Contacts of the helix formed by residues 318 - 328 (chain G) in PDB entry 4U7B
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 318 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316G ALA 4.7 2.4 - - - +
317G LYS* 1.3 78.6 - - - +
319G ASP* 1.3 70.0 + - - +
320G GLU* 3.1 13.8 - - + +
321G PHE* 2.8 32.0 + - - +
322G TYR* 3.7 6.7 - - - -
324G ARG* 5.3 3.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 319 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199G GLN 3.4 8.1 - - - +
200G SER* 4.4 21.4 - - - +
318G ASP* 1.3 73.4 - - - +
320G GLU* 1.3 63.0 + - - +
322G TYR* 3.2 12.1 + - - +
323G TRP* 3.1 18.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 320 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318G ASP* 4.2 13.6 - - + +
319G ASP* 1.3 75.9 - - - +
321G PHE* 1.3 64.3 + - - +
323G TRP* 3.2 25.9 + - - +
324G ARG* 2.9 60.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 321 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286G HIS* 3.0 59.1 + + - -
287G LEU* 4.3 15.0 - - + -
290G SER* 3.2 33.4 - - - -
313G TRP* 4.7 0.2 - + - -
317G LYS* 3.4 30.7 - - + -
318G ASP* 2.8 33.8 + - - +
320G GLU* 1.3 74.4 - - - +
322G TYR* 1.3 89.9 + + - +
324G ARG* 3.5 26.0 + - - +
325G GLY 3.2 5.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 322 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197G TRP* 3.7 23.7 - + + -
198G ASP 3.7 11.0 - - - +
199G GLN* 3.5 14.1 - - - +
201G GLY* 3.7 21.3 - - - +
202G VAL* 4.3 19.2 - - + +
286G HIS* 4.6 0.2 - - - -
287G LEU* 4.5 16.2 - - + -
313G TRP* 5.1 0.2 - - - -
314G PHE* 3.3 40.7 + + - +
317G LYS* 3.8 20.6 - - + +
318G ASP 3.7 18.6 - - - -
319G ASP* 3.2 7.7 + - - +
320G GLU 3.2 0.2 - - - -
321G PHE* 1.3 93.3 - + - +
323G TRP* 1.3 68.4 + - - +
325G GLY* 3.1 11.8 + - - -
326G ILE* 3.1 16.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 323 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199G GLN* 2.9 48.4 + - + +
319G ASP 3.1 6.8 + - - +
320G GLU* 3.5 27.1 - - - +
322G TYR* 1.3 75.9 - - - +
324G ARG* 1.3 75.6 + - + +
326G ILE* 3.4 1.0 + - - +
327G HIS* 2.9 80.2 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 324 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286G HIS* 4.4 7.4 + - - +
318G ASP* 5.3 3.6 + - - -
320G GLU* 2.9 34.3 + - - +
321G PHE* 3.5 46.5 + - - +
323G TRP* 1.3 96.7 - - + +
325G GLY* 1.3 63.2 + - - +
327G HIS* 3.0 3.4 + - - -
328G LYS* 2.9 37.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 325 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197G TRP* 4.5 5.4 - - - -
282G PRO* 4.4 1.4 - - - +
285G TYR* 2.8 29.3 + - - -
286G HIS* 3.2 37.1 + - - -
321G PHE 3.2 5.3 + - - -
322G TYR 3.1 7.2 + - - -
324G ARG* 1.3 79.8 - - - +
326G ILE* 1.3 60.2 + - - +
328G LYS* 3.6 4.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 326 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149G LEU* 3.8 42.0 - - + +
152G ILE* 4.5 15.7 - - + -
154G THR* 4.1 11.2 - - + -
197G TRP* 3.3 37.2 - - + -
198G ASP* 4.7 1.6 - - - -
199G GLN* 3.8 23.6 - - + +
282G PRO* 4.0 15.9 - - + -
322G TYR 3.1 7.2 + - - +
323G TRP 3.7 6.1 - - - +
325G GLY* 1.3 74.8 - - - +
327G HIS* 1.3 64.1 + - + +
328G LYS 3.1 1.6 - - - -
329G LEU* 3.1 30.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 327 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143G TYR* 5.8 2.6 + + - -
147G SER* 5.0 4.5 - - - -
149G LEU* 4.0 22.9 - - + +
150G HIS* 5.5 0.9 - - + -
199G GLN* 2.8 26.9 + - - -
323G TRP* 2.9 77.7 + + + +
324G ARG 3.0 2.9 + - - +
326G ILE* 1.3 82.2 - - + +
328G LYS* 1.3 58.9 + - - +
329G LEU 3.3 0.7 - - - -
330G PRO* 3.3 18.9 - - - +
331G GLU* 5.2 1.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 328 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285G TYR* 3.7 22.1 + - + +
286G HIS* 3.8 27.7 + - + +
324G ARG* 2.9 22.8 + - + +
325G GLY 3.7 9.6 - - - +
326G ILE 3.1 0.6 - - - -
327G HIS* 1.3 78.2 - - - +
329G LEU* 1.3 65.4 + - - +
330G PRO* 3.3 0.7 - - - -
331G GLU* 3.1 25.9 - - - +
332G ARG* 3.0 37.8 + - + +
----------------------------------------------------------
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