Contacts of the strand formed by residues 424 - 430 (chain A) in PDB entry 2WU4
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 ARG 424 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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322A GLN 5.2 0.6 + - - -
324A LEU 2.8 8.7 + - - +
325A GLN* 3.3 27.4 + - + +
326A VAL* 2.8 33.4 + - - +
422A GLY 3.8 1.2 + - - -
423A ALA* 1.3 72.1 - - - +
425A VAL* 1.3 56.7 + - - +
426A TYR* 3.4 33.9 + - + -
486A THR 3.7 11.1 + - - -
487A GLY* 3.4 27.8 + - - -
488A ASP* 4.3 6.1 + - - +
502A PRO* 4.7 15.5 - - + -
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Residues in contact with VAL 425 (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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326A VAL* 3.4 23.6 - - + -
328A VAL* 4.1 5.8 - - + -
415A ALA* 3.9 23.6 - - + +
418A LEU* 3.9 9.6 - - + -
419A ALA* 3.8 29.4 - - + +
423A ALA 3.5 7.2 + - - +
424A ARG* 1.3 78.3 - - - +
426A TYR* 1.3 68.9 + - - +
427A ALA* 5.0 0.2 - - + -
502A PRO* 3.3 8.4 - - - +
503A TYR* 2.6 52.7 + - + +
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Residues in contact with TYR 426 (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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326A VAL 3.0 13.9 + - - +
327A LEU* 3.4 17.1 - - + -
328A VAL* 2.8 35.0 + - - +
424A ARG* 3.4 33.0 + - + -
425A VAL* 1.3 75.5 - - - +
427A ALA* 1.3 55.9 + - - +
483A PHE* 4.3 7.2 - + - -
487A GLY 3.3 20.6 - - - -
488A ASP* 3.5 18.5 + - - -
489A PRO* 3.4 26.9 - - + -
490A ASN* 4.3 2.0 + - - -
500A TRP* 3.4 46.4 - + + +
501A PRO 3.9 4.0 - - - -
502A PRO* 3.8 20.7 - - + +
503A TYR 4.4 2.5 - - - +
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Residues in contact with ALA 427 (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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328A VAL* 3.1 18.4 - - + +
415A ALA* 5.3 1.6 - - + -
426A TYR* 1.3 76.0 - - - +
428A TYR* 1.3 62.3 + - - +
500A TRP* 3.1 14.0 + - - +
503A TYR* 4.2 25.1 - - + +
509A GLN 4.9 1.2 + - - -
510A TYR* 3.3 19.9 - - + +
511A VAL 3.0 19.1 + - - -
524A LEU* 4.8 11.0 - - + -
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Residues in contact with TYR 428 (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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228A GLN* 3.3 38.9 - - + +
327A LEU* 3.9 18.6 - - + -
328A VAL* 3.1 27.1 + - - -
329A GLY* 3.1 24.8 - - - -
330A VAL* 3.2 25.3 + - - +
427A ALA* 1.3 76.9 - - - +
429A ILE* 1.3 64.8 + - - +
430A PHE* 3.7 20.2 - + + -
450A GLU* 4.2 9.0 + - + +
480A TRP* 3.7 25.8 - + - -
500A TRP* 3.7 8.1 - + + -
510A TYR* 4.4 4.5 - - - -
511A VAL* 3.2 12.3 - - + +
513A LEU* 3.6 27.6 - - + -
524A LEU* 5.0 3.7 - - - +
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Residues in contact with ILE 429 (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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330A VAL* 3.1 23.6 - - + +
331A VAL 4.3 3.1 - - - +
332A LYS* 4.3 14.6 - - + -
428A TYR* 1.3 77.0 - - - +
430A PHE* 1.3 65.0 + - - +
431A GLU* 3.8 23.9 + - + +
510A TYR* 3.4 30.7 - - + +
511A VAL 2.9 6.4 + - - +
512A SER* 3.4 4.6 - - - -
513A LEU 2.8 23.6 + - - -
521A ARG* 4.0 15.5 - - - +
524A LEU* 5.6 4.7 - - + -
525A ARG* 5.0 14.4 - - - +
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Residues in contact with PHE 430 (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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330A VAL 2.7 14.6 + - - +
331A VAL* 3.3 6.3 - - + +
332A LYS* 2.9 25.6 + - - +
428A TYR* 3.7 13.2 - + + -
429A ILE* 1.3 72.5 - - - +
431A GLU* 1.3 61.3 + - - +
432A HIS 3.2 26.9 - - - -
445A VAL* 4.0 10.0 - - + +
449A TYR 4.2 3.8 - - - -
450A GLU* 3.5 44.4 - - + -
453A PHE* 3.8 13.0 - + + -
454A ILE* 5.2 2.9 - - + -
472A PHE* 3.7 21.8 - + - -
476A LEU* 3.5 28.7 - - + -
480A TRP* 6.1 0.2 - + - -
513A LEU* 3.6 22.2 - - + -
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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