Contacts of the helix formed by residues 280 - 287 (chain G) in PDB entry 4HY0
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 ASN 280 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278G SER 3.4 5.3 + - - +
279G VAL* 1.3 69.0 - - - +
281G LYS* 1.3 65.1 + - - +
282G GLU* 3.0 34.0 + - - +
283G GLN* 2.9 58.3 + - - +
284G LEU* 3.1 20.6 + - - +
314G GLU 5.7 0.6 + - - -
316G PRO* 4.8 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 281 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269G ILE* 3.9 11.3 + - + +
272G PHE* 3.6 56.0 + - + +
273G GLY* 4.7 5.1 - - - +
274G THR 5.6 0.2 - - - +
275G TRP* 4.3 14.8 - - + -
279G VAL 3.2 4.8 + - - -
280G ASN* 1.3 72.4 + - - +
282G GLU* 1.3 81.5 + - + +
284G LEU* 3.3 13.1 + - - +
285G ALA* 3.1 24.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 282 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265G TYR* 3.9 12.8 + - - +
269G ILE* 4.0 13.9 - - + -
280G ASN* 3.0 24.3 + - - +
281G LYS* 1.3 101.6 - - + +
283G GLN* 1.3 66.8 + - - +
284G LEU 3.3 0.2 + - - -
285G ALA* 3.3 3.6 + - - +
286G ARG* 2.9 33.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 283 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B PRO* 6.1 1.0 - - - +
280G ASN* 2.9 41.2 + - - +
282G GLU* 1.3 76.5 - - + +
284G LEU* 1.3 57.9 + - - +
286G ARG* 3.3 12.3 + - - +
287G ALA* 2.8 31.0 + - - +
314G GLU 4.7 5.5 + - - -
315G ASP* 3.8 17.9 - - - +
316G PRO* 3.7 23.2 - - + +
317G TRP* 5.2 4.9 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 284 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272G PHE* 3.9 20.9 - - + -
275G TRP* 3.7 34.1 - - + +
279G VAL* 3.7 16.2 - - + +
280G ASN 3.1 16.8 + - - +
281G LYS* 3.5 9.2 - - - +
282G GLU 3.2 0.2 - - - -
283G GLN* 1.3 76.5 - - - +
285G ALA* 1.3 60.1 + - - +
287G ALA* 3.3 3.5 + - - +
288G GLY 3.2 4.9 + - - -
289G PHE* 2.9 41.7 + - + +
298G VAL* 4.7 2.9 - - + -
310G TRP* 3.7 31.6 - - + -
316G PRO* 3.7 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 285 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265G TYR* 3.4 13.2 - - + -
268G ARG* 3.0 34.3 + - + +
269G ILE* 3.4 36.3 - - + +
272G PHE* 4.6 2.0 - - + -
281G LYS 3.1 8.0 + - - +
282G GLU 3.8 0.2 - - - +
284G LEU* 1.3 73.6 - - - +
286G ARG* 1.3 61.9 + - - +
288G GLY 2.9 15.8 + - - -
289G PHE 3.5 13.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 286 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265G TYR* 3.5 22.5 + - + -
282G GLU* 2.9 26.4 + - - +
283G GLN* 3.5 11.2 - - - +
285G ALA* 1.3 75.0 - - - +
287G ALA* 1.3 57.5 + - - +
317G TRP* 3.4 19.7 - - + +
329G TYR* 2.8 25.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 287 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283G GLN 2.8 17.9 + - - +
284G LEU 3.6 5.6 - - - +
285G ALA 3.1 0.4 - - - -
286G ARG* 1.3 75.4 - - - +
288G GLY* 1.3 57.0 + - - +
289G PHE* 3.6 10.3 - - + -
316G PRO* 3.8 22.4 - - + -
317G TRP* 3.7 31.8 - - + +
320G HIS* 3.2 22.5 + - - +
329G TYR* 3.5 11.3 - - - -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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