Contacts of the strand formed by residues 421 - 427 (chain A) in PDB entry 4H1S
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 PHE 421 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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364A ILE* 3.7 21.1 - - + -
368A MET* 3.4 48.7 - - + -
389A LEU* 5.0 3.6 - - + -
415A LEU* 4.5 6.7 - - + -
420A THR* 1.3 75.7 - - - +
422A ASP* 1.3 64.0 + - - +
423A LEU* 5.2 0.9 - - - +
496A ILE* 4.3 14.2 - - + +
497A LEU 3.6 2.0 - - - -
498A PRO* 4.3 17.7 - - + -
521A GLY* 3.3 18.7 - - - -
522A ASP 3.0 13.1 + - - +
524A ASP* 3.3 44.9 - - + -
527A VAL* 3.7 27.6 - - + -
528A VAL* 4.0 8.3 - - + -
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Residues in contact with ASP 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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420A THR* 2.7 24.7 + - - -
421A PHE* 1.3 72.3 - - - +
423A LEU* 1.3 64.7 + - - +
424A VAL 4.1 0.2 + - - -
495A VAL 3.7 0.5 - - - +
496A ILE* 3.2 6.6 - - - +
497A LEU* 2.7 44.8 + - + +
499A ASN* 3.1 23.6 - - - +
518A HIS* 2.7 31.4 + - + +
519A ASP 3.3 7.6 - - - +
520A SER* 3.4 13.9 - - - -
521A GLY 2.9 14.3 + - - +
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Residues in contact with LEU 423 (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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372A ASN* 3.4 32.5 - - - +
381A TRP* 3.3 51.4 - - + +
384A VAL* 4.2 15.9 - - + -
421A PHE 5.2 1.3 - - - +
422A ASP* 1.3 76.0 - - - +
424A VAL* 1.3 65.0 + - - +
495A VAL 3.6 3.1 - - - +
496A ILE* 3.8 30.5 - - + -
517A ARG 3.9 0.2 - - - +
518A HIS* 3.4 0.5 - - - -
519A ASP* 3.0 38.3 + - + +
520A SER 5.7 2.7 - - - +
521A GLY* 5.8 4.5 - - - -
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Residues in contact with VAL 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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381A TRP* 3.8 7.6 - - - -
422A ASP 4.1 0.2 + - - -
423A LEU* 1.3 80.1 - - - +
425A GLN* 1.3 60.4 + - - +
426A LEU* 3.7 29.4 - - + -
493A TYR 4.0 0.2 - - - +
494A LYS* 3.5 3.3 - - - -
495A VAL* 2.9 44.6 + - + +
497A LEU* 3.9 36.6 - - + -
502A ALA* 4.2 2.9 - - + -
511A ILE* 5.2 0.9 - - + -
515A LEU* 4.1 16.4 - - + -
517A ARG 3.1 12.3 - - - +
518A HIS* 4.0 16.2 - - + -
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Residues in contact with GLN 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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380A PHE* 3.5 28.5 - - - -
381A TRP* 4.5 6.3 - - + -
424A VAL* 1.3 73.7 - - - +
426A LEU* 1.3 65.0 + - - +
492A VAL* 3.6 30.2 - - + +
493A TYR 3.4 6.1 - - - +
494A LYS* 4.6 9.7 - - + +
515A LEU* 3.6 0.2 - - - -
516A LEU* 2.8 50.2 + - + +
517A ARG* 3.0 29.5 + - + +
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Residues in contact with LEU 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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424A VAL* 3.7 24.2 - - + -
425A GLN* 1.3 85.2 - - - +
427A LYS* 1.3 67.9 + - - +
430A THR* 4.5 17.3 - - + -
431A LEU* 3.9 32.3 - - + +
492A VAL* 3.4 5.1 - - - -
493A TYR* 2.6 45.8 + - - +
495A VAL* 4.7 7.6 - - + -
497A LEU* 5.0 2.2 - - + -
511A ILE* 4.3 24.2 - - + -
515A LEU* 3.5 28.5 - - + +
516A LEU* 4.8 2.2 - - - +
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Residues in contact with LYS 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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426A LEU* 1.3 77.2 - - - +
428A GLY* 1.3 67.1 + - - +
429A SER* 3.9 16.9 + - - +
430A THR* 3.1 30.9 + - - +
431A LEU* 3.2 10.6 + - - +
489A MET 4.6 3.4 - - - +
490A ASP 6.3 0.2 - - - -
491A GLU 3.5 7.0 - - - +
492A VAL* 4.3 7.4 - - + +
493A TYR* 4.5 0.2 - - - -
514A GLU* 4.4 23.7 + - - +
516A LEU* 4.4 25.5 - - + +
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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