Contacts of the helix formed by residues 434 - 445 (chain A) in PDB entry 6IY6
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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432A ILE* 3.4 2.5 - - + +
433A HIS* 1.3 80.3 + - + +
435A PRO* 1.4 76.3 - - - +
436A GLN* 3.5 13.1 + - - +
437A LEU* 3.0 30.2 + - + +
438A LEU* 3.2 23.3 + - - +
459A PHE* 5.1 0.2 - - - -
34B MET* 3.5 39.3 - - + +
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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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433A HIS 3.7 6.9 - - - +
434A ASP* 1.4 93.0 - - - +
436A GLN* 1.3 55.1 + - - +
438A LEU* 3.4 7.0 + - + +
439A THR* 2.6 34.1 + - - -
456A ILE* 4.0 12.0 - - + +
459A PHE* 3.8 9.2 - - + +
460A ARG* 3.6 61.0 - - + +
147B LEU 6.1 0.4 - - - +
149B GLU* 4.7 3.6 - - - +
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Residues in contact with GLN 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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434A ASP* 3.3 11.3 + - - +
435A PRO* 1.3 78.3 - - - +
437A LEU* 1.3 56.2 + - - +
439A THR* 3.0 10.9 + - - -
440A GLU* 2.9 47.7 + - + +
460A ARG* 5.3 1.3 - - - +
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Residues in contact with LEU 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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404A MET* 4.0 17.9 - - - -
405A PRO* 4.4 12.3 - - + -
432A ILE* 3.9 15.5 - - + -
434A ASP* 3.0 17.7 + - - +
435A PRO 3.5 0.2 - - - -
436A GLN* 1.3 73.9 - - - +
438A LEU* 1.3 56.1 + - - +
440A GLU* 3.3 23.6 + - + +
441A ARG* 3.0 44.2 + - + +
34B MET* 3.6 33.0 - - + -
36B GLN* 4.6 7.4 - - - +
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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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401A PHE* 3.7 27.7 - - + -
402A TYR* 4.0 17.7 - - + -
432A ILE* 3.4 25.9 - - + +
434A ASP 3.2 19.3 + - - +
435A PRO* 3.4 6.1 - - + +
437A LEU* 1.3 76.0 - - - +
439A THR* 1.3 57.2 + - - +
441A ARG* 3.8 2.1 + - - +
442A ALA* 3.2 25.8 + - - +
455A TYR* 3.8 15.7 - - + +
456A ILE* 4.3 16.8 - - + -
459A PHE* 3.6 38.8 - - + -
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Residues in contact with THR 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 PRO 2.6 23.1 + - - -
436A GLN* 3.0 9.1 + - - -
438A LEU* 1.3 74.2 - - - +
440A GLU* 1.3 59.1 + - - +
442A ALA* 3.2 8.9 + - - +
443A LEU* 3.0 37.0 + - + +
449A LEU* 3.4 37.5 - - + -
456A ILE* 3.7 21.9 - - + +
460A ARG* 4.7 5.5 + - - +
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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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436A GLN* 2.9 44.7 + - + +
437A LEU* 3.5 26.0 + - + +
439A THR* 1.3 76.3 - - - +
441A ARG* 1.3 52.4 + - + +
443A LEU* 3.1 15.5 + - + +
444A HIS* 2.9 31.3 + - - +
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Residues in contact with ARG 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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396A LEU* 3.9 43.6 + - - +
397A ALA* 5.5 1.4 - - - +
399A ARG 5.1 0.6 + - - -
400A PRO 5.1 0.8 + - - -
401A PHE* 3.4 24.6 + - - +
405A PRO* 4.3 14.6 - - + +
432A ILE* 3.8 17.5 - - + -
437A LEU* 3.0 29.8 + - + +
438A LEU 4.0 4.5 - - - +
440A GLU* 1.3 74.9 - - - +
442A ALA* 1.3 57.2 + - - +
444A HIS* 3.4 43.7 + - - +
445A HIS* 3.1 65.3 + - - +
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Residues in contact with ALA 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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401A PHE* 4.1 5.6 - - + +
438A LEU 3.2 15.9 + - - +
439A THR* 3.2 12.1 + - - +
441A ARG* 1.3 76.4 - - - +
443A LEU* 1.3 52.7 + - - +
445A HIS 3.5 0.5 + - - -
446A GLY 3.1 6.8 + - - -
447A ILE* 2.8 50.3 + - + +
449A LEU* 3.8 16.8 - - + -
452A ILE* 3.9 20.0 - - + -
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Residues in contact with LEU 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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439A THR* 3.0 23.8 + - + +
440A GLU* 3.1 11.9 + - + +
442A ALA* 1.3 72.3 - - - +
444A HIS* 1.3 61.5 + - - +
445A HIS 3.2 0.2 - - - -
446A GLY* 3.0 20.1 + - - +
447A ILE 4.2 7.6 - - - +
449A LEU* 3.7 35.4 - - + -
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Residues in contact with HIS 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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397A ALA* 6.0 5.8 - - + -
440A GLU 2.9 12.7 + - - +
441A ARG* 3.4 50.3 + - - +
443A LEU* 1.3 76.6 - - - +
445A HIS* 1.3 61.8 + + - +
446A GLY 3.3 0.8 + - - -
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Residues in contact with HIS 445 (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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397A ALA 4.6 10.6 + - - -
399A ARG 3.4 24.4 + - - -
400A PRO* 4.2 2.4 - - + +
401A PHE* 3.8 27.1 + - + +
441A ARG* 3.1 51.3 + - - +
442A ALA 3.5 4.5 + - - +
443A LEU 3.2 0.2 - - - -
444A HIS* 1.3 81.7 + - - +
446A GLY* 1.3 62.5 + - - +
447A ILE* 3.5 12.1 + - + +
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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