Contacts of the helix formed by residues 433 - 443 (chain A) in PDB entry 3C98
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 PRO 433 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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401A THR* 4.1 11.4 - - + +
431A GLN 4.5 1.3 - - - +
432A ILE* 1.3 90.3 - - + +
434A PRO* 1.3 75.7 - - + +
435A GLU* 4.3 8.1 - - + +
436A ASP* 2.9 38.3 + - - +
437A SER* 3.3 8.5 + - - -
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Residues in contact with PRO 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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432A ILE 3.6 3.5 - - - +
433A PRO* 1.3 84.2 - - + +
435A GLU* 1.3 64.5 + - + +
437A SER* 2.7 26.4 + - - +
438A GLU* 3.3 14.3 + - - +
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Residues in contact with GLU 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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433A PRO* 3.1 7.0 + - + +
434A PRO* 1.3 81.6 - - + +
436A ASP* 1.3 59.7 + - - +
438A GLU* 3.9 15.3 - - - +
439A ILE 4.6 0.2 + - - -
583A LYS* 3.0 47.9 + - + +
587A LYS* 4.4 20.0 + - - +
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Residues in contact with ASP 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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401A THR* 3.8 27.6 - - + +
402A TYR* 3.5 14.8 - - - -
405A ILE* 3.4 13.6 - - + +
432A ILE* 4.8 1.1 - - + -
433A PRO* 2.9 38.4 + - + +
435A GLU* 1.3 75.9 - - - +
437A SER* 1.3 67.8 + - - +
438A GLU 3.1 2.0 - - - -
439A ILE* 3.0 27.0 + - - +
583A LYS* 3.0 31.3 + - - +
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Residues in contact with SER 437 (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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427A ILE* 3.9 37.1 - - - +
432A ILE* 4.2 16.0 - - - +
433A PRO 3.3 5.3 + - - -
434A PRO* 2.7 29.8 + - - +
436A ASP* 1.3 77.7 - - - +
438A GLU* 1.3 62.5 + - - +
439A ILE 2.9 1.8 + - - -
440A ILE* 2.9 26.2 + - - +
441A THR* 3.9 3.9 + - - +
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Residues in contact with GLU 438 (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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434A PRO 3.3 13.2 + - - +
435A GLU* 3.9 14.1 - - - +
436A ASP 3.1 0.2 - - - -
437A SER* 1.3 80.8 + - - +
439A ILE* 1.3 55.2 + - - +
440A ILE 3.2 0.4 + - - -
441A THR* 3.3 19.2 + - - -
442A ASN* 2.8 48.7 + - - +
583A LYS* 5.5 2.7 - - - +
586A ASN* 3.4 24.9 + - - +
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Residues in contact with ILE 439 (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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402A TYR* 4.1 15.9 - - + +
405A ILE* 4.2 22.2 - - + -
409A LEU* 5.0 3.0 - - + +
436A ASP* 3.0 21.3 + - - +
437A SER 2.9 0.4 + - - -
438A GLU* 1.3 77.4 - - - +
440A ILE* 1.3 61.6 + - - +
442A ASN* 3.4 8.4 + - - +
443A MET* 3.2 20.8 + - - +
579A LEU* 3.4 43.3 - - + +
582A LEU* 3.8 27.4 - - + +
583A LYS* 3.8 27.8 - - + -
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Residues in contact with ILE 440 (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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405A ILE* 4.1 26.5 - - + -
408A ILE* 3.9 33.2 - - + -
409A LEU* 4.1 18.4 - - + -
412A ILE* 4.0 17.7 - - + -
423A LEU* 4.4 9.9 - - + -
427A ILE* 4.3 19.7 - - + -
432A ILE* 5.0 1.3 - - + -
437A SER* 2.9 20.7 + - - +
439A ILE* 1.3 76.3 - - - +
441A THR* 1.3 63.6 + - + +
443A MET* 3.2 19.1 + - - +
450A ILE* 3.8 25.2 - - + +
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Residues in contact with THR 441 (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 GLU* 5.8 1.1 - - - +
423A LEU* 3.9 28.3 - - + -
437A SER 3.9 3.5 + - - +
438A GLU* 3.3 26.6 + - - -
440A ILE* 1.3 76.9 - - + +
442A ASN* 1.3 61.2 + - - +
444A ALA* 3.1 28.1 + - - +
445A HIS* 4.5 3.2 + - - -
450A ILE* 4.5 7.0 - - + -
451A VAL* 4.9 7.6 - - + -
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Residues in contact with ASN 442 (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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438A GLU* 2.8 39.5 + - - +
439A ILE 3.7 4.7 - - - +
440A ILE 3.2 0.4 - - - -
441A THR* 1.3 74.2 + - - +
443A MET* 1.3 62.0 + - - +
444A ALA 3.0 6.4 + - - -
445A HIS* 3.2 37.1 + - - +
446A LEU* 4.4 0.2 - - - +
582A LEU* 2.9 32.5 + - + +
583A LYS 4.2 4.0 + - - -
585A LEU* 3.8 13.0 - - + +
586A ASN* 3.2 40.1 + - - +
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Residues in contact with MET 443 (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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235A ARG* 6.4 1.1 - - - -
239A PRO* 4.4 17.7 - - + -
243A VAL* 4.8 2.9 - - + -
409A LEU* 4.0 24.9 - - + -
413A PHE* 4.4 10.5 - - + -
439A ILE 3.2 9.8 + - - +
440A ILE 3.2 15.8 + - - +
441A THR 3.1 0.8 - - - -
442A ASN* 1.3 77.8 - - - +
444A ALA* 1.3 60.0 + - - +
445A HIS 3.1 0.2 - - - -
446A LEU* 3.1 36.0 + - - +
448A VAL* 3.9 14.8 - - + +
450A ILE* 3.8 17.3 - - + -
578A LEU* 4.6 16.6 - - + -
582A LEU* 3.5 30.7 - - + -
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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