Contacts of the helix formed by residues 335 - 342 (chain B) in PDB entry 4CZ8
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 LEU 335 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B ILE* 4.8 9.0 - - + -
107B ILE* 4.8 15.5 - - + -
331B GLY* 2.8 22.6 + - - +
334B ILE* 1.3 77.5 - - + +
336B ALA* 1.3 60.9 + - - +
338B PRO* 3.9 0.7 - - - +
339B LEU* 3.1 44.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 336 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B THR* 4.0 21.6 - - + +
103B ILE* 3.5 28.4 - - + +
104B ALA 4.2 2.0 - - - +
331B GLY 3.3 3.4 + - - -
332B VAL* 3.2 28.4 + - + +
335B LEU* 1.3 77.5 - - - +
337B ARG* 1.3 68.5 + - - +
339B LEU* 3.1 5.2 + - - +
340B ALA* 2.9 25.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 337 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B LEU* 5.1 4.0 - - - +
96B GLY 6.1 2.4 - - - -
100B THR* 4.4 16.4 + - - +
127B GLY 5.8 0.4 + - - -
129B THR* 4.3 15.3 - - - +
151B ILE* 5.7 3.8 - - - +
154B GLU* 2.9 40.6 + - - -
332B VAL 3.0 11.6 + - - +
333B MSE 4.1 7.0 - - - +
336B ALA* 1.3 80.0 - - - +
338B PRO* 1.3 58.7 - - + +
340B ALA* 3.3 2.6 + - - +
341B THR* 2.2 40.9 + - - -
356B ILE* 3.2 23.0 + - - +
357B ALA* 2.9 31.3 + - - +
358B LEU* 5.0 0.7 - - - +
360B GLY* 4.1 23.1 - - - +
362B ARG* 4.1 21.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 338 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333B MSE 3.6 6.3 - - - +
334B ILE 3.2 28.9 - - - +
335B LEU 3.9 0.7 - - - +
336B ALA 3.6 1.3 - - - -
337B ARG* 1.3 94.7 - - + +
339B LEU* 1.3 57.7 + - + +
341B THR* 3.0 6.0 + - - +
342B LEU* 2.9 16.8 + - - -
353B TYR* 2.8 26.8 + - + +
354B LEU* 5.2 6.1 - - + -
357B ALA* 3.8 12.8 - - + -
358B LEU* 3.9 26.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 339 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B LEU* 4.6 7.1 - - - +
103B ILE* 3.9 30.3 - - + -
335B LEU* 3.1 36.8 + - + +
336B ALA 3.1 4.2 + - - +
338B PRO* 1.3 78.1 - - + +
340B ALA* 1.3 61.5 + - - +
342B LEU* 3.2 29.7 - - + +
343B PRO* 4.6 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 340 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B ILE* 5.1 0.3 - - - +
96B GLY* 3.2 41.7 + - - +
99B LEU* 3.5 20.0 - - + +
100B THR* 3.2 25.4 - - - +
103B ILE* 5.8 0.6 - - - +
336B ALA 2.9 13.0 + - - +
337B ARG 3.7 2.9 - - - +
339B LEU* 1.3 75.8 - - - +
341B THR* 1.3 61.9 + - - +
342B LEU 3.1 1.2 + - - -
343B PRO* 3.4 12.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 341 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B LEU* 4.6 10.8 - - + -
96B GLY* 5.4 1.1 - - - -
337B ARG* 2.2 38.9 + - - +
338B PRO 3.0 6.2 + - - -
340B ALA* 1.3 76.2 - - - +
342B LEU* 1.3 51.7 + - - +
343B PRO* 3.0 1.9 - - - +
344B LEU* 2.8 64.2 + - + +
353B TYR* 3.1 19.1 - - + -
356B ILE* 4.7 1.8 - - + -
357B ALA* 3.4 27.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 342 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338B PRO 2.9 5.3 + - - +
339B LEU* 3.2 28.0 - - + +
340B ALA 3.1 0.2 - - - -
341B THR* 1.3 75.0 - - - +
343B PRO* 1.3 63.6 - - + +
344B LEU 2.9 5.4 + - - -
345B LEU* 3.3 39.5 + - + +
346B LYS* 4.4 9.1 - - - +
353B TYR* 3.5 20.2 - - + +
----------------------------------------------------------
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