Contacts of the helix formed by residues 237 - 248 (chain A) in PDB entry 1Z59
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 237 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A GLY 3.9 1.0 + - - +
236A VAL* 1.3 72.1 - - - +
238A ARG* 1.3 66.0 + - - +
239A GLU* 3.2 9.9 + - - +
240A GLU* 2.9 46.8 + - - +
241A ILE* 3.1 23.7 + - - +
297A VAL* 4.2 12.1 - - + -
301A LYS* 5.6 4.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 238 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A ASP* 1.3 76.6 - - - +
239A GLU* 1.3 69.7 + - + +
241A ILE* 3.2 5.6 + - - +
242A LYS* 3.0 41.0 + - - +
290A GLU* 2.7 46.4 + - - +
293A ILE* 3.9 20.2 - - + +
294A THR* 2.2 41.7 + - - +
297A VAL* 4.0 17.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 239 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A ASP* 3.2 8.8 + - - +
238A ARG* 1.3 82.7 - - + +
240A GLU* 1.3 58.8 + - + +
242A LYS* 3.4 32.7 + - - +
243A ILE* 3.0 40.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 240 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A TYR* 3.7 32.0 - - + -
235A GLY 3.7 5.8 - - - +
236A VAL* 3.5 16.0 - - + -
237A ASP* 2.9 50.8 + - - +
239A GLU* 1.3 76.6 - - + +
241A ILE* 1.3 58.4 + - - +
243A ILE* 3.3 15.6 + - + +
244A LEU* 3.0 35.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 241 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A VAL* 3.8 18.4 - - + -
237A ASP 3.1 16.0 + - - +
238A ARG 3.2 7.6 + - - +
240A GLU* 1.3 75.1 - - - +
242A LYS* 1.3 57.1 + - - +
244A LEU* 3.2 7.5 + - + +
245A ILE* 3.0 46.8 + - + +
257A PHE* 4.6 7.9 - - + -
262A PHE* 3.7 30.1 - - + -
288A LEU* 5.4 0.9 - - + -
293A ILE* 4.2 18.6 - - + -
296A LEU* 4.2 13.9 - - + -
297A VAL* 4.1 16.8 - - + -
300A PHE* 4.0 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 242 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238A ARG* 3.0 33.3 + - - +
239A GLU* 3.4 34.4 + - - +
241A ILE* 1.3 75.4 - - - +
243A ILE* 1.3 58.1 + - - +
245A ILE* 3.3 7.8 + - + +
246A ASN* 3.0 41.3 + - - +
290A GLU* 3.1 40.0 + - - +
293A ILE* 4.5 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 243 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A SER* 5.5 6.3 - - - +
239A GLU* 3.0 37.4 + - + +
240A GLU* 3.6 16.8 - - + +
241A ILE 3.3 0.2 - - - -
242A LYS* 1.3 75.0 - - - +
244A LEU* 1.3 66.9 + - + +
246A ASN* 3.5 5.6 + - - +
247A ASN* 3.2 38.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 244 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A PRO* 4.2 27.8 - - + -
236A VAL* 4.7 6.5 - - + -
240A GLU* 3.0 23.0 + - + +
241A ILE* 3.2 9.8 + - - +
243A ILE* 1.3 81.3 - - + +
245A ILE* 1.3 61.7 + - - +
247A ASN* 3.4 14.8 + - + +
248A LEU* 3.6 16.8 + - - +
257A PHE* 4.2 14.6 - - + -
261A GLU* 4.1 23.4 - - + +
262A PHE* 4.1 27.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 245 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A ILE* 3.0 36.7 + - + +
242A LYS* 3.7 6.3 - - - +
244A LEU* 1.3 75.6 - - - +
246A ASN* 1.3 72.0 + - - +
247A ASN 3.2 1.0 + - - -
248A LEU* 3.2 27.9 + - + +
257A PHE* 4.0 17.7 - - + -
285A VAL* 4.1 37.0 - - + +
286A LYS* 4.1 17.8 - - + +
288A LEU* 4.4 14.6 - - + -
293A ILE* 4.6 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 246 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A LYS* 3.0 26.7 + - - +
243A ILE* 4.0 6.0 - - - +
244A LEU 3.4 0.4 - - - -
245A ILE* 1.3 84.0 - - - +
247A ASN* 1.3 66.0 + - - +
248A LEU 3.4 3.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 247 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A ILE* 3.2 30.0 + - - +
244A LEU* 3.7 9.6 - - + +
245A ILE 3.1 1.0 - - - -
246A ASN* 1.3 83.5 + - - +
248A LEU* 1.3 65.4 + - - +
249A LYS* 3.4 2.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 248 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A LEU 3.6 8.3 - - - +
245A ILE* 3.2 25.3 + - + +
246A ASN 3.4 3.7 - - - +
247A ASN* 1.3 80.0 - - - +
249A LYS* 1.3 62.3 + - - +
250A ARG 3.7 18.6 - - - +
252A TYR* 3.8 27.8 - - + -
257A PHE* 4.1 5.4 - - + -
261A GLU* 3.9 28.7 - - + +
285A VAL* 3.5 32.3 - - + -
286A LYS* 6.2 1.1 - - + -
----------------------------------------------------------
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