Contacts of the helix formed by residues 256 - 268 (chain G) in PDB entry 6MZL
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 HIS 256 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211G PRO* 4.4 20.9 - - + +
251G LEU* 3.5 11.7 + - + +
252G VAL* 5.6 0.6 - - - -
254G ASN* 3.2 39.8 + - + +
255G GLN* 1.3 77.9 + - - +
257G GLU* 1.3 63.7 + - - +
259G GLU* 3.1 31.7 + - + +
260G ALA* 3.4 23.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 257 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255G GLN 3.9 3.1 + - - +
256G HIS* 1.3 72.6 - - - +
258G ASN* 1.3 78.3 + - - +
259G GLU* 3.3 2.2 + - - -
260G ALA* 3.4 3.1 + - - +
261G LYS* 2.9 30.0 + - + +
286G THR* 4.5 29.6 + - + +
38I LEU* 3.4 32.6 - - - +
41I ASP* 4.4 5.0 - - - +
45I TYR* 5.1 2.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 258 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257G GLU* 1.3 88.6 - - - +
259G GLU* 1.3 65.3 + - - +
261G LYS* 3.4 24.4 - - + +
262G SER* 2.8 31.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 259 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211G PRO* 6.2 1.1 - - + -
212G THR* 4.4 19.5 - - + -
215G GLU* 3.5 16.7 - - - +
251G LEU* 5.5 2.9 - - + -
256G HIS* 3.1 44.5 + - + +
257G GLU 3.3 2.8 + - - -
258G ASN* 1.3 77.7 + - - +
260G ALA* 1.3 57.3 + - - +
262G SER* 3.4 4.9 + - - -
263G PHE* 2.9 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 260 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215G GLU* 4.4 0.2 + - - -
248G TYR* 3.5 20.0 - - + +
251G LEU* 3.6 40.5 - - + +
252G VAL* 4.8 4.3 - - + +
256G HIS 3.4 17.2 + - - +
257G GLU* 3.7 3.1 - - - +
259G GLU* 1.3 75.7 - - - +
261G LYS* 1.3 58.9 + - - +
263G PHE* 3.9 0.9 - - - +
264G PHE* 2.9 32.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 261 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248G TYR* 5.3 2.7 + - - -
257G GLU* 2.9 22.3 + - + +
258G ASN* 3.4 26.9 - - + +
260G ALA* 1.3 77.1 - - - +
262G SER* 1.3 57.3 + - - +
264G PHE* 3.7 4.9 - - - +
265G GLU* 2.9 59.2 + - + +
10I SER* 6.1 1.4 - - - +
11I ASN* 4.1 26.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 262 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258G ASN 2.8 19.3 + - - -
259G GLU* 3.8 4.3 - - - -
261G LYS* 1.3 73.5 - - - +
263G PHE* 1.3 57.3 + - - +
265G GLU* 3.3 12.4 + - - +
266G LYS* 2.9 30.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 263 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215G GLU* 3.5 50.3 - - + +
218G TYR* 3.4 35.4 - + + -
244G PHE* 3.6 25.7 - + - -
247G MET* 5.1 11.2 - - + -
251G LEU* 3.8 20.9 - - + -
259G GLU 2.9 18.1 + - - +
260G ALA* 3.9 5.2 - - - +
262G SER* 1.3 74.8 - - - +
264G PHE* 1.3 61.4 + - - +
266G LYS* 3.3 3.8 + - + +
267G PHE* 2.9 53.6 + + - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 264 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244G PHE* 3.6 25.8 - + + -
248G TYR* 4.0 16.8 - + + +
260G ALA 2.9 17.7 + - - +
261G LYS* 3.7 4.3 - - - +
263G PHE* 1.3 78.2 - - - +
265G GLU* 1.3 59.7 + - + +
268G HIS* 2.5 73.4 + + + +
279G LEU* 4.2 26.5 - - + -
282G LEU* 3.7 31.4 - - + -
283G SER* 4.3 19.7 - - - -
9I LEU* 4.9 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 265 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261G LYS* 2.9 55.9 + - + +
262G SER* 3.7 11.3 - - - +
264G PHE* 1.3 84.4 - - + +
266G LYS* 1.3 59.1 + - - +
268G HIS* 3.2 25.6 - - + -
10I SER* 5.5 8.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 266 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219G SER* 5.4 2.4 + - - -
262G SER* 2.9 18.8 + - - +
263G PHE* 3.8 3.6 - - + +
264G PHE 3.1 0.2 - - - -
265G GLU* 1.3 81.5 - - - +
267G PHE* 1.3 97.8 + - + +
268G HIS* 3.6 2.3 + - - -
269G GLY 4.9 1.2 + - - -
270G ASP* 4.4 6.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 267 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218G TYR* 3.8 15.1 + + + -
219G SER* 3.2 36.3 - - - -
222G LYS* 3.6 29.2 - - + -
244G PHE* 3.7 25.8 - - + -
263G PHE* 2.9 35.0 + + - +
264G PHE 3.7 0.7 - - - -
266G LYS* 1.3 116.3 - - + +
268G HIS* 1.3 61.6 + - - +
269G GLY 3.5 0.4 - - - -
270G ASP* 3.0 33.3 - - - +
271G GLN* 5.0 2.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 268 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244G PHE* 4.4 7.2 - - - -
264G PHE* 2.5 62.9 + + + +
265G GLU* 3.2 29.6 + - + -
266G LYS 3.6 0.9 - - - -
267G PHE* 1.3 77.8 - - - +
269G GLY* 1.3 70.3 + - - +
270G ASP 2.9 11.8 + - - -
271G GLN* 4.1 12.3 + - - +
279G LEU* 5.0 14.4 - - + +
7I LEU 3.1 27.5 + - - -
8I LYS* 3.4 23.7 - - + +
----------------------------------------------------------
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