Contacts of the strand formed by residues 239 - 246 (chain A) in PDB entry 2WP9
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 239 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205A ALA* 3.5 28.0 - - + -
206A GLY* 4.0 8.7 - - - -
208A ILE* 3.6 21.7 - - + +
209A TYR* 4.0 11.9 - + - +
214A ASN* 5.3 0.4 - - - -
236A MET* 3.2 22.4 + - + +
237A GLU 3.1 10.3 + - - -
238A MET* 1.3 71.7 - - - +
240A GLN* 1.3 62.0 + - - +
241A PHE* 3.3 30.3 + - + -
353A CYS* 3.6 27.8 - - - -
355A TYR* 3.6 18.6 - - - -
356A MET* 3.6 42.8 - - + -
357A MET* 3.7 3.1 - - - +
475A ARG* 4.1 7.6 + - - +
522A THR* 4.3 7.2 - - + -
526A THR* 3.1 32.1 + - + +
539A ALA* 3.3 15.1 - - - +
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Residues in contact with GLN 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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239A TRP* 1.3 72.2 - - - +
241A PHE* 1.3 69.6 + - - +
242A HIS 4.1 2.9 - - - +
286A ARG* 2.7 45.0 + - + +
353A CYS* 3.9 2.1 - - - -
354A HIS* 2.9 30.6 + - + +
355A TYR* 2.9 24.8 + - + +
357A MET* 3.4 17.1 - - - +
398A ASN* 3.4 13.5 + - - +
399A ARG* 2.9 52.2 + - - +
539A ALA* 4.5 3.6 - - - -
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Residues in contact with PHE 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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209A TYR* 3.7 24.9 - + - -
239A TRP* 3.3 28.9 + - + -
240A GLN* 1.3 77.1 - - - +
242A HIS* 1.3 66.6 + - - +
243A PRO* 3.3 4.7 - - - +
286A ARG* 4.4 2.9 - - - +
287A ASP* 5.8 0.2 - - - -
290A ALA* 3.6 16.2 - - + +
351A PRO* 4.5 3.8 - - + -
352A THR* 3.4 14.1 - - - +
353A CYS* 3.3 35.0 - - + -
468A GLN* 4.7 7.0 - - - -
471A PHE 3.9 3.1 - - - -
472A SER* 3.6 42.0 - - - -
473A VAL* 3.7 28.5 - - + -
475A ARG* 4.3 3.1 - - - -
539A ALA* 5.3 4.8 - - + +
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Residues in contact with HIS 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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213A THR* 4.8 3.4 - - + -
240A GLN* 3.7 4.4 - - - +
241A PHE* 1.3 69.4 - - - +
243A PRO* 1.3 73.5 - - + +
244A THR* 3.1 41.4 + - - -
245A GLY 4.3 0.7 + - - +
252A LEU* 3.4 32.4 - - + +
253A VAL 3.8 3.8 - - - -
255A GLU* 4.0 13.3 + - + +
258A ARG* 4.3 4.9 - - - -
286A ARG* 3.3 40.1 + - - -
351A PRO* 3.0 2.4 - - - +
352A THR 2.8 34.2 + - - +
354A HIS* 3.4 36.9 - + + +
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Residues in contact with PRO 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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241A PHE 3.3 5.6 - - - +
242A HIS* 1.3 95.2 - - + +
244A THR* 1.3 62.7 + - + +
245A GLY 3.8 0.2 - - - -
258A ARG* 3.8 22.2 - - - +
286A ARG* 3.5 28.9 - - + +
289A VAL* 3.5 33.7 - - + -
290A ALA* 4.3 3.8 - - + +
293A ILE* 3.6 13.0 - - + +
349A VAL* 4.7 0.2 - - - +
350A ILE* 3.3 2.8 - - - -
351A PRO* 3.2 31.5 - - + +
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Residues in contact with THR 244 (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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242A HIS* 3.1 17.5 + - - -
243A PRO* 1.3 84.5 - - + +
245A GLY* 1.3 59.6 + - - +
252A LEU* 3.7 2.8 - - - +
253A VAL* 2.8 52.1 + - - +
254A THR 4.5 0.7 + - - -
258A ARG* 3.5 21.8 + - - +
264A LEU* 4.1 15.7 - - + -
293A ILE* 5.0 0.2 - - + -
313A LEU* 4.3 8.2 - - + +
349A VAL* 3.8 26.2 - - + -
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Residues in contact with GLY 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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213A THR* 4.8 2.2 - - - -
242A HIS* 4.3 3.2 + - - +
243A PRO 3.8 0.2 - - - -
244A THR* 1.3 75.1 - - - +
246A ILE* 1.3 62.3 + - - -
250A GLY 4.3 4.0 - - - -
251A VAL 3.6 7.6 - - - -
252A LEU* 4.4 3.4 - - - -
349A VAL* 3.1 7.5 - - - -
350A ILE 2.9 35.1 + - - -
352A THR* 3.5 23.1 + - - -
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Residues in contact with ILE 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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245A GLY* 1.3 71.0 - - - -
247A ALA* 1.3 76.2 + - - +
248A GLY 3.3 0.3 + - - -
249A ALA* 3.1 15.6 + - + -
250A GLY* 2.9 26.5 + - - -
251A VAL* 2.7 32.2 + - + +
253A VAL* 3.9 26.2 - - + -
333A LEU 3.6 28.0 - - - +
334A SER* 4.2 6.7 - - - -
337A PHE* 4.2 11.7 - - + +
338A ALA* 3.8 22.0 - - + -
347A ILE* 4.4 10.1 - - + -
348A PRO 3.6 7.4 - - - +
349A VAL* 4.5 0.7 - - - +
350A ILE* 4.8 2.5 - - - +
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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