Contacts of the strand formed by residues 431 - 435 (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 TYR 431 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288A MET* 4.7 5.2 - - - +
289A ASN* 4.6 5.9 + - - -
292A THR* 4.2 3.1 + - - +
374A TYR* 3.4 43.4 - + + +
375A ASN 3.4 7.1 + - - +
376A ASN 3.4 34.5 - - - -
377A GLY* 3.6 5.1 - - - -
430A GLY* 1.3 72.0 - - - -
432A ALA* 1.3 58.5 + - - +
433A GLN* 2.8 35.9 + - + +
440A TYR 3.9 17.7 - - - -
441A ILE* 3.1 10.7 - - - +
442A TYR* 2.9 80.1 + + + +
444A SER* 4.6 2.2 - - - +
452A GLN* 4.2 1.4 + - - -
454A VAL* 4.6 0.4 - - - -
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Residues in contact with ALA 432 (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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377A GLY* 3.1 16.0 - - - -
426A TYR* 3.1 40.2 + - + -
431A TYR* 1.3 78.1 - - - +
433A GLN* 1.3 60.2 + - - +
439A TRP* 3.9 10.7 - - + -
440A TYR 3.2 7.0 - - - +
441A ILE* 4.2 6.1 - - + -
454A VAL* 4.5 2.7 - - + -
456A LEU* 3.7 30.3 - - + -
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Residues in contact with GLN 433 (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* 2.9 33.9 + - - +
342A ARG* 3.8 6.6 + - - -
377A GLY* 3.6 12.8 - - - +
380A HIS* 2.8 48.9 - - + +
381A ILE 4.9 0.3 + - - -
431A TYR* 2.8 34.7 + - + +
432A ALA* 1.3 76.0 - - - +
434A ARG* 1.3 62.2 + - - +
435A VAL* 3.6 17.7 + - + +
439A TRP* 3.5 6.5 - - - -
440A TYR* 2.8 38.3 + - + +
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Residues in contact with ARG 434 (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* 5.7 0.2 - - - -
377A GLY 4.9 1.6 + - - -
380A HIS* 3.3 23.8 + - - -
425A LEU* 3.8 25.3 - - + +
433A GLN* 1.3 72.5 - - - +
435A VAL* 1.3 60.4 + - - +
436A GLY 3.0 19.1 + - - +
437A ASN* 3.5 27.9 - - - +
438A SER 3.3 12.0 + - - -
439A TRP* 3.2 43.6 - - + +
459A TYR* 3.2 48.4 - - + +
480A GLU* 2.8 33.1 + - - +
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Residues in contact with VAL 435 (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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291A TYR* 5.6 0.9 - - + -
292A THR* 4.1 8.5 - - + -
334A PRO* 3.6 31.9 - - + -
342A ARG* 4.6 8.3 - - - +
433A GLN* 3.6 32.8 - - + +
434A ARG* 1.3 75.9 - - - +
436A GLY* 1.3 66.3 + - - +
437A ASN* 3.1 1.2 + - - +
438A SER* 2.8 27.9 + - - +
440A TYR* 3.8 32.8 - - + -
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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