Contacts of the strand formed by residues 423 - 430 (chain A) in PDB entry 4UHW
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 GLU 423 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329A GLU* 4.2 2.9 - - - +
332A GLN* 3.6 14.0 - - - +
376A ASN* 4.7 2.8 - - - +
418A TYR 4.5 1.6 - - - +
419A SER* 3.4 14.9 - - - -
420A ARG* 2.7 62.4 + - - +
422A TRP* 1.3 78.3 - - - +
424A PHE* 1.3 75.3 + - - +
425A VAL* 5.0 2.2 - - + -
446A ARG* 2.7 43.1 + - + +
447A VAL 3.4 11.7 - - - +
448A PHE* 3.9 9.0 - - + -
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Residues in contact with PHE 424 (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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329A GLU* 3.2 28.7 - - + -
332A GLN* 3.7 17.7 - - - +
422A TRP* 3.7 17.7 - + - -
423A GLU* 1.3 81.2 - - - +
425A VAL* 1.3 64.1 + - - +
445A MET 4.0 0.2 - - - +
446A ARG* 3.4 4.9 - - - +
447A VAL* 3.1 40.0 + - + +
449A PHE* 3.8 23.6 - + - -
526A PHE* 4.3 3.2 - - + -
530A VAL* 3.2 34.3 - - + -
533A ILE* 3.5 32.1 - - + -
534A LEU* 4.0 10.3 - - + -
537A MET* 3.8 13.7 - - - -
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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
----------------------------------------------------------
332A GLN* 3.2 43.9 + - + +
333A MET* 3.9 31.2 - - + -
336A ALA* 4.0 21.2 - - + +
371A ILE* 4.7 4.7 - - + -
374A VAL* 4.7 7.0 - - + -
419A SER* 5.5 1.1 - - - -
423A GLU* 5.0 3.4 - - + -
424A PHE* 1.3 81.8 - - - +
426A SER* 1.3 67.6 + - - +
445A MET 3.4 9.4 - - - +
446A ARG* 3.9 23.8 - - + -
526A PHE* 4.6 0.7 - - - -
529A GLU* 4.6 3.8 - - - +
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Residues in contact with SER 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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336A ALA* 4.7 2.2 - - - -
339A LYS* 5.3 1.0 + - - -
425A VAL* 1.3 80.0 - - - +
427A ALA* 1.3 60.6 + - - +
428A PHE* 3.4 14.3 - - - -
443A SER 4.1 0.2 - - - +
444A GLY* 3.5 1.9 - - - -
445A MET* 2.9 35.1 + - - +
526A PHE* 3.4 29.1 - - - -
529A GLU* 2.7 36.4 + - - -
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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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336A ALA* 4.0 13.6 - - + +
339A LYS* 2.7 39.6 + - + +
340A HIS* 3.6 11.2 - - + +
371A ILE* 3.3 38.1 - - + -
426A SER* 1.3 76.1 + - - +
428A PHE* 1.3 58.1 + - - +
443A SER 3.1 10.5 - - - +
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Residues in contact with PHE 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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339A LYS* 3.8 16.2 - - - +
340A HIS* 3.2 12.3 - - - -
426A SER* 3.4 33.4 - - - -
427A ALA* 1.3 78.8 - - - +
429A ARG* 1.3 61.6 + - - +
442A ASN* 3.2 1.6 - - - -
443A SER* 2.9 30.7 + - - +
445A MET* 4.6 8.1 - - + -
522A PHE* 3.4 51.1 - + + -
525A LYS* 3.9 29.8 - - + -
526A PHE* 3.8 23.8 - + + -
529A GLU* 3.5 16.6 - - - -
553A LEU 6.1 1.1 - - - -
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Residues in contact with ARG 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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339A LYS* 5.9 0.8 - - - +
340A HIS* 3.8 20.6 + - + +
343A THR* 3.5 33.6 + - + -
367A ASP* 2.9 39.2 + - - -
428A PHE* 1.3 78.5 - - - +
430A GLN* 1.3 67.9 + - - +
431A ALA* 4.0 13.3 - - - +
434A GLN 4.1 16.4 + - - -
435A GLU* 5.2 0.4 - - - +
437A ALA 3.1 26.9 + - - -
439A ALA* 3.6 18.9 - - + +
441A VAL 3.5 7.6 - - - +
442A ASN* 3.8 11.9 - - + -
522A PHE* 3.8 7.6 - - - -
1177A THR* 5.5 0.7 - - - +
3006A FAD 3.9 4.8 + - - -
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Residues in contact with GLN 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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429A ARG* 1.3 80.9 - - - +
431A ALA* 1.3 78.4 + - - +
432A GLN 5.4 0.6 - - - -
433A ARG 5.6 1.8 + - - -
439A ALA* 3.7 2.4 - - - -
440A ILE* 2.7 36.1 + - + +
441A VAL 3.0 8.7 + - - -
514A PHE* 4.1 14.6 - - + -
518A LEU* 3.8 19.3 - - + -
522A PHE* 4.1 6.7 - - + -
1177A THR* 3.3 43.1 + - - +
1179A ASP* 3.6 25.1 + - - +
1308A PRO* 3.9 14.3 - - + +
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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