Contacts of the helix formed by residues 433 - 443 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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304D GLU* 3.5 20.6 - - - +
367D LYS* 3.7 16.8 - - - +
370D VAL* 4.8 0.4 - - - -
432D PRO* 1.3 76.3 - - - +
434D PHE* 1.3 60.0 + - - +
435D LYS* 3.7 7.9 + - - +
436D ALA* 3.1 26.4 + - - +
437D LEU* 2.9 27.8 + - - +
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Residues in contact with PHE 434 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297D ALA* 4.3 7.9 - - - +
300D MET* 3.5 51.4 - - + -
301D CYS* 3.3 27.0 - - - +
304D GLU* 3.0 15.2 + - - +
366D THR* 3.7 29.4 - - + -
369D ASP* 3.7 9.9 - - + -
370D VAL* 3.6 32.1 - - + +
373D PHE* 3.5 31.6 - + + -
432D PRO 4.1 0.2 + - - -
433D THR* 1.3 69.4 - - - +
435D LYS* 1.3 60.2 + - - +
437D LEU* 3.6 15.8 - - + +
438D ARG* 2.8 26.2 + - - +
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Residues in contact with LYS 435 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301D CYS* 3.6 12.7 - - + -
304D GLU* 3.3 12.7 + - - +
433D THR* 3.7 9.0 - - - +
434D PHE* 1.3 76.5 - - - +
436D ALA* 1.3 56.1 + - - +
438D ARG* 3.5 21.8 + - - +
439D GLU* 3.1 36.5 + - - +
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Residues in contact with ALA 436 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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432D PRO* 4.4 9.0 - - + -
433D THR* 3.1 24.3 + - - +
435D LYS* 1.3 77.5 - - - +
437D LEU* 1.3 64.8 + - - +
439D GLU* 3.0 17.4 + - - +
440D ARG* 2.9 25.1 + - - +
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Residues in contact with LEU 437 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297D ALA* 4.7 2.9 - - + -
370D VAL* 4.0 21.8 - - + -
373D PHE* 3.7 35.0 - - + -
377D LEU* 5.8 0.9 - - + -
419D LEU* 3.7 29.2 - - + -
423D CYS* 3.8 11.7 - - - -
432D PRO* 3.6 23.3 - - + +
433D THR 2.9 16.9 + - - +
434D PHE* 3.3 24.9 + - + +
436D ALA* 1.3 75.2 - - - +
438D ARG* 1.3 57.0 + - - +
440D ARG* 3.3 4.9 + - - +
441D LEU* 2.9 37.3 + - + +
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Residues in contact with ARG 438 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244D HIS* 5.6 1.8 + - - -
294D TRP* 3.4 28.9 - - + +
297D ALA* 4.0 14.1 - - + +
298D GLU* 2.6 37.9 + - - +
301D CYS* 3.5 35.0 - - - +
434D PHE 2.8 17.7 + - - +
435D LYS* 3.6 24.6 - - - +
437D LEU* 1.3 77.8 - - - +
439D GLU* 1.3 57.7 + - - +
441D LEU* 4.6 0.9 - - - +
442D SER* 3.0 30.9 + - - -
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Residues in contact with GLU 439 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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435D LYS* 3.1 24.0 + - - +
436D ALA* 3.0 20.7 + - - +
438D ARG* 1.3 80.1 - - - +
440D ARG* 1.3 60.0 + - - +
442D SER* 3.6 15.0 - - - -
443D SER* 3.9 8.0 + - - -
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Residues in contact with ARG 440 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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415D SER* 4.2 7.8 + - - +
419D LEU* 3.8 32.5 - - + -
436D ALA 2.9 14.5 + - - +
437D LEU 3.8 3.6 - - - +
439D GLU* 1.3 73.8 - - - +
441D LEU* 1.3 66.0 + - - +
442D SER 3.3 0.7 + - - -
443D SER* 3.0 29.5 + - - -
444D PHE* 3.2 32.2 - - + -
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Residues in contact with LEU 441 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290D LEU* 4.9 6.3 - - + +
293D ALA* 4.2 22.2 - - + +
294D TRP* 4.3 12.3 - - + +
297D ALA* 4.0 11.9 - - + -
373D PHE* 3.8 34.8 - - + -
377D LEU* 4.9 4.3 - - + -
416D VAL* 4.6 19.3 - - + -
419D LEU* 4.0 20.2 - - + -
437D LEU* 2.9 21.7 + - + +
438D ARG* 4.1 2.9 - - - +
440D ARG* 1.3 74.3 - - - +
442D SER* 1.3 63.5 + - - +
443D SER 3.2 0.2 - - - -
444D PHE* 3.1 27.9 + - + +
445D THR* 3.2 16.7 + - - +
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Residues in contact with SER 442 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294D TRP* 3.9 19.2 + - - -
438D ARG* 3.0 18.9 + - - -
439D GLU* 3.6 10.1 - - - -
440D ARG 3.2 0.2 - - - -
441D LEU* 1.3 77.4 - - - +
443D SER* 1.3 60.9 + - - +
445D THR* 2.9 24.0 + - - -
447D HIS* 4.7 9.0 + - - -
448D HIS* 3.2 15.7 - - - +
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Residues in contact with SER 443 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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439D GLU 3.9 7.1 + - - -
440D ARG* 3.0 34.3 + - - -
442D SER* 1.3 78.1 - - - +
444D PHE* 1.3 61.4 + - - +
445D THR 3.4 0.6 - - - +
448D HIS* 3.3 41.3 + - - +
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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