Contacts of the helix formed by residues 434 - 444 (chain A) in PDB entry 3K5M
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 ASP 434 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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377A TYR* 2.7 23.6 + - - -
432A LEU 3.2 7.0 + - - +
433A ILE* 1.3 81.0 - - - +
435A PRO* 1.3 67.8 - - - +
436A VAL* 3.1 1.9 + - - +
437A GLY* 2.7 24.6 + - - +
438A LEU* 2.8 31.0 + - - +
459A PHE* 3.7 2.8 - - - -
464A HIS* 3.3 15.7 - - + -
465A CYS 3.2 20.1 + - - -
466A LEU* 2.8 22.2 + - - +
467A PRO* 4.0 2.7 - - + -
515A LEU* 3.5 5.4 - - - +
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Residues in contact with PRO 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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73A PHE* 3.8 20.4 - - + -
373A PHE* 4.2 2.9 - - + -
377A TYR* 3.1 22.0 - - + +
434A ASP* 1.3 97.6 - - - +
436A VAL* 1.3 60.6 + - - +
438A LEU* 3.4 4.5 + - + +
439A VAL* 3.4 22.9 + - - +
466A LEU* 4.5 9.6 - - + -
503A LEU* 4.1 24.2 - - + -
510A PHE* 4.1 15.0 - - + +
515A LEU* 3.8 18.8 - - + -
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Residues in contact with VAL 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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73A PHE* 4.0 18.8 - - + -
377A TYR* 2.9 17.5 + - + +
381A MET* 4.0 23.6 - - + -
384A ALA* 4.3 6.7 - - + -
386A TYR* 4.1 26.0 - - + -
434A ASP* 3.3 8.5 - - - +
435A PRO* 1.3 73.0 - - - +
437A GLY* 1.3 68.0 + - - +
439A VAL* 3.1 7.8 + - - +
440A GLU* 3.0 20.5 + - + +
463A LYS* 4.0 30.1 - - + +
464A HIS* 4.6 1.3 - - - -
465A CYS* 4.4 5.6 - - - -
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Residues in contact with GLY 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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432A LEU 5.3 0.2 - - - -
434A ASP* 2.7 25.8 + - - -
436A VAL* 1.3 72.2 - - - +
438A LEU* 1.3 52.1 + - - +
441A GLY* 2.5 31.4 + - - -
459A PHE* 4.0 3.8 - - - -
460A SER* 2.9 22.4 + - - -
463A LYS 3.3 21.1 - - - -
464A HIS* 4.6 1.6 - - - -
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Residues in contact with LEU 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 ASP 2.8 17.5 + - - +
435A PRO 3.6 5.8 - - - +
436A VAL 3.1 0.2 - - - -
437A GLY* 1.3 76.4 - - - +
439A VAL* 1.3 67.2 + - + +
442A MET* 2.9 52.2 + - + +
457A ALA* 4.2 6.7 - - + -
458A TRP 3.2 24.5 - - - +
459A PHE* 3.7 13.4 - - + -
512A ASP* 3.8 18.2 - - + +
514A ARG* 3.8 32.8 - - + +
515A LEU* 4.1 15.7 - - + -
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Residues in contact with VAL 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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73A PHE* 3.4 53.6 - - + +
74A HIS 5.4 0.2 - - - -
75A ARG* 3.8 15.1 - - + -
386A TYR* 3.7 29.2 - - + +
435A PRO 3.5 14.4 - - - +
436A VAL* 3.1 8.1 + - - +
438A LEU* 1.3 78.8 - - + +
440A GLU* 1.3 64.1 + - - +
442A MET* 3.5 5.6 + - - +
443A ALA* 3.3 18.7 + - - +
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Residues in contact with GLU 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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75A ARG* 5.9 1.1 - - - -
386A TYR* 2.9 30.8 + - + +
436A VAL 3.0 15.6 + - - +
439A VAL* 1.3 74.7 - - - +
441A GLY* 1.3 65.9 + - - +
443A ALA* 3.3 11.7 + - - +
444A GLN* 3.3 28.2 + - - +
450A SER* 4.6 0.2 + - - -
460A SER* 3.4 22.0 + - - -
463A LYS* 3.9 36.0 + - + +
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Residues in contact with GLY 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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437A GLY 2.5 18.6 + - - -
440A GLU* 1.3 73.4 - - - +
442A MET* 1.3 55.6 + - - +
444A GLN 2.9 30.5 + - - +
445A PRO* 3.1 4.7 - - - +
450A SER* 3.4 18.2 - - - -
458A TRP* 3.2 26.1 - - - +
460A SER 3.7 2.6 - - - +
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Residues in contact with MET 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 LEU* 2.9 39.5 + - + +
439A VAL* 4.0 5.8 - - - +
441A GLY* 1.3 71.4 - - - +
443A ALA* 1.3 60.6 + - - +
445A PRO* 3.3 17.9 - - + +
456A ASP* 3.5 20.4 - - + +
457A ALA* 4.1 1.3 - - - -
458A TRP* 3.4 38.4 - - + -
514A ARG* 4.1 21.8 - - - +
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Residues in contact with ALA 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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75A ARG* 3.5 41.0 + - - +
439A VAL 3.3 9.7 + - - +
440A GLU* 3.5 15.0 - - - +
441A GLY 3.2 0.8 - - - -
442A MET* 1.3 78.0 - - - +
444A GLN* 1.3 66.6 + - + +
445A PRO* 3.4 6.6 - - - +
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Residues in contact with GLN 444 (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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440A GLU* 3.3 18.4 + - - +
441A GLY 2.9 10.4 + - - +
443A ALA* 1.3 85.4 - - + +
445A PRO* 1.3 59.0 - - - +
446A ASP* 2.8 21.4 + - - +
449A HIS* 3.4 49.5 + - + +
450A SER* 3.0 14.6 + - - +
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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