Contacts of the strand formed by residues 401 - 409 (chain A) in PDB entry 3H13
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 401 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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337A ARG* 3.4 41.1 - - + -
340A PHE* 3.6 22.2 - - + -
341A MET* 3.8 21.5 - - + -
353A LYS* 3.5 20.6 - - + -
355A PHE* 3.6 34.3 - + - -
397A ARG 4.1 7.4 - - - -
398A GLU* 3.6 20.2 - - + +
399A ALA 3.3 6.2 - - - -
400A ASP* 1.3 79.8 - - - +
402A PHE* 1.3 60.3 + - - +
403A TRP* 4.2 6.7 - + + -
469A HIS* 3.3 5.7 - - - +
470A THR* 2.9 35.4 + - + +
471A LEU* 3.8 4.2 - - - +
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Residues in contact with PHE 402 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352A PRO* 6.4 0.2 - - + -
353A LYS 2.9 7.5 + - - +
354A MET* 3.8 19.5 - - + -
355A PHE* 2.8 35.8 + - - +
356A PHE* 3.8 24.5 - + - -
401A PHE* 1.3 73.0 - - - +
403A TRP* 1.3 58.6 + - - +
404A SER* 4.1 6.1 - - - -
439A LEU* 3.6 39.0 - - + -
440A LEU* 3.9 22.2 - - + -
443A HIS* 3.8 22.0 - + + -
467A LEU* 3.6 26.0 - - + -
469A HIS* 3.9 10.1 - - + -
471A LEU* 4.0 25.6 - - + -
475A LEU* 5.0 0.2 - - + -
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Residues in contact with TRP 403 (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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333A LEU* 3.6 37.9 - - + +
336A ILE* 4.5 4.7 - - + -
337A ARG* 3.2 54.4 - - + +
355A PHE* 3.4 47.1 - + + -
357A ILE* 3.3 26.2 - - + -
401A PHE* 5.2 5.6 - + + -
402A PHE* 1.3 74.5 - - - +
404A SER* 1.3 59.1 + - - +
405A LEU* 4.2 13.0 - - + +
466A TRP* 3.3 35.3 - + - +
467A LEU* 3.4 6.3 - - - +
468A GLN* 2.9 42.9 + - + +
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Residues in contact with SER 404 (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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355A PHE 2.9 15.6 + - - +
356A PHE* 3.5 12.7 - - - -
357A ILE* 2.8 28.2 + - - +
402A PHE* 4.1 5.8 - - - -
403A TRP* 1.3 73.7 - - - +
405A LEU* 1.3 59.4 + - - +
423A TYR* 2.7 27.7 + - - -
443A HIS* 2.7 36.0 + - - -
465A VAL* 4.2 1.2 - - - +
466A TRP 3.6 3.4 - - - -
467A LEU* 4.2 2.0 - - - -
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Residues in contact with LEU 405 (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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319A GLN* 5.2 9.4 - - + +
333A LEU* 4.0 25.8 - - + -
357A ILE* 3.5 31.0 - - + +
359A ASN* 4.0 13.0 - - + +
403A TRP* 4.0 14.1 + - - +
404A SER* 1.3 74.9 + - - +
406A CYS* 1.3 69.1 + - - +
407A THR* 4.1 13.8 + - - +
464A TYR 3.6 1.6 - - - +
465A VAL* 3.5 2.9 - - - -
466A TRP* 2.8 63.1 + - + +
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Residues in contact with CYS 406 (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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357A ILE 2.7 10.3 + - - +
358A GLN* 3.3 23.0 + - - +
359A ASN* 2.7 31.4 + - - +
404A SER 4.2 0.4 - - - -
405A LEU* 1.3 73.9 - - - +
407A THR* 1.3 64.6 + - - +
423A TYR* 3.5 45.3 - - + -
463A TYR* 3.8 24.5 - - - -
464A TYR 3.2 10.3 - - - -
465A VAL* 4.1 6.3 - - + +
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Residues in contact with THR 407 (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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318A SER* 6.1 1.5 - - - -
358A GLN* 4.2 0.4 - - - -
359A ASN* 3.5 9.8 + - - +
361A VAL* 3.8 32.5 - - + +
405A LEU* 4.1 17.0 + - - +
406A CYS* 1.3 76.4 + - - +
408A ALA* 1.3 67.2 + - - +
463A TYR* 3.7 2.1 - - - -
464A TYR* 2.8 48.9 + - + +
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Residues in contact with ALA 408 (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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358A GLN* 3.8 9.9 - - - +
359A ASN 3.0 6.3 + - - -
360A TYR* 3.3 10.5 - - + -
361A VAL* 2.9 27.2 + - - +
407A THR* 1.3 79.0 - - - +
409A ASP* 1.3 63.1 + - - +
412A LEU* 4.0 11.0 - - + -
462A LYS 4.0 6.3 - - - +
463A TYR* 3.6 32.8 - - + -
464A TYR* 5.5 1.8 - - - -
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Residues in contact with ASP 409 (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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360A TYR* 3.8 4.7 - - - -
361A VAL 3.5 7.4 - - - -
363A SER* 3.1 34.2 + - - -
408A ALA* 1.3 74.8 - - - +
410A MET* 1.3 66.2 + - - +
411A SER* 2.6 42.0 + - - +
412A LEU* 3.0 24.7 + - - +
459A ALA 5.3 1.1 - - - +
460A LYS* 3.6 37.2 - - - +
462A LYS 4.5 4.0 + - - -
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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