Contacts of the helix formed by residues 354 - 363 (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 354 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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306D ARG* 5.7 1.7 - - - +
307D VAL* 3.9 34.5 + - + +
350D THR* 3.1 14.5 + - + +
351D ALA 3.0 7.9 + - - +
353D ALA* 1.3 77.9 - - - +
355D PRO* 1.3 73.0 - - - +
356D GLN* 2.9 35.5 + - - +
357D PHE* 3.1 9.8 + - + -
358D VAL* 3.2 23.6 + - - +
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Residues in contact with PRO 355 (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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353D ALA 3.5 8.5 - - - +
354D ASP* 1.3 93.3 - - - +
356D GLN* 1.3 71.5 + - - +
358D VAL* 3.6 7.6 + - + +
359D ALA* 3.1 27.0 + - - +
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Residues in contact with GLN 356 (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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307D VAL* 5.1 2.7 - - + -
309D GLU* 5.4 5.8 - - - +
312D LEU* 3.7 24.7 - - + +
354D ASP* 2.9 14.6 + - - +
355D PRO* 1.3 93.4 - - - +
357D PHE* 1.3 61.5 + - - +
359D ALA* 3.5 5.4 + - - +
360D TRP* 2.9 27.9 + - - +
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Residues in contact with PHE 357 (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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307D VAL* 4.3 12.1 - - + +
311D MET* 5.6 3.1 - - + -
312D LEU* 4.1 17.2 - - + +
318D LEU* 4.5 4.7 - - + -
335D ILE* 4.0 30.3 - - + -
337D VAL* 4.3 7.6 - - + -
346D LEU* 3.7 25.1 - - + -
351D ALA* 3.4 37.0 - - + +
352D LEU* 4.3 2.0 - - + -
354D ASP* 3.1 10.9 + - - +
356D GLN* 1.3 75.7 - - - +
358D VAL* 1.3 57.6 + - - +
360D TRP* 3.1 29.5 + + - +
361D LEU* 2.9 60.8 + - + +
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Residues in contact with VAL 358 (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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351D ALA 4.3 1.3 - - - +
352D LEU* 3.4 26.9 - - - +
353D ALA 5.0 0.9 - - - -
354D ASP 3.2 18.5 + - - +
355D PRO* 3.9 7.9 - - + +
357D PHE* 1.3 76.1 - - - +
359D ALA* 1.3 62.1 + - - +
361D LEU* 3.3 12.5 + - + +
362D GLY* 3.1 18.0 + - - -
384D GLY 6.0 0.2 - - - +
385D ILE* 4.5 29.2 - - + -
386D GLU 4.5 3.1 - - - +
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Residues in contact with ALA 359 (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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355D PRO 3.1 17.7 + - - +
356D GLN* 3.7 7.4 - - - +
358D VAL* 1.3 73.3 - - - +
360D TRP* 1.3 67.2 + - - +
362D GLY* 2.9 4.4 + - - -
363D ASP* 2.9 26.1 + - - +
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Residues in contact with TRP 360 (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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311D MET 4.5 9.0 - - - -
312D LEU* 3.6 35.8 - - + -
313D ALA 3.0 21.3 + - - -
316D ALA* 3.9 27.1 - - + -
318D LEU* 4.0 22.7 - - + -
337D VAL* 4.7 5.8 - - + -
356D GLN 2.9 15.4 + - - +
357D PHE* 3.2 28.7 - + - +
359D ALA* 1.3 78.7 - - - +
361D LEU* 1.3 90.9 + - + +
363D ASP* 3.5 10.3 + - - +
366D LYS* 3.7 22.7 - - + +
367D LYS 5.1 2.5 - - - -
368D LYS* 2.8 50.6 + - + -
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Residues in contact with LEU 361 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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318D LEU* 3.9 19.1 - - + -
320D VAL* 5.4 2.0 - - + -
352D LEU* 4.4 10.5 - - + -
357D PHE* 2.9 42.4 + - + +
358D VAL* 3.5 11.0 - - + +
359D ALA 3.2 0.2 - - - -
360D TRP* 1.3 99.3 - - + +
362D GLY* 1.3 52.5 - - - +
368D LYS* 3.3 4.5 + - - +
380D LEU* 4.6 11.0 - - + -
385D ILE* 3.8 23.8 - - + -
386D GLU 3.6 9.4 - - - +
387D LEU* 3.5 13.2 - - + +
388D CYS 2.8 39.0 + - - +
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Residues in contact with GLY 362 (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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358D VAL 3.1 9.1 + - - -
359D ALA* 2.9 8.6 + - - -
361D LEU* 1.3 75.3 - - - +
363D ASP* 1.3 63.3 + - - +
364D GLU 3.5 2.4 + - - -
386D GLU* 3.5 20.8 + - - +
388D CYS* 3.6 19.3 - - - +
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Residues in contact with ASP 363 (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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359D ALA 2.9 15.0 + - - +
360D TRP* 3.9 2.0 - - - +
361D LEU 3.4 0.8 - - - -
362D GLY* 1.3 76.9 - - - +
364D GLU* 1.3 62.0 + - - +
365D THR* 2.7 37.1 + - - +
366D LYS* 3.2 35.8 + - + +
368D LYS* 3.0 22.9 + - - -
388D CYS* 4.2 0.9 - - - -
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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