Contacts of the helix formed by residues 351 - 359 (chain A) in PDB entry 2WMN
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 PRO 351 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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314A MET* 4.3 8.3 - - + -
342A SER 3.6 24.9 - - - +
345A VAL* 4.4 8.1 - - + -
350A GLY* 1.3 79.8 - - - +
352A LEU* 1.3 62.0 + - + +
353A ALA 3.2 0.4 - - - -
354A TYR* 3.3 11.9 + - + +
379A PHE* 3.3 26.3 - - + -
382A PHE* 4.0 22.9 - - + -
415A MET* 4.7 9.6 - - - -
419A LEU* 5.8 0.2 - - - -
36B VAL* 3.9 17.9 - - + +
37B PHE* 4.0 26.0 - - + -
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Residues in contact with LEU 352 (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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350A GLY* 2.6 8.9 + - - +
351A PRO* 1.3 73.7 - - + +
353A ALA* 1.3 52.2 + - - +
354A TYR 3.1 0.9 - - - -
355A ALA* 2.9 8.2 + - + +
356A ARG* 2.8 74.1 + - - +
415A MET* 4.0 28.7 - - + +
418A GLU* 3.2 31.9 - - + +
419A LEU* 3.7 31.2 - - + -
422A ILE* 5.1 0.2 - - + -
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Residues in contact with ALA 353 (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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271A VAL* 3.8 19.6 - - + +
349A ALA* 4.1 20.6 - - + -
350A GLY 2.7 22.7 + - - +
352A LEU* 1.3 72.4 - - - +
354A TYR* 1.3 59.8 + - - +
356A ARG* 3.5 15.2 - - - +
357A ALA* 3.1 28.1 + - - +
36B VAL* 4.7 1.6 - - + -
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Residues in contact with TYR 354 (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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271A VAL* 3.9 26.4 - - + +
306A PRO 5.2 0.9 - - - -
309A VAL* 4.9 5.2 - - + +
310A ALA* 3.5 35.9 - - + -
313A GLU* 3.7 23.9 - - + +
314A MET* 3.6 33.0 - - + -
351A PRO 3.3 11.4 + - - +
352A LEU 3.1 0.4 - - - -
353A ALA* 1.3 79.0 - - - +
355A ALA* 1.3 56.9 + - - +
358A PHE* 2.9 42.1 + + - +
359A LEU* 5.3 0.2 - - - -
375A LEU* 4.7 0.8 - - + +
379A PHE* 3.8 12.6 - - + -
34B PRO 4.8 6.4 + - - -
35B THR* 5.1 0.5 - - - -
36B VAL* 3.4 46.9 + - + +
37B PHE* 5.0 0.2 - + - -
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Residues in contact with ALA 355 (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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351A PRO 3.7 0.8 + - - -
352A LEU* 2.9 9.8 + - - +
354A TYR* 1.3 80.1 - - - +
356A ARG* 1.3 59.3 + - - +
359A LEU* 2.7 52.7 + - + +
379A PHE* 4.1 10.3 - - + -
419A LEU* 3.8 29.4 - - + -
422A ILE* 4.4 14.8 - - + +
423A MET* 6.1 0.9 - - + -
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Residues in contact with ARG 356 (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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349A ALA 5.6 3.4 + - - -
350A GLY* 5.0 1.0 + - - -
352A LEU* 2.8 74.0 + - + +
353A ALA* 3.5 13.4 - - - +
355A ALA* 1.3 75.7 - - - +
357A ALA* 1.3 61.6 + - + +
358A PHE 3.6 0.3 + - - -
360A ASP* 4.0 17.4 - - - +
418A GLU* 3.2 25.9 + - - +
422A ILE* 4.3 12.1 - - + -
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Residues in contact with ALA 357 (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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271A VAL* 3.8 20.2 - - + -
272A GLU* 4.7 14.8 - - + +
353A ALA 3.1 18.4 + - - +
356A ARG* 1.3 78.1 - - - +
358A PHE* 1.3 72.4 + - + +
360A ASP* 5.9 0.4 - - - -
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Residues in contact with PHE 358 (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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271A VAL* 3.6 37.0 - - + -
272A GLU* 4.1 11.4 - - + -
306A PRO* 3.6 28.5 - - + -
307A ILE* 3.6 29.0 - - + +
310A ALA* 4.2 14.4 - - + -
354A TYR* 2.9 31.7 + + - +
357A ALA* 1.3 86.9 - - + +
359A LEU* 1.3 63.3 + - - +
360A ASP 3.4 9.2 + - - +
368A PRO* 6.1 0.9 - - - +
372A VAL* 5.0 6.1 - - - +
375A LEU* 3.5 19.7 - - + -
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Residues in contact with LEU 359 (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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355A ALA* 2.7 35.3 + - + +
358A PHE* 1.3 78.3 - - - +
360A ASP* 1.3 58.2 + - - +
372A VAL* 3.3 33.7 - - + -
375A LEU* 3.7 20.0 - - + -
376A LYS* 3.8 26.3 - - + -
379A PHE* 3.8 28.7 - - + -
422A ILE* 3.1 26.9 - - + +
423A MET* 4.0 19.1 - - + +
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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