Contacts of the helix formed by residues 349 - 356 (chain B) in PDB entry 2WO6
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 CYS 349 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326B PHE 4.1 10.1 - - - +
327B TYR* 4.0 18.4 - - + -
345B TRP* 3.1 43.1 + - - -
346B SER 3.6 6.7 - - - +
348B GLY* 1.3 75.2 - - - +
350B ILE* 1.3 63.6 + - - +
352B VAL* 3.5 2.4 + - - +
353B GLU* 3.2 23.8 + - - +
360B LEU* 4.4 20.0 + - + +
361B PHE* 3.8 26.7 - - - -
460B LEU* 4.1 2.8 - - - +
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Residues in contact with ILE 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B LEU* 5.4 1.8 - - + -
269B MET* 6.3 0.2 - - + -
288B LEU* 3.7 14.8 - - + +
289B LYS* 3.6 33.9 - - - +
290B PRO* 4.0 11.0 - - + -
293B ILE* 4.1 22.4 - - + -
327B TYR* 3.9 17.3 - - + -
346B SER 2.9 26.0 + - - +
347B LEU* 3.5 16.4 - - + +
348B GLY 3.2 0.2 - - - -
349B CYS* 1.3 76.3 - - - +
351B LEU* 1.3 62.3 + - + +
353B GLU* 3.1 8.5 + - - +
354B MET* 2.8 41.2 + - + +
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Residues in contact with LEU 351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262B THR* 3.8 19.8 - - + +
265B PHE* 4.5 7.6 - - + -
266B ALA* 3.6 42.6 - - + +
269B MET* 5.7 0.7 - - + -
347B LEU* 2.9 44.3 + - + +
349B CYS 3.4 0.2 - - - -
350B ILE* 1.3 76.7 - - + +
352B VAL* 1.3 67.3 + - - +
354B MET* 3.4 7.0 + - + +
355B HIS 3.4 13.3 + - - -
452B PHE* 3.6 19.3 - - + -
455B LEU* 5.4 1.6 - - + -
456B ILE* 3.9 16.2 - - + -
459B MET* 4.0 20.4 - - + -
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Residues in contact with VAL 352 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348B GLY 3.3 14.9 + - - +
349B CYS 4.0 5.8 - - - +
350B ILE 3.3 0.2 - - - -
351B LEU* 1.3 76.5 - - - +
353B GLU* 1.3 58.3 + - - +
355B HIS* 3.1 3.5 + - - +
356B THR* 2.9 46.0 + - + +
360B LEU* 4.3 24.5 - - + -
423B LEU* 4.0 22.0 - - + -
426B ILE* 4.5 4.3 - - + -
427B LEU* 4.0 14.1 - - + -
452B PHE* 4.4 5.6 - - - -
456B ILE* 3.7 29.2 - - + -
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Residues in contact with GLU 353 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B TYR* 4.8 2.3 - - - -
249B LEU* 3.5 14.5 - - + +
290B PRO* 3.9 10.7 - - + +
327B TYR* 2.5 36.1 + - - -
349B CYS 3.2 9.0 + - - +
350B ILE* 3.1 8.8 + - - +
352B VAL* 1.3 79.6 - - - +
354B MET* 1.3 55.9 + - - +
357B GLY* 2.7 34.8 + - - +
358B GLU* 3.3 28.1 - - - +
359B PRO* 3.6 21.6 - - + +
360B LEU 4.6 0.8 - - - +
6C ARG* 2.6 28.4 + - - -
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Residues in contact with MET 354 (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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245B LEU* 3.6 50.0 - - + +
248B LEU* 4.0 19.1 - - + -
249B LEU* 3.2 35.3 - - + +
257B VAL* 2.9 37.0 + - + +
262B THR* 4.3 7.2 - - + +
265B PHE* 4.2 13.0 - - + -
290B PRO* 4.8 10.8 - - - -
350B ILE* 2.8 31.9 + - + +
351B LEU* 3.8 11.4 - - + +
352B VAL 3.3 0.4 - - - -
353B GLU* 1.3 75.9 - - - +
355B HIS* 1.3 57.7 + - - +
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Residues in contact with HIS 355 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255B ARG 3.7 3.5 - - - +
256B GLY* 3.5 12.8 - - - -
257B VAL 2.8 24.5 + - - -
258B SER 3.7 1.0 - - - -
259B LEU* 3.6 31.6 + - + -
262B THR* 3.7 10.3 + - + +
351B LEU 3.4 7.3 + - - +
352B VAL 3.1 7.3 + - - +
354B MET* 1.3 80.8 - - - +
356B THR* 1.3 59.1 + - + +
427B LEU* 4.7 8.5 - - + -
434B PRO* 3.2 32.9 - - + +
438B ARG* 3.9 12.0 + - - -
444B HIS* 3.9 7.6 - - - -
449B TYR* 2.7 39.5 + + - -
452B PHE* 4.4 9.0 - - + -
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Residues in contact with THR 356 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254B PHE 3.5 9.0 - - - +
255B ARG 3.9 7.8 - - - +
352B VAL* 2.9 36.6 + - + +
353B GLU* 3.8 0.2 - - - -
355B HIS* 1.3 78.4 - - - +
357B GLY* 1.3 57.2 + - - +
358B GLU* 3.1 34.4 + - - +
426B ILE* 4.3 17.8 - - + +
427B LEU* 4.2 11.0 - - + -
434B PRO* 4.2 21.7 - - + +
437B ARG* 4.2 5.9 + - - -
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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
------------------------------------------------------------
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