Contacts of the helix formed by residues 337 - 350 (chain A) in PDB entry 2WVL
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 THR 337 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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235A GLY* 3.1 34.5 - - - +
236A VAL* 5.6 0.4 - - + -
335A LEU 3.2 6.2 + - - +
336A ALA* 1.3 76.4 - - - +
338A GLU* 1.3 67.1 + - - +
339A GLU* 3.2 16.0 + - - +
340A VAL* 3.2 25.0 + - - +
341A ARG* 3.1 21.2 + - - +
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Residues in contact with GLU 338 (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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336A ALA 4.0 0.2 + - - -
337A THR* 1.3 75.2 - - - +
339A GLU* 1.3 76.9 + - - +
341A ARG* 3.5 27.5 + - - +
342A GLN* 3.3 33.6 + - + +
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Residues in contact with GLU 339 (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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337A THR* 3.8 14.1 - - - +
338A GLU* 1.3 95.4 + - - +
340A VAL* 1.3 64.1 + - + +
342A GLN* 3.0 28.7 - - - +
343A SER* 3.1 11.4 + - - -
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Residues in contact with VAL 340 (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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231A GLN* 3.5 40.8 - - + +
232A LEU* 4.2 9.6 - - + +
235A GLY* 4.3 5.6 - - - -
330A VAL* 3.9 27.8 - - + -
336A ALA* 4.9 3.1 - - + -
337A THR* 3.2 30.9 + - - +
339A GLU* 1.3 73.9 - - + +
341A ARG* 1.3 69.0 + - - +
342A GLN 3.0 0.5 + - - -
343A SER* 3.0 8.5 + - - -
344A VAL* 3.0 27.6 + - + +
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Residues in contact with ARG 341 (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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331A TYR* 3.0 86.0 + - + +
333A SER 6.0 0.2 - - - -
336A ALA* 3.8 21.1 + - + +
337A THR 3.1 6.8 + - - +
338A GLU* 3.7 30.3 + - - +
340A VAL* 1.3 78.3 - - - +
342A GLN* 1.3 58.7 + - - +
344A VAL* 3.5 3.9 - - - +
345A LEU* 3.1 27.0 + - - +
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Residues in contact with GLN 342 (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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338A GLU* 3.3 19.4 + - + +
339A GLU* 3.0 27.9 - - - +
341A ARG* 1.3 77.3 - - - +
343A SER* 1.3 70.8 + - - +
344A VAL 3.0 1.6 - - - -
345A LEU* 3.2 10.3 + - + +
346A GLU* 3.1 40.2 + - + +
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Residues in contact with SER 343 (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 ARG* 3.6 13.9 + - - -
231A GLN* 2.8 33.5 + - - -
339A GLU 3.1 13.3 + - - -
340A VAL* 3.0 11.8 + - - -
342A GLN* 1.3 79.3 + - - +
344A VAL* 1.3 61.7 + - - +
346A GLU* 3.3 13.9 + - - +
347A GLU* 3.3 19.1 + - - +
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Residues in contact with VAL 344 (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 ARG* 4.6 6.7 - - - +
228A ALA* 4.2 18.8 - - + -
231A GLN* 4.8 0.2 - - - +
327A LEU* 3.5 40.3 - - + +
330A VAL* 4.2 22.9 - - + -
331A TYR* 4.0 13.0 - - + -
340A VAL* 3.0 20.5 + - + +
341A ARG* 3.5 7.0 - - - +
343A SER* 1.3 75.2 - - - +
345A LEU* 1.3 67.2 + - - +
346A GLU 3.1 1.6 - - - -
347A GLU* 3.2 6.9 + - - +
348A LEU* 3.1 29.2 + - + +
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Residues in contact with LEU 345 (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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331A TYR* 3.6 33.9 - - + +
341A ARG* 3.1 18.4 + - - +
342A GLN* 3.2 8.7 + - + +
344A VAL* 1.3 80.2 - - - +
346A GLU* 1.3 57.4 + - + +
348A LEU* 3.7 7.7 - - - +
349A GLN* 3.1 57.5 + - - +
358A GLU* 3.9 27.6 - - + +
359A GLU* 6.0 0.2 - - - -
360A PRO* 5.2 3.1 - - + -
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Residues in contact with GLU 346 (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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342A GLN* 3.1 32.1 + - + +
343A SER* 3.4 14.3 - - - +
345A LEU* 1.3 76.8 - - + +
347A GLU* 1.3 66.1 + - - +
349A GLN* 4.7 7.6 - - - +
350A ALA* 3.0 29.5 + - - +
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Residues in contact with GLU 347 (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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220A ARG* 3.4 27.4 + - - -
224A ARG* 3.1 49.8 + - - +
227A ARG* 5.4 1.7 + - - -
323A LEU* 4.4 9.8 - - - +
327A LEU* 3.7 13.9 - - + -
343A SER 3.3 4.0 + - - +
344A VAL 3.2 9.0 + - - +
346A GLU* 1.3 78.1 - - - +
348A LEU* 1.3 60.6 + - - +
350A ALA* 2.9 32.1 - - - +
351A ALA* 3.6 5.2 - - - +
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Residues in contact with LEU 348 (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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323A LEU* 4.8 7.6 - - + -
324A LEU* 3.7 39.3 - - + +
327A LEU* 3.7 31.2 - - + -
344A VAL* 3.1 20.5 + - + +
345A LEU* 3.7 11.0 - - - +
347A GLU* 1.3 76.0 - - - +
349A GLN* 1.3 70.6 + - - +
351A ALA* 3.6 1.3 - - - +
352A GLY 3.0 22.7 + - - +
353A ALA* 3.8 5.2 + - + -
358A GLU* 3.8 17.3 - - + +
360A PRO* 4.0 31.9 - - + -
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Residues in contact with GLN 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A LEU* 3.1 33.8 + - - +
346A GLU* 4.4 7.2 - - - +
348A LEU* 1.3 76.7 - - - +
350A ALA* 1.3 52.0 + - - +
351A ALA 2.5 22.3 + - - -
352A GLY 3.7 0.5 + - - -
353A ALA 3.8 11.8 + - - +
354A LEU 3.5 11.7 - - - +
355A ALA* 2.7 30.1 + - - +
356A PRO 2.8 21.2 + - - -
358A GLU* 3.5 18.0 + - + +
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Residues in contact with ALA 350 (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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220A ARG* 5.9 0.7 + - - -
346A GLU 3.0 21.0 + - - +
347A GLU* 2.9 18.3 - - - +
349A GLN* 1.3 70.8 - - - +
351A ALA* 1.3 59.7 + - - +
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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