Contacts of the helix formed by residues 372 - 382 (chain D) in PDB entry 2HVH
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 372 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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370D MET* 5.4 0.2 - - - +
371D PHE* 1.3 88.4 - - + +
373D SER* 1.3 59.8 + - - +
374D LYS* 3.8 9.2 + - - +
375D ARG* 3.2 42.1 + - + +
376D ALA* 3.6 5.2 + - - +
393D ASP* 2.9 21.0 + - - -
395D LEU* 3.7 26.3 - - + +
2I FRU 2.7 36.7 + - - +
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Residues in contact with SER 373 (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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370D MET* 4.0 19.5 - - - -
371D PHE 3.5 1.2 - - - -
372D ASP* 1.3 71.4 - - - +
374D LYS* 1.3 54.9 + - - +
376D ALA* 3.2 2.3 + - - +
377D ALA* 2.7 38.0 + - - +
387D LEU* 4.3 1.6 - - - +
390D VAL* 3.7 39.2 - - - +
393D ASP* 2.7 26.1 + - - +
482D SER* 3.8 11.8 + - - -
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Residues in contact with LYS 374 (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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327D TYR* 2.8 22.6 + - - +
372D ASP* 3.2 7.7 + - - +
373D SER* 1.3 80.4 + - - +
375D ARG* 1.3 65.4 + - - +
377D ALA* 3.1 6.6 + - - +
378D VAL* 2.8 25.7 + - + +
393D ASP* 4.4 0.2 + - - -
482D SER* 3.4 32.8 + - - +
485D LEU* 3.7 17.0 - - + -
486D ALA* 3.7 24.0 - - + +
489D GLU* 2.7 28.2 + - - +
605D ILE* 4.5 1.2 - - - +
606D PHE 2.9 21.7 + - - -
608D GLN* 4.5 10.8 - - - +
2I FRU 5.5 4.4 - - - -
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Residues in contact with ARG 375 (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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320D VAL 5.6 1.6 - - - +
322D VAL* 3.1 33.9 + - + +
323D VAL 4.7 0.6 + - - -
324D GLU 2.9 24.7 + - - -
325D GLU* 2.9 25.1 + - - +
327D TYR* 3.7 37.7 - - + +
372D ASP* 3.2 32.0 + - - +
374D LYS* 1.3 78.4 - - - +
376D ALA* 1.3 58.3 + - + +
378D VAL* 4.1 0.3 - - - -
379D ALA* 3.0 29.5 + - - +
1I GLC 3.0 16.8 + - - -
2I FRU 2.9 29.1 + - - -
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Residues in contact with ALA 376 (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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320D VAL* 3.8 30.3 - - + +
322D VAL* 5.2 0.4 - - - -
370D MET* 3.8 26.7 - - + -
372D ASP 3.6 2.8 + - - +
373D SER 3.2 7.9 + - - +
374D LYS 3.1 0.6 - - - -
375D ARG* 1.3 78.2 - - - +
377D ALA* 1.3 60.8 + - - +
379D ALA* 3.2 5.9 + - - +
380D LEU* 2.8 37.7 + - + +
387D LEU* 4.3 4.9 - - + -
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Residues in contact with ALA 377 (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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373D SER 2.7 21.9 + - - +
374D LYS* 3.6 7.9 - - - +
376D ALA* 1.3 72.4 - - - +
378D VAL* 1.3 62.4 + - - +
380D LEU* 3.9 2.5 - - - +
381D LYS* 3.1 31.9 + - - +
385D ILE 4.8 0.5 - - - +
387D LEU* 3.8 28.5 + - + +
390D VAL* 6.4 0.4 - - + -
483D SER* 6.2 1.8 - - - +
486D ALA* 4.4 12.3 - - + -
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Residues in contact with VAL 378 (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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327D TYR* 3.7 18.2 - - + -
328D HIS* 3.7 29.6 - - + +
374D LYS* 2.8 23.5 + - + +
377D ALA* 1.3 67.6 - - - +
379D ALA* 1.3 60.7 + - - +
380D LEU 3.0 2.0 - - - -
381D LYS* 2.8 24.2 + - + +
382D TRP* 3.0 22.4 + - + +
486D ALA* 3.7 37.5 - - + +
489D GLU* 3.8 16.2 - - + +
490D PHE* 4.9 6.5 - - + -
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Residues in contact with ALA 379 (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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322D VAL* 3.6 29.8 - - + -
327D TYR* 4.0 19.5 + - + +
330D ALA 4.7 5.8 - - - +
332D ILE* 4.0 11.9 - - + +
375D ARG 3.0 19.2 + - - +
376D ALA* 3.8 3.6 - - - +
378D VAL* 1.3 76.5 - - - +
380D LEU* 1.3 57.7 + - - +
382D TRP* 3.8 10.2 + - - +
383D LYS* 3.3 23.6 - - - +
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Residues in contact with LEU 380 (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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320D VAL* 4.4 18.8 - - + -
332D ILE* 3.8 22.0 - - + -
352D LEU* 4.1 23.1 - - + -
361D LEU* 4.6 9.2 - - + -
376D ALA 2.8 20.7 + - - +
377D ALA* 3.9 3.6 - - - +
379D ALA* 1.3 75.6 - - - +
381D LYS* 1.3 56.5 + - - +
382D TRP 3.1 1.6 - - - -
383D LYS* 2.7 26.3 + - + +
385D ILE* 3.1 53.4 + - + +
387D LEU* 4.1 31.4 - - + -
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Residues in contact with LYS 381 (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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377D ALA* 3.1 23.7 + - - +
378D VAL* 2.8 10.8 + - - +
380D LEU* 1.3 75.4 - - - +
382D TRP* 1.3 57.5 + - - +
383D LYS 2.9 5.4 + - - -
384D GLY* 3.0 13.4 + - - +
385D ILE 3.6 11.0 + - - +
386D GLU* 5.1 16.0 + - + +
387D LEU 6.2 0.2 - - - +
483D SER 5.4 0.4 + - - -
486D ALA* 4.1 30.1 - - - +
487D GLU* 3.9 22.9 + - - +
490D PHE* 3.6 53.9 - - + -
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Residues in contact with TRP 382 (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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327D TYR 4.6 0.7 - - - -
328D HIS* 3.0 26.9 + - + -
329D ASP* 3.2 51.6 - - + +
330D ALA 6.0 0.4 - - - +
378D VAL* 3.0 34.9 + - + +
379D ALA* 4.0 9.0 - - - +
380D LEU 3.1 0.6 - - - -
381D LYS* 1.3 74.2 - - - +
383D LYS* 1.3 64.0 + - + +
384D GLY 3.6 0.7 - - - -
490D PHE* 3.9 23.1 - + - -
596D ARG* 3.7 34.1 - - - -
603D HIS* 3.6 46.7 - + - -
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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