Contacts of the helix formed by residues 431 - 441 (chain A) in PDB entry 5HAN
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 HIS 431 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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413A GLN* 3.3 33.4 - - + +
416A GLN* 4.9 4.6 + - - -
420A GLN* 5.9 0.4 + - - -
427A PHE* 2.8 68.1 + + + +
428A ALA 3.0 11.0 + - - +
429A LYS 3.6 0.4 - - - -
430A ASP* 1.3 93.0 + - + +
432A ARG* 1.3 60.3 + - - +
433A GLU 3.4 2.0 - - - -
434A PHE* 3.6 3.3 + - + +
435A ALA 3.0 21.7 + - - -
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Residues in contact with ARG 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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402A ASP* 4.9 4.9 + - - +
428A ALA 4.9 0.2 - - - -
430A ASP 4.1 2.0 + - - -
431A HIS* 1.3 71.6 - - - +
433A GLU* 1.3 72.6 + - + +
435A ALA* 3.2 9.1 + - - +
436A ARG* 2.8 76.1 + - + +
439A GLU* 5.4 0.8 + - - -
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Residues in contact with GLU 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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400A HIS* 2.9 28.0 + - - -
402A ASP* 5.9 0.2 - - - -
406A ALA* 3.7 30.3 - - + +
409A LYS* 3.7 40.0 + - + +
410A SER* 3.5 6.5 - - - +
413A GLN* 3.0 22.1 + - - +
431A HIS* 5.0 0.2 - - - -
432A ARG* 1.3 89.7 + - + +
434A PHE* 1.3 64.0 + - - +
436A ARG* 3.2 7.0 + - - -
437A ALA 3.2 1.9 + - - -
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Residues in contact with PHE 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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374A ALA* 3.4 42.8 - - + -
375A LEU* 4.4 7.4 - - + -
378A PRO* 5.2 3.6 - - + -
410A SER* 3.8 14.1 - - - +
413A GLN* 2.9 27.0 + - + +
414A ALA* 3.9 12.1 - - + -
417A CYS* 4.6 2.5 - - + -
424A PRO* 3.3 39.7 - - + -
427A PHE* 3.7 26.2 - + - -
428A ALA* 3.7 15.3 - - + -
431A HIS* 3.8 6.7 - - + +
432A ARG 3.3 0.2 - - - -
433A GLU* 1.3 74.4 - - - +
435A ALA* 1.3 62.0 + - - +
437A ALA* 3.2 16.3 + - - +
438A PHE* 3.3 26.4 - + - -
449A TYR* 5.3 0.7 - - - -
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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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428A ALA* 3.3 22.0 - - + +
431A HIS 3.0 18.2 + - - +
432A ARG* 3.2 10.3 + - + +
434A PHE* 1.3 78.8 - - - +
436A ARG* 1.3 61.6 + - + +
438A PHE* 3.4 29.0 - - - +
439A GLU* 3.5 11.1 - - - +
456A LEU* 4.3 11.1 - - + +
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Residues in contact with ARG 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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400A HIS* 3.7 14.1 - - + -
401A VAL* 3.6 26.0 - - + +
402A ASP* 3.0 42.6 + - - +
432A ARG* 2.8 63.5 + - + +
433A GLU* 3.2 0.6 + - - -
435A ALA* 1.3 70.5 - - + +
437A ALA* 1.4 58.2 + - - +
438A PHE 3.2 2.2 - - - -
439A GLU* 2.9 37.9 + - - +
440A SER* 2.9 28.4 + - - -
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Residues in contact with ALA 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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374A ALA* 3.9 25.6 - - + -
375A LEU* 3.7 10.7 - - + +
400A HIS* 4.0 11.9 - - + -
410A SER* 4.1 1.3 - - - +
433A GLU 3.2 9.4 + - - +
434A PHE 3.2 14.3 + - - +
436A ARG* 1.4 74.4 - - - +
438A PHE* 1.4 58.6 + - - +
440A SER* 3.9 8.3 - - - -
441A PHE* 3.0 42.7 + - + -
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Residues in contact with PHE 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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375A LEU* 3.3 24.7 - - + -
424A PRO 4.2 11.2 - - - -
425A VAL* 3.9 13.9 - - + -
428A ALA* 3.9 15.3 - - + -
434A PHE* 3.3 25.6 - + - -
435A ALA* 3.4 13.7 - - - +
436A ARG 3.2 0.2 - - - -
437A ALA* 1.4 77.6 - - - +
439A GLU* 1.3 56.8 + - - +
441A PHE 3.3 1.7 - - - +
442A PRO* 3.3 29.8 - - - +
445A ALA* 3.6 15.5 - - + +
449A TYR* 3.6 36.1 - + + -
452A TRP* 3.7 40.9 - + + -
456A LEU* 4.0 9.6 - - + -
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Residues in contact with GLU 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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401A VAL* 5.4 5.8 - - + +
432A ARG* 5.4 0.9 + - - -
435A ALA* 3.5 18.6 - - - +
436A ARG* 2.9 49.4 + - - +
438A PHE* 1.3 73.5 - - - +
440A SER* 1.3 62.2 + - - +
441A PHE 3.4 0.2 - - - -
442A PRO* 3.5 13.5 - - - +
452A TRP* 3.9 25.9 - - + -
453A ARG* 5.7 1.3 - - - +
456A LEU* 5.8 3.1 - - - +
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Residues in contact with SER 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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399A GLY 3.8 18.2 - - - +
400A HIS* 3.5 6.1 - - - -
401A VAL* 2.9 31.9 + - - +
436A ARG 2.9 19.3 + - - -
437A ALA* 3.5 7.9 - - - -
438A PHE 3.3 0.4 - - - -
439A GLU* 1.3 80.3 - - - +
441A PHE* 1.4 80.3 + - - +
442A PRO* 3.5 5.5 - - - +
56B VAL* 5.4 1.4 - - - +
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Residues in contact with PHE 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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373A ASN* 3.8 28.7 - - + +
374A ALA 5.5 0.2 - - - -
375A LEU* 3.5 6.2 - - + +
395A GLY 3.5 25.4 - - - -
396A GLY* 3.7 22.7 - - - -
399A GLY 3.8 20.2 - - - -
400A HIS* 4.8 2.2 - + + -
437A ALA* 3.0 31.9 + - + +
438A PHE 3.3 5.7 - - - +
440A SER* 1.4 92.6 - - - +
442A PRO* 1.3 60.9 - - - +
443A GLN* 3.3 5.4 - - - -
444A ASP* 3.2 19.9 + - + +
445A ALA 3.0 21.5 + - - -
56B VAL* 3.9 27.4 - - + -
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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