Contacts of the helix formed by residues 292 - 302 (chain A) in PDB entry 1L0N
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 SER 292 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A ILE 3.3 20.1 + - - -
277A ILE* 2.6 27.4 + - - -
278A GLY* 5.0 2.0 - - - -
279A HIS 6.0 0.2 - - - -
290A LEU* 3.5 1.8 - - - +
291A SER* 1.3 79.2 - - - +
293A PRO* 1.3 64.5 - - - +
294A LEU* 3.5 4.0 + - - +
295A ALA* 3.2 22.7 + - - +
296A SER* 2.8 27.9 + - - -
356A ARG* 3.8 2.1 - - - +
90B GLU* 5.5 0.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 293 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A ILE* 4.8 3.6 - - + +
277A ILE* 5.9 0.7 - - - -
291A SER 3.0 9.1 - - - +
292A SER* 1.3 85.5 - - - +
294A LEU* 1.3 57.4 + - - +
296A SER* 4.3 5.6 - - - -
297A ILE* 2.8 46.7 + - + +
337A VAL* 5.4 0.2 - - - -
341A GLN* 3.3 35.0 - - - +
344A ARG* 4.5 11.9 - - - +
353A GLU* 5.4 2.0 - - - +
356A ARG* 4.8 5.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 294 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A ILE* 3.7 14.8 - - + -
292A SER* 3.2 8.1 + - - +
293A PRO* 1.3 77.9 - - - +
295A ALA* 1.3 58.4 + - - +
297A ILE* 3.2 0.7 + - - -
298A ALA* 2.8 34.2 + - + +
307A PHE* 3.4 29.4 - - + -
334A MET* 3.7 27.8 - - + -
337A VAL* 3.5 29.6 - - + -
338A LEU* 3.6 36.3 - - + +
341A GLN* 4.2 16.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 295 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A HIS 4.5 5.6 - - - +
280A TYR* 4.3 9.4 - - + -
290A LEU* 3.9 25.1 - - + -
292A SER* 3.2 24.9 + - - +
294A LEU* 1.3 77.5 - - - +
296A SER* 1.3 58.9 + - - +
298A ALA* 3.1 3.5 + - - +
299A ALA* 2.9 31.2 + - - +
307A PHE* 3.7 20.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 296 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A GLY 4.1 11.4 - - - -
288A ALA* 3.1 19.9 + - - -
290A LEU* 3.7 17.6 - - - +
292A SER 2.8 16.8 + - - -
293A PRO* 3.6 7.2 - - - -
295A ALA* 1.3 76.0 - - - +
297A ILE* 1.3 66.2 + - - +
298A ALA 3.2 0.3 + - - -
299A ALA* 3.2 2.3 + - - +
300A THR* 2.8 31.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 297 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A PRO* 2.8 35.3 + - + +
294A LEU 4.1 1.6 - - - +
296A SER* 1.3 77.0 - - - +
298A ALA* 1.3 62.5 + - - +
300A THR* 3.6 4.9 - - - +
301A ASN* 3.1 41.3 + - - +
303A LEU* 4.0 15.3 - - + +
337A VAL* 4.6 22.9 - - + -
341A GLN* 5.8 1.8 - - - +
3C ASN* 5.4 8.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 298 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A TYR* 4.6 5.3 - - + -
294A LEU* 2.8 21.0 + - + +
295A ALA* 3.4 6.3 - - - +
297A ILE* 1.3 77.9 - - - +
299A ALA* 1.3 58.1 + - - +
302A LYS* 2.9 24.4 + - - -
303A LEU* 2.9 20.7 + - + +
304A CYS* 4.1 26.4 + - - +
307A PHE* 4.4 6.7 - - + -
334A MET* 4.5 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 299 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A TYR* 3.4 35.3 + - + +
287A GLY* 3.9 26.2 - - - -
295A ALA 2.9 15.6 + - - +
296A SER 3.9 2.2 - - - +
298A ALA* 1.3 78.4 - - - +
300A THR* 1.3 63.7 + - - +
302A LYS* 3.4 17.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 300 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A ALA* 3.4 36.1 - - + +
296A SER* 2.8 19.0 + - - +
297A ILE* 3.5 9.7 + - - +
299A ALA* 1.3 78.7 - - - +
301A ASN* 1.3 69.7 + - - +
302A LYS* 3.2 9.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 301 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A ILE* 3.1 33.0 + - - +
300A THR* 1.3 85.5 + - - +
302A LYS* 1.3 72.3 + - - +
303A LEU* 3.3 22.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 302 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A ALA 2.9 14.1 + - - -
299A ALA* 3.8 12.8 - - - +
300A THR 3.2 8.8 - - - +
301A ASN* 1.3 80.9 - - - +
303A LEU* 1.3 58.1 + - - +
304A CYS 3.3 11.5 + - - +
330A SER* 4.3 4.9 + - - -
----------------------------------------------------------
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