Contacts of the helix formed by residues 337 - 352 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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235B GLY* 3.3 37.5 - - - +
236B VAL* 5.2 0.7 - - + -
335B LEU 3.8 7.4 - - - +
336B ALA* 1.3 77.0 - - - +
338B GLU* 1.3 67.3 - - - +
339B GLU* 3.0 22.7 + - - +
340B VAL* 3.0 24.9 + - + +
341B ARG* 2.8 22.1 + - - +
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Residues in contact with GLU 338 (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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337B THR* 1.3 68.9 - - - +
339B GLU* 1.3 62.2 + - - +
341B ARG* 2.7 48.2 + - - +
342B GLN* 2.8 39.5 + - + +
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Residues in contact with GLU 339 (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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337B THR* 3.0 20.2 + - - +
338B GLU* 1.3 83.8 + - - +
340B VAL* 1.3 57.8 + - + +
342B GLN* 3.3 4.9 + - - +
343B SER* 3.0 30.9 + - - -
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Residues in contact with VAL 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B GLN* 3.4 32.9 - - + +
232B LEU* 4.1 23.1 - - + +
235B GLY* 4.1 9.4 - - - -
330B VAL* 3.9 26.7 - - + -
336B ALA* 4.4 2.9 - - + -
337B THR* 3.0 31.1 + - + +
339B GLU* 1.3 76.6 - - + +
341B ARG* 1.3 67.7 + - - +
343B SER* 3.5 5.4 + - - -
344B VAL* 3.3 22.3 + - + +
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Residues in contact with ARG 341 (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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331B TYR* 3.5 66.9 + - + +
332B HIS* 5.4 0.2 - - - +
333B SER 3.7 8.9 + - - -
336B ALA* 3.5 34.3 + - + +
337B THR 2.8 14.1 + - - +
338B GLU* 2.7 43.6 + - - +
340B VAL* 1.3 73.9 - - - +
342B GLN* 1.3 63.2 + - - +
344B VAL* 3.2 14.5 + - - +
345B LEU* 3.2 13.3 + - - +
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Residues in contact with GLN 342 (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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338B GLU* 2.8 21.6 + - + +
339B GLU* 3.8 4.9 - - - +
341B ARG* 1.3 74.1 - - - +
343B SER* 1.3 64.5 + - - +
345B LEU* 3.3 18.0 + - + +
346B GLU* 3.1 43.6 + - - +
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Residues in contact with SER 343 (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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224B ARG* 3.3 8.7 + - - -
231B GLN* 3.3 29.4 + - - -
339B GLU 3.0 16.8 + - - -
340B VAL* 3.9 6.5 - - - -
341B ARG 3.3 0.2 - - - -
342B GLN* 1.3 77.9 - - - +
344B VAL* 1.3 62.6 + - - +
346B GLU* 3.5 13.3 + - - +
347B GLU* 3.3 23.2 + - - +
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Residues in contact with VAL 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224B ARG* 4.1 11.7 - - - +
228B ALA* 4.9 4.7 - - + -
231B GLN* 5.0 3.1 - - - +
327B LEU* 3.3 46.8 - - + +
330B VAL* 4.1 23.6 - - + -
331B TYR* 4.2 14.8 - - + +
340B VAL* 3.3 15.9 + - + +
341B ARG* 3.3 8.5 - - - +
342B GLN 3.1 0.4 - - - -
343B SER* 1.3 74.3 - - - +
345B LEU* 1.3 68.0 + - - +
346B GLU 2.8 3.5 + - - -
347B GLU* 3.0 6.1 + - - +
348B LEU* 3.0 25.6 + - + +
360B PRO* 5.5 2.5 - - + -
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Residues in contact with LEU 345 (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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331B TYR* 3.3 35.2 - - + +
341B ARG 3.2 7.2 + - - +
342B GLN* 3.3 25.6 - - - +
344B VAL* 1.3 80.2 - - + +
346B GLU* 1.3 56.7 + - + +
348B LEU* 3.8 6.8 - - + +
349B GLN* 3.0 75.5 + - - +
358B GLU* 3.9 27.6 - - + +
360B PRO* 4.1 12.8 - - + -
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Residues in contact with GLU 346 (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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342B GLN* 3.1 34.0 + - - +
343B SER* 3.6 14.7 - - - +
344B VAL 2.8 5.3 + - - -
345B LEU* 1.3 70.3 - - - +
347B GLU* 1.3 54.7 + - + +
348B LEU 3.1 1.6 - - - -
349B GLN* 3.4 8.6 + - - +
350B ALA* 2.7 35.5 + - - +
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Residues in contact with GLU 347 (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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220B ARG* 4.3 9.2 + - - +
224B ARG* 2.7 59.0 + - + +
227B ARG* 3.0 19.0 + - - -
323B LEU* 4.9 4.3 - - + +
327B LEU* 4.1 8.3 - - + -
343B SER* 3.3 7.4 - - - +
344B VAL 3.0 5.1 + - - +
346B GLU* 1.3 75.6 - - + +
348B LEU* 1.3 58.1 - - - +
350B ALA* 3.4 8.6 - - - +
351B ALA* 3.0 30.0 + - - +
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Residues in contact with LEU 348 (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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323B LEU* 4.3 7.9 - - + -
324B LEU* 3.9 42.0 - - + +
327B LEU* 3.4 37.2 - - + -
344B VAL* 3.0 19.0 + - + +
345B LEU* 3.8 8.3 - - + +
347B GLU* 1.3 76.6 - - - +
349B GLN* 1.3 61.4 + - - +
351B ALA* 4.5 1.2 - - - +
352B GLY 3.4 16.7 + - - +
353B ALA* 3.2 26.0 - - + +
358B GLU* 3.5 26.0 - - + +
360B PRO* 4.8 7.9 - - + -
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Residues in contact with GLN 349 (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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345B LEU* 3.0 46.4 + - - +
346B GLU* 3.8 7.4 - - - +
348B LEU* 1.3 76.8 - - - +
350B ALA* 1.3 67.0 + - - +
351B ALA 3.0 7.1 + - - +
352B GLY* 3.7 1.2 + - - -
353B ALA 3.7 24.1 + - - +
354B LEU 4.0 1.6 - - - +
355B ALA* 2.9 30.0 + - - +
356B PRO 4.0 1.6 + - - -
358B GLU* 3.3 19.3 - - + +
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Residues in contact with ALA 350 (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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346B GLU 2.7 22.0 + - - +
347B GLU* 3.4 12.3 - - - +
349B GLN* 1.3 74.1 - - - +
351B ALA* 1.3 60.5 + - - +
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Residues in contact with ALA 351 (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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220B ARG* 5.1 11.9 - - - +
320B ARG* 5.8 4.9 - - + -
323B LEU* 4.1 22.9 - - + -
347B GLU 3.0 16.3 + - - +
348B LEU 4.5 1.1 - - - +
349B GLN 3.0 2.1 + - - +
350B ALA* 1.3 79.8 - - - +
352B GLY* 1.3 58.9 + - - +
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Residues in contact with GLY 352 (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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320B ARG* 4.4 33.2 + - - +
324B LEU* 5.3 5.0 - - - +
348B LEU* 3.4 10.8 + - - +
349B GLN 3.7 1.3 + - - -
351B ALA* 1.3 82.2 - - - +
353B ALA* 1.3 65.1 + - - +
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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