Contacts of the helix formed by residues 433 - 443 (chain A) in PDB entry 5H2U
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 433 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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304A GLU* 3.5 21.5 - - - +
367A LYS* 3.5 20.2 - - - +
370A VAL* 4.7 0.7 - - - -
431A ARG 3.7 0.2 + - - -
432A PRO* 1.3 77.0 - - - +
434A PHE* 1.3 58.4 + - - +
435A LYS* 3.4 10.1 - - + +
436A ALA* 3.1 24.2 + - - +
437A LEU* 3.0 26.8 + - - +
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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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297A ALA* 4.3 8.4 - - - +
300A MET* 3.5 52.0 - - + -
301A CYS* 3.2 26.8 - - - +
304A GLU* 2.9 27.3 + - - +
313A LEU* 4.3 0.2 - - + -
366A THR* 3.7 21.1 - - + -
369A ASP* 3.6 9.9 - - + -
370A VAL* 3.6 35.2 - - + -
373A PHE* 3.6 30.5 - + + -
432A PRO 4.0 0.2 + - - -
433A THR* 1.3 68.5 - - - +
435A LYS* 1.3 67.3 + - - +
437A LEU* 3.7 13.4 - - + +
438A ARG* 2.8 22.5 + - - +
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Residues in contact with LYS 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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301A CYS* 3.5 12.3 - - - -
304A GLU* 3.1 13.7 + - - +
433A THR* 3.4 12.6 - - + +
434A PHE* 1.3 76.3 - - - +
436A ALA* 1.3 56.7 + - - +
438A ARG* 3.6 18.4 + - - +
439A GLU* 3.2 36.8 + - - +
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Residues in contact with ALA 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 PRO* 4.5 8.3 - - + -
433A THR* 3.1 22.0 + - - +
435A LYS* 1.3 77.5 - - - +
437A LEU* 1.3 61.2 + - - +
439A GLU* 3.3 10.8 - - - +
440A ARG* 2.9 54.1 + - - +
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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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297A ALA* 4.9 0.9 - - + -
370A VAL* 3.9 14.4 - - + -
373A PHE* 3.7 33.0 - - + -
419A LEU* 3.4 36.8 - - + -
422A THR* 4.8 0.2 - - - +
423A CYS* 3.8 11.7 - - - -
432A PRO* 3.5 23.3 - - + -
433A THR 3.0 20.6 + - - +
434A PHE* 3.2 21.1 + - + +
436A ALA* 1.3 72.3 - - - +
438A ARG* 1.3 56.2 + - - +
440A ARG* 3.3 6.8 + - + +
441A LEU* 2.7 41.6 + - + +
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Residues in contact with ARG 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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244A HIS* 5.9 0.8 + - - -
294A TRP* 3.6 24.5 - - + +
297A ALA* 3.9 16.0 - - + +
298A GLU* 2.5 36.9 + - - +
301A CYS* 3.5 33.9 - - - +
434A PHE 2.8 20.9 + - - +
435A LYS* 3.6 20.3 + - - +
437A LEU* 1.3 72.2 - - - +
439A GLU* 1.3 55.8 + - - +
441A LEU* 3.1 1.9 + - - -
442A SER* 2.8 36.9 + - - -
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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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435A LYS* 3.2 28.3 + - - +
436A ALA* 3.3 13.4 - - - +
438A ARG* 1.3 81.5 - - - +
440A ARG* 1.3 84.9 + - - +
442A SER* 3.3 19.3 - - - -
443A SER* 3.7 7.6 + - - -
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Residues in contact with ARG 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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419A LEU* 3.8 22.0 - - + -
432A PRO* 6.1 2.4 - - - +
436A ALA* 2.9 44.7 + - - +
437A LEU* 3.3 7.8 + - - +
439A GLU* 1.3 104.4 + - - +
441A LEU* 1.3 61.4 + - - +
443A SER* 3.4 15.5 + - - -
444A PHE* 3.3 21.0 - - + -
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Residues in contact with LEU 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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290A LEU* 5.1 6.1 - - + +
293A ALA* 4.0 28.0 - - + +
294A TRP* 4.4 13.2 - - + +
297A ALA* 4.0 6.7 - - + -
373A PHE* 3.7 35.7 - - + -
377A LEU* 4.7 5.6 - - + -
416A VAL* 4.7 12.8 - - + -
419A LEU* 4.1 20.2 - - + -
437A LEU* 2.7 25.0 + - + +
438A ARG 3.8 3.4 - - - +
440A ARG* 1.3 68.4 - - - +
442A SER* 1.3 64.9 + - - +
443A SER 3.1 2.2 - - - -
444A PHE* 2.9 32.9 + - + +
445A THR* 3.4 13.6 - - - +
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Residues in contact with SER 442 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A TRP* 3.8 19.8 + - - -
438A ARG* 2.8 13.8 + - - -
439A GLU* 3.3 17.5 - - - -
440A ARG 3.3 0.2 - - - -
441A LEU* 1.3 75.8 - - - +
443A SER* 1.3 60.2 + - - +
445A THR* 2.7 26.8 + - - -
447A HIS* 4.5 9.4 + - - -
448A HIS* 3.5 13.3 - - - +
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Residues in contact with SER 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 GLU 3.7 8.0 + - - -
440A ARG* 3.4 14.6 + - - -
441A LEU 3.1 1.0 - - - -
442A SER* 1.3 77.4 - - - +
444A PHE* 1.3 68.3 + - - +
445A THR 3.4 0.4 - - - +
448A HIS* 3.6 38.4 + - - +
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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