A CYS* 6.0 0.7 - - - -
294A ILE* 3.7 23.6 - - + -
312A ILE* 3.9 26.2 - - + -
314A PRO* 4.3 7.6 - - + -
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Residues in contact with VAL 246 (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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188A THR* 3.9 11.7 - - + -
197A MET* 3.7 30.1 - - + -
199A ILE* 3.8 9.9 - - + -
232A THR* 3.4 22.7 - - - +
233A GLN* 3.5 6.5 - - - +
237A CYS* 4.1 9.6 - - + -
245A PRO* 1.3 80.6 - - - +
247A VAL* 1.3 66.3 + - - +
248A MET* 3.8 19.0 + - + +
260A LYS 3.7 0.7 - - - +
261A ILE* 3.5 3.8 - - - -
262A ILE* 2.8 31.9 + - - +
264A PHE* 3.8 15.7 - - + -
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Residues in contact with VAL 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A THR* 2.8 29.8 + - - -
233A GLN* 3.0 21.8 + - - +
245A PRO 5.9 0.2 - - - -
246A VAL* 1.3 72.9 - - - +
248A MET* 1.3 59.2 + - - +
249A THR* 5.0 0.2 - - - +
259A THR* 3.6 25.8 - - + -
260A LYS 3.6 2.7 - - - -
261A ILE* 3.8 22.0 - - + -
282A ILE* 3.7 19.1 - - + -
285A CYS* 3.8 20.2 - - + -
296A CYS* 4.1 17.3 - - - -
310A ILE* 4.2 4.7 - - + -
312A ILE* 4.5 6.1 - - + -
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Residues in contact with MET 248 (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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199A ILE* 4.3 12.6 - - + -
201A MET* 3.6 29.4 - - + -
210A ALA* 5.1 1.8 - - + -
222A ILE* 4.2 10.3 - - + -
225A TRP* 3.7 24.7 - - + -
230A LEU* 4.5 2.2 - - + -
231A ARG 3.3 6.5 - - - +
232A THR* 3.8 4.9 - - - +
246A VAL* 3.8 23.6 - - + +
247A VAL* 1.3 78.9 - - - +
249A THR* 1.3 62.8 + - - +
258A ALA 4.1 0.2 - - - +
259A THR* 3.2 7.0 - - - +
260A LYS 2.8 35.0 + - - +
262A ILE* 3.6 23.8 - - + -
264A PHE* 4.0 25.6 - - + -
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Residues in contact with THR 249 (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 TRP* 4.5 0.2 - - - -
230A LEU* 3.4 3.4 - - - +
231A ARG* 2.8 62.6 + - - +
232A THR* 5.0 0.2 - - - +
247A VAL* 5.0 0.5 - - - +
248A MET* 1.3 73.0 + - - +
250A ASP* 1.3 62.3 + - - +
257A ALA* 3.8 24.2 - - + -
258A ALA 3.7 4.7 - - - +
259A THR* 2.7 26.9 + - - +
281A HIS* 5.3 0.2 - - + -
282A ILE* 2.8 25.3 + - - +
283A GLU* 4.6 3.7 - - - -
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Residues in contact with ASP 250 (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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224A SER* 2.6 26.9 + - - -
225A TRP* 2.8 39.5 + - + +
226A ALA* 3.3 19.0 - - - +
227A GLY 3.4 0.9 + - - -
228A ASN 2.8 36.0 + - - +
230A LEU* 3.8 12.8 - - + +
231A ARG* 4.1 0.7 - - - +
249A THR* 1.3 78.1 - - - +
251A GLY* 1.3 57.6 + - - +
258A ALA 3.0 25.5 + - - +
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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