Contacts of the helix formed by residues 328 - 339 (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 LYS 328 (chain G).
----------------------------------------------------------
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
Residues in contact with LEU 329 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149G LEU* 3.9 6.3 - - + -
152G ILE* 3.9 25.6 - - + -
247G LEU* 5.1 4.9 - - + -
280G LEU* 4.3 5.6 - - - +
282G PRO* 3.5 30.7 - - + -
285G TYR* 2.8 34.1 - - + +
326G ILE* 3.1 18.0 + - + +
328G LYS* 1.3 76.0 - - - +
330G PRO* 1.3 65.6 - - + +
332G ARG* 2.8 10.3 + - + +
333G TRP* 2.7 66.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 330 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140G LEU* 3.5 9.4 - - + +
143G TYR* 3.8 50.5 - - + +
149G LEU* 4.4 7.6 - - + -
326G ILE 4.3 1.1 - - - +
327G HIS* 3.3 22.0 - - + +
328G LYS 3.4 1.1 - - - -
329G LEU* 1.3 94.9 - - + +
331G GLU* 1.3 56.7 + - - +
333G TRP* 3.8 13.7 - - + -
334G GLU* 3.1 31.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 331 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327G HIS 5.2 1.2 + - - +
328G LYS* 3.1 38.6 + - - +
329G LEU 3.1 0.8 - - - -
330G PRO* 1.3 77.3 - - - +
332G ARG* 1.3 65.6 + - + +
334G GLU* 3.1 13.1 + - - +
335G LYS* 2.9 56.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 332 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279G ASP* 3.1 35.7 + - - +
280G LEU* 4.1 12.3 - - + -
285G TYR* 3.2 51.4 + - + +
328G LYS* 3.0 37.5 + - + +
329G LEU* 2.8 13.4 + - + +
331G GLU* 1.3 77.2 - - - +
333G TRP* 1.3 57.7 + - + +
335G LYS* 3.4 7.1 + - - +
336G CYS* 2.9 28.6 + - - +
344G PHE* 3.5 30.1 - - + -
345G GLU 5.2 6.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 333 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136G CYS* 3.7 22.6 - - + +
139G LEU* 3.8 47.3 - - + +
140G LEU* 3.3 36.8 - - + -
143G TYR* 4.2 14.1 - - + -
148G PHE* 4.0 24.5 - + - -
149G LEU* 4.4 3.8 - - + -
271G LEU* 4.8 5.8 - - + -
280G LEU* 3.6 29.0 + - + +
329G LEU* 2.7 56.9 + - + +
330G PRO* 3.8 14.1 - - + -
332G ARG* 1.3 73.6 - - + +
334G GLU* 1.3 57.0 + - - +
336G CYS* 3.1 7.3 + - - +
337G VAL* 2.9 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 334 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140G LEU* 3.9 15.9 - - + -
144G LYS* 4.0 23.4 + - - -
330G PRO* 3.1 24.0 + - - +
331G GLU* 3.1 15.7 + - - +
333G TRP* 1.3 75.0 - - - +
335G LYS* 1.3 62.6 + - + +
337G VAL* 3.3 8.8 - - + +
338G ALA* 3.0 25.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 335 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331G GLU* 2.9 41.9 + - - +
332G ARG* 3.7 8.7 - - - +
334G GLU* 1.3 77.2 - - + +
336G CYS* 1.3 52.2 + - - +
338G ALA* 3.0 7.6 + - - +
339G SER* 2.8 41.1 + - - +
344G PHE* 3.8 27.3 - - + -
345G GLU* 3.5 32.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 336 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132G ARG* 3.4 29.8 - - - +
133G LYS* 4.2 0.9 - - - -
136G CYS* 2.1 48.5 - - - -
280G LEU* 4.4 7.0 - - + -
332G ARG 2.9 14.9 + - - +
333G TRP 3.3 4.5 - - - +
335G LYS* 1.3 77.1 - - - +
337G VAL* 1.3 59.3 + - - +
339G SER* 3.2 5.9 + - - -
341G GLY* 3.0 25.7 + - - -
342G LYS 4.7 2.5 - - - -
344G PHE* 3.6 18.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 337 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133G LYS* 4.2 31.7 - - + +
137G GLU* 4.0 27.6 - - + +
140G LEU* 3.6 23.1 - - + -
333G TRP 2.9 23.2 + - - +
334G GLU* 3.3 13.7 - - + +
336G CYS* 1.3 74.1 - - - +
338G ALA* 1.3 56.5 + - - +
340G ASP* 3.0 25.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 338 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334G GLU 3.0 20.6 + - - +
335G LYS* 3.0 7.6 + - - +
337G VAL* 1.3 77.2 - - + +
339G SER* 1.3 56.7 + - - +
340G ASP* 3.1 7.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 339 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335G LYS* 2.8 23.3 + - - +
336G CYS 3.2 3.1 + - - -
338G ALA* 1.3 71.9 - - - +
340G ASP* 1.3 68.8 - - - +
342G LYS* 3.2 46.8 + - - +
343G TYR 4.6 2.9 - - - -
344G PHE* 3.7 20.8 - - - +
----------------------------------------------------------
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