Contacts of the helix formed by residues 335 - 343 (chain A) in PDB entry 2WMH
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 SER 335 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43A ASN* 3.7 21.1 - - - +
238A TRP* 4.0 1.6 - - - -
333A ALA 3.2 2.2 + - - -
334A PRO* 1.3 75.8 - - - +
336A LYS* 1.3 65.9 + - - +
337A GLU* 3.0 33.2 + - - -
338A GLU* 2.8 32.7 + - - +
339A VAL* 3.0 20.8 + - - +
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Residues in contact with LYS 336 (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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238A TRP* 3.5 51.3 + - + +
239A LEU* 3.5 34.6 + - + +
241A GLY* 4.1 14.8 - - - -
335A SER* 1.3 72.5 - - - +
337A GLU* 1.3 64.1 + - - +
339A VAL* 3.1 3.8 + - - +
340A VAL* 2.9 38.2 + - + +
397A ILE* 5.6 2.0 - - - -
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Residues in contact with GLU 337 (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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335A SER* 3.0 28.7 + - - +
336A LYS* 1.3 83.3 + - - +
338A GLU* 1.3 58.3 + - + +
340A VAL* 3.8 7.7 - - - +
341A ASN* 2.9 44.7 + - - +
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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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43A ASN* 4.7 1.2 + - - -
332A PRO 5.5 0.3 - - - +
333A ALA 4.1 2.9 - - - +
334A PRO* 3.4 14.9 - - + +
335A SER* 2.8 47.8 + - - +
337A GLU* 1.3 77.8 - - + +
339A VAL* 1.3 64.1 + - - +
341A ASN* 3.3 4.8 + - - +
342A ARG* 3.1 28.1 + - - +
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Residues in contact with VAL 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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238A TRP* 4.0 18.6 - - + -
239A LEU* 3.7 32.3 - - + -
293A GLY 4.2 8.5 - - - +
294A GLY* 4.3 0.4 - - - -
334A PRO* 3.8 20.9 - - + -
335A SER 3.0 17.2 + - - +
336A LYS 3.7 5.6 - - - +
338A GLU* 1.3 73.7 - - - +
340A VAL* 1.3 58.6 + - - +
342A ARG* 3.2 40.6 - - - +
343A THR* 2.7 28.0 + - - +
381A ILE 6.0 1.6 - - - +
383A PRO* 5.5 1.6 - - + -
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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
----------------------------------------------------------
239A LEU* 3.8 16.6 - - + -
336A LYS* 2.9 31.1 + - + +
337A GLU* 3.8 7.6 - - - +
339A VAL* 1.3 75.8 - - - +
341A ASN* 1.3 72.1 + - - +
343A THR* 3.2 23.5 + - - +
397A ILE* 3.3 35.2 - - + +
398A PHE* 4.1 22.8 - - + -
399A PRO* 5.4 2.0 - - + -
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Residues in contact with ASN 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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337A GLU* 2.9 32.8 + - - +
338A GLU* 4.0 5.1 - - - +
339A VAL 3.2 0.2 - - - -
340A VAL* 1.3 86.4 - - - +
342A ARG* 1.3 59.6 + - - +
343A THR 3.6 2.6 + - - +
344A LYS* 4.6 9.7 + - - +
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Residues in contact with ARG 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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292A THR 3.0 29.1 + - - -
293A GLY* 3.8 12.9 - - - -
334A PRO* 4.0 16.6 - - - +
338A GLU* 3.1 18.6 + - - +
339A VAL* 3.2 33.2 - - - +
341A ASN* 1.3 74.3 - - - +
343A THR* 1.3 64.1 + - - +
344A LYS* 3.4 20.8 + - - +
380A HIS* 3.5 54.7 + - + +
381A ILE* 4.7 6.3 + - - +
422A TYR* 4.0 8.0 - - - -
433A GLN* 3.8 8.5 + - - -
434A ARG 5.7 0.4 - - - -
435A VAL* 4.6 8.5 - - - +
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Residues in contact with THR 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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339A VAL* 2.7 24.4 + - - +
340A VAL* 3.2 16.2 + - - +
341A ASN 4.5 2.3 - - - +
342A ARG* 1.3 78.2 + - - +
344A LYS* 1.3 63.0 + - - +
345A ALA 3.2 27.4 - - - +
346A VAL* 3.7 18.8 - - + -
380A HIS* 5.7 0.7 - - - -
381A ILE 5.6 0.2 + - - -
383A PRO* 3.9 21.5 - - + +
398A PHE* 4.2 10.8 - - + -
400A ASN* 4.8 3.1 - - - +
401A ALA* 3.7 13.5 + - + +
422A TYR* 3.8 4.7 - - - +
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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