Contacts of the helix formed by residues 413 - 422 (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 413 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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410A GLU 3.1 12.3 + - - +
412A SER* 1.3 81.8 + - - +
414A LYS* 1.3 58.4 + - - +
415A VAL 3.4 2.0 - - - -
416A ASN* 3.3 27.7 + - - +
417A TYR* 2.9 24.9 + - - +
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Residues in contact with LYS 414 (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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359A GLY 3.1 13.7 + - - -
360A PHE* 2.8 45.2 + - + +
362A GLN* 2.8 23.2 + - - +
364A LEU* 4.1 15.0 - - + -
410A GLU 3.9 8.1 - - - -
411A LEU* 3.5 33.4 + - + +
413A SER* 1.3 75.0 - - - +
415A VAL* 1.3 76.8 + - + +
417A TYR* 3.4 2.6 + - - +
418A LEU* 3.0 30.1 + - + +
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Residues in contact with VAL 415 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A GLN 4.4 0.2 - - - +
363A GLY* 3.5 38.4 - - - +
364A LEU* 4.2 9.0 - - + -
379A TYR* 4.6 2.9 - - - +
413A SER 3.4 0.6 - - - -
414A LYS* 1.3 90.5 - - + +
416A ASN* 1.3 64.9 + - - +
418A LEU* 3.3 0.9 + - - +
419A ASN* 2.9 54.7 + - - +
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Residues in contact with ASN 416 (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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413A SER* 3.3 26.2 + - - +
415A VAL* 1.3 82.6 - - - +
417A TYR* 1.3 63.2 + - - +
419A ASN* 3.4 9.7 + - - +
420A SER* 3.1 22.0 + - - -
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Residues in contact with TYR 417 (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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402A LYS* 3.2 31.2 + - + +
404A LEU* 3.9 31.2 - - + -
410A GLU* 3.7 43.3 - - + +
411A LEU* 6.1 1.1 - - + -
413A SER* 2.9 20.2 + - - +
414A LYS* 3.8 3.4 - - - +
416A ASN* 1.3 77.8 - - - +
418A LEU* 1.3 68.7 + - + +
420A SER* 2.7 35.5 + - - -
421A LEU* 3.5 31.0 + - + +
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Residues in contact with LEU 418 (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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345A ALA* 3.9 28.3 - - + -
360A PHE* 4.7 7.0 - - + -
364A LEU* 3.4 47.1 - - + -
379A TYR* 4.1 7.2 - - + -
382A LEU* 4.0 15.7 - - + -
404A LEU* 4.3 16.6 - - + -
411A LEU* 6.2 0.2 - - + -
414A LYS* 3.0 24.7 + - + +
417A TYR* 1.3 78.9 - - + +
419A ASN* 1.3 59.7 + - - +
421A LEU* 3.0 11.3 + - + +
422A TYR* 2.9 44.2 + - + +
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Residues in contact with ASN 419 (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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378A ARG* 3.2 34.8 + - - +
379A TYR* 2.5 29.5 + - - -
415A VAL* 2.9 35.8 + - - +
416A ASN* 3.6 11.6 + - - +
418A LEU* 1.3 78.1 - - - +
420A SER* 1.3 57.3 + - - +
422A TYR 3.3 16.4 - - - +
423A PRO* 4.4 2.9 - - - +
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Residues in contact with SER 420 (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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416A ASN 3.1 11.8 + - - -
417A TYR* 2.7 36.0 + - - -
419A ASN* 1.3 76.2 - - - +
421A LEU* 1.3 65.5 + - - +
423A PRO 5.7 0.2 - - - -
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Residues in contact with LEU 421 (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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344A LYS* 3.5 50.6 - - + +
345A ALA* 3.9 15.7 - - + -
402A LYS* 4.0 5.6 - - + -
417A TYR* 3.8 44.9 - - + +
418A LEU* 3.0 9.3 + - + +
420A SER* 1.3 89.9 - - - +
422A TYR* 1.3 63.5 + - + +
423A PRO* 3.5 9.9 - - - +
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Residues in contact with TYR 422 (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 ARG 4.0 8.3 - - - -
343A THR* 3.7 5.7 - - - +
344A LYS* 2.8 48.0 + - + -
345A ALA* 3.1 19.8 + - + -
378A ARG* 2.8 53.7 + - + +
379A TYR* 3.8 35.6 + + + -
380A HIS* 4.3 7.6 - + - -
382A LEU* 3.6 25.3 - - + +
383A PRO* 5.2 0.9 - - - +
418A LEU* 2.9 27.7 + - + +
419A ASN* 3.3 6.0 - - - +
421A LEU* 1.3 77.2 - - + +
423A PRO* 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