Contacts of the helix formed by residues 335 - 343 (chain A) in PDB entry 1ORZ
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 PRO 335 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A LYS* 3.2 31.6 - - + +
333A HIS 3.7 5.6 - - - +
334A LEU* 1.3 90.6 - - + +
336A PRO* 1.3 73.2 - - + +
337A GLU* 3.9 11.4 - - + +
338A VAL* 2.9 21.2 + - + +
339A LEU* 2.7 19.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 336 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334A LEU 3.5 2.5 - - - +
335A PRO* 1.3 89.8 - - + +
337A GLU* 1.3 65.9 + - + +
339A LEU* 3.3 12.4 + - + +
340A LYS* 3.0 22.7 + - - +
359A THR* 3.7 23.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 337 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A LYS* 3.1 30.8 + - - -
335A PRO* 3.0 9.1 - - + +
336A PRO* 1.3 81.9 - - + +
338A VAL* 1.3 75.4 + - + +
340A LYS* 3.0 7.8 + - - +
341A GLU* 2.7 36.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 338 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A LYS* 4.2 13.0 - - + +
277A GLU* 3.9 13.7 - - + +
334A LEU* 4.7 15.3 - - + -
335A PRO* 2.9 30.1 + - + +
337A GLU* 1.3 87.9 - - + +
339A LEU* 1.3 66.4 + - + +
341A GLU* 4.5 5.8 - - - +
342A ARG* 2.9 41.5 + - + +
343A LEU* 6.1 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 339 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A LEU* 3.9 24.5 - - + +
334A LEU* 3.5 29.8 - - + +
335A PRO 2.7 34.8 - - - +
336A PRO* 3.6 9.6 - - + +
337A GLU 3.2 0.4 - - - -
338A VAL* 1.3 80.4 - - - +
340A LYS* 1.3 57.4 + - - +
343A LEU* 2.7 74.9 + - + +
347A SER* 4.3 12.0 + - - +
358A VAL* 4.5 15.9 - - + -
359A THR* 5.2 7.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 340 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A PRO 3.0 13.7 + - - +
337A GLU* 3.0 10.3 + - - +
339A LEU* 1.3 77.6 - - - +
341A GLU* 1.3 64.3 + - - +
344A PRO* 3.0 38.2 + - + +
347A SER* 4.7 18.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 341 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A SER* 4.8 1.4 + - - -
125A ARG 5.6 1.4 - - - +
156A ALA* 4.6 6.2 - - - +
337A GLU 2.7 19.6 + - - +
338A VAL* 4.0 5.4 - - - +
340A LYS* 1.3 78.6 - - - +
342A ARG* 1.3 97.6 + - + +
344A PRO* 3.3 7.6 - - - +
147B ILE* 4.9 17.3 - - - +
151B LYS* 5.7 4.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 342 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A SER* 2.9 27.8 + - - -
139A GLN* 3.6 20.6 + - - +
141A LYS* 3.4 54.6 + - - +
154A ALA 4.7 0.8 + - - -
156A ALA* 3.4 21.7 - - - +
157A ASP* 3.2 19.9 + - - -
277A GLU* 3.6 22.9 - - - +
338A VAL* 2.9 27.3 + - + +
341A GLU* 1.3 112.8 + - + +
343A LEU* 1.3 62.7 + - + +
344A PRO* 3.0 14.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 343 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A LYS* 4.8 4.5 - - - +
157A ASP* 4.2 4.9 - - - +
271A THR* 3.9 20.9 - - + -
273A GLY 5.1 0.2 - - - -
274A ALA* 4.5 3.8 - - - +
277A GLU* 4.5 20.2 - - + -
331A LEU* 4.0 13.0 - - + -
334A LEU* 4.8 1.1 - - + -
338A VAL* 5.5 0.9 - - + -
339A LEU* 2.7 52.5 + - + +
342A ARG* 1.3 82.8 - - + +
344A PRO* 1.3 65.8 - - - +
345A GLY 3.2 2.2 - - - -
346A ILE* 2.7 54.1 + - + +
347A SER* 3.3 2.6 + - - +
----------------------------------------------------------
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