Contacts of the helix formed by residues 430 - 439 (chain A) in PDB entry 3C5R
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 THR 430 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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-2A PRO 5.3 7.9 - - - -
-1A PHE 3.9 11.4 - - - +
0A THR* 3.9 19.1 - - + -
429A GLU* 1.3 76.9 - - - +
431A LEU* 1.3 63.8 + - - +
432A LEU* 3.3 12.7 + - - +
433A HIS* 2.9 35.1 + - + +
434A ILE* 3.1 24.3 + - - +
456A VAL* 4.2 25.5 - - + +
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Residues in contact with LEU 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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-1A PHE 4.8 2.4 + - - -
430A THR* 1.3 73.4 - - - +
432A LEU* 1.3 56.5 + - - +
434A ILE* 3.3 16.9 + - + +
435A ALA* 2.8 31.7 + - + +
443A SER* 6.4 0.9 - - - -
447A LEU* 4.0 31.0 - - + -
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Residues in contact with LEU 432 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430A THR* 3.1 10.8 + - - +
431A LEU* 1.3 77.0 - - - +
433A HIS* 1.3 65.4 + - - +
435A ALA* 3.4 1.3 + - - -
436A SER* 2.9 29.5 + - - +
444A VAL* 4.2 26.0 - - + +
447A LEU* 3.8 33.0 - - + +
448A LEU* 4.1 19.1 - - + -
452A SER* 4.4 12.1 - - - +
453A ASP 4.2 6.1 - - - +
454A PRO* 3.8 30.3 - - + -
456A VAL* 5.1 1.1 - - + -
464A PRO* 3.9 18.4 - - + -
480A LEU* 4.2 2.7 - - + -
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Residues in contact with HIS 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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428A GLY 4.0 6.7 - - - -
429A GLU* 3.8 15.0 - - + -
430A THR* 2.9 46.1 + - + +
432A LEU* 1.3 76.7 - - - +
434A ILE* 1.3 57.9 + - - +
436A SER* 3.0 6.3 + - - -
437A ILE* 2.8 37.2 + - + +
456A VAL* 3.4 29.0 + - + -
457A LYS 4.0 1.8 - - - -
458A ASP* 3.5 24.2 + - + -
462A TRP 2.8 29.6 + - - -
463A THR 4.0 2.5 - - - -
464A PRO* 3.6 20.0 - - + +
467A GLU* 4.6 7.0 - - + +
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Residues in contact with ILE 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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425A ASN* 3.7 25.4 - - + +
427A ARG* 5.7 0.7 - - - +
429A GLU* 4.0 17.7 - - + +
430A THR 3.1 16.0 + - - +
431A LEU* 3.7 20.0 - - + +
433A HIS* 1.3 81.1 - - - +
435A ALA* 1.3 61.5 + - - +
437A ILE* 3.4 10.8 + - + +
438A LYS* 3.1 48.9 + - + +
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Residues in contact with ALA 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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431A LEU* 2.8 20.9 + - + +
432A LEU 4.0 1.8 - - - +
434A ILE* 1.3 74.4 - - - +
436A SER* 1.3 57.0 + - - +
438A LYS* 4.6 2.5 - - - -
439A GLY* 3.0 5.7 + - - -
440A ASP* 2.9 36.1 + - + +
443A SER* 3.6 31.4 - - - -
444A VAL* 3.7 17.5 - - + +
447A LEU* 4.6 4.7 - - + -
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Residues in contact with SER 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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432A LEU* 2.9 23.8 + - - +
433A HIS 3.0 4.5 + - - -
435A ALA* 1.3 73.9 - - - +
437A ILE* 1.3 66.5 + - - +
439A GLY* 3.4 1.6 + - - -
444A VAL* 4.0 5.2 - - - +
464A PRO* 3.4 38.6 + - - +
467A GLU* 4.4 3.8 - - - -
468A ALA* 3.9 8.9 - - - +
473A HIS* 3.1 20.6 - - - -
476A VAL* 3.8 22.2 - - - +
480A LEU* 3.8 3.5 - - - +
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Residues in contact with ILE 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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429A GLU* 4.7 20.0 - - - +
433A HIS* 2.8 25.9 + - + +
434A ILE* 3.6 12.3 - - + +
436A SER* 1.3 75.7 - - - +
438A LYS* 1.3 61.0 + - + +
467A GLU* 3.5 36.8 - - + +
471A HIS* 3.6 33.9 - - + +
473A HIS* 2.9 20.4 + - - -
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Residues in contact with LYS 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 ILE* 3.1 35.9 + - + +
435A ALA* 4.1 4.9 - - - +
437A ILE* 1.3 81.3 - - + +
439A GLY* 1.3 61.9 + - - +
440A ASP* 4.2 13.2 - - + +
473A HIS* 3.5 9.5 + - - -
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Residues in contact with GLY 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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435A ALA 3.0 6.5 + - - -
436A SER 3.4 1.6 + - - -
437A ILE 3.3 4.0 - - - -
438A LYS* 1.3 78.9 - - - +
440A ASP* 1.3 59.6 + - - +
441A ILE* 3.1 17.9 + - - +
473A HIS* 3.3 29.6 + - - +
476A VAL* 3.9 11.8 - - - +
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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