Contacts of the helix formed by residues 424 - 436 (chain A) in PDB entry 3N51
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 424 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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361A THR* 4.1 24.1 + - + +
364A PHE* 3.4 37.9 - + + -
365A HIS* 3.6 32.9 + - - +
368A ASP* 3.7 29.9 + - + -
373A GLY* 3.0 31.0 + - - -
375A LEU* 3.8 24.5 - - + -
380A LEU* 4.1 6.5 - - + -
422A ILE 2.9 7.9 + - - +
423A GLU* 1.3 71.1 - - - +
425A SER* 1.3 68.1 + - - +
427A PHE* 3.0 10.3 + - - +
428A VAL* 2.8 35.3 + - + +
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Residues in contact with SER 425 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361A THR* 6.3 1.3 - - - -
373A GLY 4.6 0.8 + - - -
423A GLU* 3.1 15.5 + - - -
424A TYR* 1.3 91.6 - - - +
426A GLU* 1.3 74.1 + - - +
428A VAL* 3.3 15.0 + - - +
429A THR* 3.2 18.4 + - - -
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Residues in contact with GLU 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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414A VAL* 3.9 27.6 - - + +
423A GLU* 3.0 36.1 + - + +
425A SER* 1.3 85.9 + - - +
427A PHE* 1.3 61.5 + - - +
429A THR* 3.7 6.6 + - - -
430A VAL* 3.3 28.6 + - + +
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Residues in contact with PHE 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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360A LEU* 4.4 1.3 - - + -
364A PHE* 3.6 28.3 - + - -
380A LEU* 3.9 23.1 - - + -
384A TYR* 3.5 40.6 - + - -
407A VAL* 3.8 32.5 - - + -
410A VAL* 3.3 36.8 - - + -
411A LEU* 4.3 6.3 - - + -
414A VAL* 4.5 3.1 - - + +
422A ILE* 4.2 5.4 - - + -
423A GLU 3.2 6.4 + - - +
424A TYR* 3.0 18.5 + - - +
426A GLU* 1.3 74.5 - - - +
428A VAL* 1.3 69.2 + - - +
430A VAL* 3.3 1.0 + - - +
431A ALA* 2.8 28.8 + - + +
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Residues in contact with VAL 428 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357A THR* 4.0 27.6 - - + +
360A LEU* 3.9 20.2 - - + -
361A THR* 3.7 25.6 - - - +
364A PHE* 3.7 24.9 - - + -
424A TYR* 2.8 25.5 + - + +
425A SER* 3.3 11.2 + - - +
427A PHE* 1.3 76.9 - - - +
429A THR* 1.3 63.6 + - - +
431A ALA* 3.5 0.5 - - - +
432A MET* 3.1 29.9 + - + +
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Residues in contact with THR 429 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357A THR* 5.8 0.9 - - - -
425A SER 3.2 12.9 + - - -
426A GLU* 3.7 9.4 - - - -
428A VAL* 1.3 77.6 - - - +
430A VAL* 1.3 55.8 + - + +
432A MET* 5.2 1.1 - - - -
433A ASP* 2.5 58.2 + - + +
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Residues in contact with VAL 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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410A VAL* 3.4 33.4 - - + +
413A ALA* 4.5 12.3 - - + -
414A VAL* 4.0 14.6 - - + -
426A GLU* 3.3 15.8 + - + +
427A PHE 3.3 1.6 + - - -
429A THR* 1.3 82.0 - - + +
431A ALA* 1.3 63.8 + - - +
433A ASP* 4.5 3.4 - - - -
434A ARG* 2.8 55.2 + - + +
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Residues in contact with ALA 431 (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 LEU* 4.4 2.9 - - + -
384A TYR* 3.4 36.0 + - + +
406A GLU* 4.8 4.3 - - - +
410A VAL* 4.1 12.3 - - + +
427A PHE* 2.8 33.1 + - + +
428A VAL 3.5 4.3 - - - +
430A VAL* 1.3 73.6 - - - +
432A MET* 1.3 62.2 + - + +
434A ARG* 4.1 1.9 - - - +
435A LYS* 3.0 29.5 + - - +
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Residues in contact with MET 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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353A SER* 4.4 13.9 - - - +
356A GLU* 3.8 37.0 - - + +
357A THR* 3.4 31.4 - - - +
360A LEU* 4.6 6.3 - - + -
384A TYR* 2.9 38.1 - - + +
387A LEU* 4.8 1.6 - - + -
428A VAL* 3.1 20.2 + - + +
429A THR* 4.1 0.9 - - - +
431A ALA* 1.3 75.5 - - + +
433A ASP* 1.3 58.1 + - - +
434A ARG 3.1 7.9 + - - -
435A LYS* 3.3 21.8 + - + +
436A THR* 3.2 28.3 + - - +
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Residues in contact with ASP 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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429A THR* 2.5 42.5 + - + +
430A VAL* 3.7 2.5 - - - +
432A MET* 1.3 71.6 - - - +
434A ARG* 1.3 54.1 + - - +
436A THR* 4.2 2.7 - - - -
440A ARG* 2.7 23.9 + - - -
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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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406A GLU* 2.5 33.5 + - - -
409A GLN* 3.8 35.5 + - - +
410A VAL* 4.2 12.3 - - - +
413A ALA* 5.7 3.1 - - - -
430A VAL* 2.8 40.2 + - + +
431A ALA 4.1 1.2 + - - +
433A ASP* 1.3 80.2 - - - +
435A LYS* 1.3 50.3 + - - +
436A THR 3.0 4.7 - - - -
437A LEU* 2.6 45.6 + - + +
440A ARG* 3.0 4.2 + - - +
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Residues in contact with LYS 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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352A THR* 6.4 0.7 - - - -
356A GLU* 3.3 27.0 + - - +
384A TYR* 4.2 14.0 - - + +
387A LEU* 5.8 0.8 - - - +
388A MET* 5.5 7.5 - - - +
406A GLU* 5.2 7.0 - - + +
431A ALA 3.0 21.6 + - - +
432A MET* 3.3 22.6 + - + +
434A ARG* 1.3 74.7 - - - +
436A THR* 1.3 58.2 + - + +
437A LEU* 3.1 4.6 + - - +
438A LEU* 4.3 7.8 + - - +
439A SER 5.5 0.2 + - - -
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Residues in contact with THR 436 (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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349A SER* 4.4 11.9 - - - +
350A LYS* 5.5 4.5 - - + +
353A SER* 3.6 33.0 - - - +
432A MET 3.2 14.2 + - - +
433A ASP* 4.0 3.1 + - - -
434A ARG 2.8 1.6 + - - -
435A LYS* 1.3 73.8 - - + +
437A LEU* 1.3 66.2 + - - +
438A LEU 3.4 0.7 - - - -
439A SER* 2.9 26.1 + - - +
440A ARG* 2.8 41.1 + - - +
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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