Contacts of the strand formed by residues 438 - 442 (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 438 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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434A ARG* 3.3 12.9 - - - +
435A VAL 2.8 39.2 + - - -
436A GLY 3.3 0.8 + - - -
437A ASN* 1.3 83.3 + - - +
439A TRP* 1.3 59.9 + - - +
440A TYR* 3.7 24.4 + - - -
477A VAL* 4.6 2.3 - - - +
478A VAL 3.1 11.4 - - - -
479A LYS* 3.4 28.3 - - - +
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Residues in contact with TRP 439 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425A LEU* 3.5 40.4 - - + -
426A TYR* 4.1 8.3 - + + -
432A ALA* 3.9 26.9 - - + -
433A GLN 3.5 20.9 - - - -
434A ARG* 3.2 47.2 - - + +
438A SER* 1.3 73.4 - - - +
440A TYR* 1.3 60.1 + - - +
441A ILE* 3.9 17.1 - - + +
456A LEU* 3.7 23.8 - - + +
457A PRO* 3.0 29.4 + - + -
458A MET* 3.7 18.3 - - + -
459A TYR* 4.0 12.1 - + - -
477A VAL* 3.3 8.5 - - - +
478A VAL* 2.8 40.3 + - + +
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Residues in contact with TYR 440 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A MET* 3.9 24.0 - - + -
291A TYR* 3.3 29.6 + + - -
292A THR* 3.7 19.7 - - + -
324A PHE* 4.9 0.9 - + - -
327A HIS* 2.7 29.6 + + - -
331A ASN* 4.8 1.7 - - - +
431A TYR* 3.9 5.6 - - + -
432A ALA* 3.2 2.4 - - - -
433A GLN* 2.8 44.6 + - + +
435A VAL* 3.8 30.5 - - + -
438A SER* 3.7 23.5 + - - -
439A TRP* 1.3 73.9 - - - +
441A ILE* 1.3 59.4 + - - +
476A ALA 3.8 1.6 - - - -
477A VAL* 3.5 32.4 - - + +
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Residues in contact with ILE 441 (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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288A MET* 4.2 4.1 - - - +
431A TYR* 3.1 11.2 - - - +
432A ALA* 4.2 8.1 - - + -
439A TRP* 3.9 20.2 - - + +
440A TYR* 1.3 77.3 - - - +
442A TYR* 1.3 71.8 + - - +
454A VAL* 4.2 12.3 - - + -
456A LEU* 3.6 30.5 - - + -
468A LEU* 3.7 20.2 - - + -
470A LEU* 3.6 29.6 - - + -
475A TYR* 3.2 4.2 - - - +
476A ALA* 2.9 39.5 + - + +
478A VAL* 4.0 11.4 - - + -
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Residues in contact with TYR 442 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A MET* 3.8 34.3 - - + -
288A MET* 3.8 22.4 - - - -
289A ASN* 2.7 32.0 + - - -
373A LEU* 3.6 16.6 - - + -
374A TYR* 2.9 46.3 + - - +
430A GLY* 4.0 1.7 - - - -
431A TYR* 2.9 58.4 + + + +
441A ILE* 1.3 75.6 - - - +
443A ASN* 1.3 72.8 + - - +
444A SER* 4.3 0.9 - - - -
452A GLN* 4.0 0.2 - - - +
470A LEU* 4.3 7.6 - - - +
474A THR 3.3 15.0 - - - +
475A TYR* 3.9 6.3 - - + -
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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