Contacts of the helix formed by residues 282 - 288 (chain D) in PDB entry 3HB0
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 PHE 282 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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276D ASP* 4.5 1.3 - - - +
277D GLU* 3.1 6.9 + - - -
280D ILE* 4.0 15.3 + - + +
281D ILE* 1.3 75.3 - - - +
283D HIS* 1.3 105.8 + + - +
284D SER 3.2 1.1 - - - -
285D LEU* 3.0 25.3 + - + +
286D LEU* 3.7 16.4 + - + +
305D GLY* 3.6 24.5 - - - -
308D MET* 4.1 8.7 - - + -
309D GLU* 3.6 28.7 - - + -
312D ILE* 3.6 22.7 - - + -
313D PHE* 5.2 7.4 - + - -
457D LYS* 3.8 18.4 - - + -
461D TYR* 3.3 17.0 - - - +
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Residues in contact with HIS 283 (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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276D ASP* 3.9 14.4 + - + +
277D GLU* 3.6 13.8 + - - +
282D PHE* 1.3 99.0 - + - +
284D SER* 1.3 58.4 + - - +
285D LEU 3.0 0.2 - - - -
286D LEU* 2.9 32.7 + - + +
287D THR* 3.2 22.5 + - + +
309D GLU* 5.9 0.6 + - - -
313D PHE* 6.4 1.3 - + - -
449D THR* 4.6 2.9 - - + -
457D LYS* 3.4 30.2 + - - -
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Residues in contact with SER 284 (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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277D GLU* 2.8 37.1 + - - +
281D ILE* 3.4 14.9 - - - +
283D HIS* 1.3 77.0 - - - +
285D LEU* 1.3 58.0 + - - +
287D THR* 3.7 9.9 - - - -
288D GLY* 3.4 11.8 + - - -
289D THR* 3.6 14.8 + - - -
290D PHE* 3.2 39.9 + - - +
293D ARG* 5.8 3.6 - - - -
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Residues in contact with LEU 285 (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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281D ILE* 3.9 25.1 - - + +
282D PHE* 3.0 16.9 + - + +
284D SER* 1.3 79.0 - - - +
286D LEU* 1.3 59.9 + - - +
288D GLY* 4.1 3.2 + - - -
290D PHE* 3.7 28.9 - - + -
301D SER* 3.5 19.9 - - - +
302D VAL* 3.1 29.3 + - - +
304D ILE* 4.3 4.7 - - + -
305D GLY* 3.8 24.7 - - - +
308D MET* 5.8 1.1 - - + -
417D LEU* 3.8 26.7 - - + -
420D LEU* 4.0 17.3 - - + -
461D TYR* 5.1 0.7 - - - +
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Residues in contact with LEU 286 (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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282D PHE* 4.0 28.9 - - + +
283D HIS* 2.9 22.4 + - + +
285D LEU* 1.3 80.6 - - - +
287D THR* 1.3 63.0 + - + +
288D GLY 3.3 1.1 + - - -
302D VAL* 4.2 14.1 - - + +
305D GLY* 3.5 30.5 - - - -
306D LEU* 3.6 24.5 - - + +
309D GLU* 3.6 23.1 - - - +
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Residues in contact with THR 287 (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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283D HIS* 3.4 18.6 - - + +
284D SER* 3.7 6.8 + - - -
286D LEU* 1.3 79.4 - - + +
288D GLY* 1.3 60.9 + - - +
289D THR* 3.2 35.5 + - - +
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Residues in contact with GLY 288 (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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284D SER 3.4 5.8 + - - -
285D LEU 4.1 4.4 + - - -
286D LEU 3.3 4.9 + - - -
287D THR* 1.3 78.0 + - - +
289D THR* 1.3 62.3 + - - +
290D PHE 3.3 2.2 - - - -
291D ALA* 3.6 10.3 + - - +
292D SER* 3.3 22.9 + - - -
298D THR* 5.5 4.6 - - - +
301D SER* 6.3 1.3 - - - -
302D VAL* 5.5 5.6 - - - -
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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