Contacts of the helix formed by residues 252 - 262 (chain G) in PDB entry 1QZW
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 LYS 252 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37G SER* 2.6 30.9 - - - +
38G ASP* 2.9 31.4 - - + +
220G ALA 3.8 7.9 - - - +
221G SER* 4.7 8.0 - - - +
250G THR* 3.1 47.4 + - + +
251G ALA* 1.3 86.4 - - - +
253G GLY* 1.3 66.5 + - - +
254G GLY 2.9 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 253 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1G MET* 6.0 1.1 - - - +
38G ASP* 4.1 1.0 - - - +
220G ALA* 3.4 25.2 - - - +
247G MET* 4.9 9.2 - - - -
250G THR* 4.6 0.4 - - - -
251G ALA 3.8 1.8 - - - +
252G LYS* 1.3 75.5 - - - +
254G GLY* 1.3 70.3 + - - -
255G GLY 2.9 0.5 + - - -
256G ALA* 2.4 23.7 + - - +
257G LEU* 4.1 7.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 254 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37G SER* 5.7 1.0 - - - -
39G VAL* 3.9 11.9 - - - -
82G PHE* 4.9 5.2 - - - -
252G LYS 2.9 7.2 + - - -
253G GLY* 1.3 69.2 - - - -
255G GLY* 1.3 54.1 + - - -
256G ALA 2.4 16.5 + - - -
257G LEU* 2.6 37.6 + - - +
258G SER* 2.6 14.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 255 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38G ASP* 2.9 19.3 - - - -
39G VAL* 3.0 23.2 - - - +
40G ASN 3.8 0.2 - - - -
224G GLN* 3.0 19.9 - - - -
253G GLY 2.9 2.0 + - - -
254G GLY* 1.3 70.7 - - - -
256G ALA* 1.3 66.8 + - - +
258G SER* 2.7 12.7 + - - -
259G ALA 2.6 17.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 256 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38G ASP* 4.0 0.2 + - - -
218G ILE* 6.1 1.6 - - + -
219G ASP 5.2 0.4 - - - +
220G ALA* 3.6 24.2 - - + -
222G ILE* 5.9 0.2 - - + -
223G GLY* 3.2 28.0 - - - +
224G GLN 3.0 3.6 - - - +
226G ALA* 5.4 2.4 - - + +
244G ILE* 4.5 10.5 - - + -
247G MET* 6.4 0.2 - - + -
253G GLY 2.4 18.9 + - - +
254G GLY 2.4 6.3 + - - -
255G GLY* 1.3 76.6 - - - +
257G LEU* 1.3 56.5 + - + +
259G ALA* 3.1 6.4 + - - +
260G VAL* 2.8 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 257 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82G PHE* 3.0 41.1 - - + -
244G ILE* 4.5 13.3 - - + +
247G MET* 4.5 18.8 - - + -
253G GLY* 4.1 2.5 - - - -
254G GLY* 2.6 47.0 + - - +
256G ALA* 1.3 74.8 - - + +
258G SER* 1.3 74.5 + - - +
260G VAL* 2.9 18.0 - - - +
261G VAL* 2.8 20.4 - - + +
267G ILE* 5.4 2.4 - - + +
270G ILE* 5.9 3.1 - - + -
287G PHE* 4.9 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 258 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39G VAL* 4.3 6.6 - - - +
40G ASN* 4.8 7.0 - - - -
43G LEU* 4.9 12.1 - - - -
81G LEU* 5.1 6.1 - - - +
82G PHE* 3.8 12.9 - - - -
224G GLN* 5.3 0.2 - - - -
254G GLY* 2.6 36.6 + - - -
255G GLY* 2.7 13.9 + - - -
256G ALA 2.9 0.4 + - - -
257G LEU* 1.3 83.1 - - - +
259G ALA* 1.3 72.5 + - - +
260G VAL 2.9 0.2 + - - -
261G VAL* 3.0 19.2 + - - +
262G ALA* 3.3 5.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 259 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40G ASN* 5.8 2.6 - - + +
224G GLN* 3.0 35.2 - - + +
227G TYR* 3.1 41.6 - - + +
255G GLY 2.6 17.8 + - - +
256G ALA 3.4 2.2 - - - +
258G SER* 1.3 73.7 - - - +
260G VAL* 1.3 71.7 + - - +
262G ALA* 2.9 11.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 260 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218G ILE* 5.8 4.5 - - + -
226G ALA* 6.0 4.3 - - + -
227G TYR* 4.6 4.4 - - - +
242G VAL* 4.6 10.5 - - + -
244G ILE* 4.3 13.5 - - + -
256G ALA 2.8 21.3 - - - +
257G LEU* 2.9 19.7 - - - +
259G ALA* 1.3 79.1 - - - +
261G VAL* 1.3 59.9 + - - +
263G THR* 2.3 30.2 + - - -
265G ALA* 3.0 20.2 - - + -
267G ILE* 3.2 29.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 261 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80G LYS 4.2 3.4 - - - +
81G LEU 3.9 8.1 - - - +
82G PHE* 2.9 34.8 - - + +
83G GLY* 3.4 26.7 - - - +
84G GLY 4.2 2.0 - - - +
257G LEU* 2.8 22.0 - - + +
258G SER* 3.0 7.3 + - - +
260G VAL* 1.3 79.3 - - + +
262G ALA* 1.3 53.5 - - - +
263G THR 2.2 19.9 + - - -
264G GLY* 2.5 17.8 + - - -
265G ALA* 3.0 11.6 + - - +
267G ILE* 5.1 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 262 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43G LEU* 6.3 5.8 - - + -
81G LEU 6.1 0.2 - - - +
227G TYR* 2.8 23.6 + - + +
258G SER 3.3 5.6 + - - +
259G ALA* 2.9 12.6 + - - +
260G VAL 2.9 2.0 + - - -
261G VAL* 1.3 73.1 - - + +
263G THR* 1.3 70.2 + - - +
----------------------------------------------------------
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