Contacts of the helix formed by residues 323 - 334 (chain F) in PDB entry 2Y1M
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 323 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249F GLN* 3.4 42.2 - - + +
250F PRO* 3.8 13.2 - - + -
319F PRO* 6.2 0.2 - - - -
321F ASN* 4.7 0.9 - - - +
322F LYS* 1.3 93.4 - - + +
324F LEU* 1.3 66.4 + - - +
325F PHE* 3.6 24.0 - - + -
326F GLN* 2.9 25.1 + - + +
327F ALA* 3.4 3.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 324 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247F LEU 4.7 6.4 + - - +
249F GLN 5.0 0.4 + - - -
261F LEU* 4.1 19.7 - - + +
293F PHE* 3.9 22.9 - - + -
303F TRP* 3.5 63.2 - - + +
305F ILE* 4.1 21.1 - - + -
319F PRO* 4.2 13.9 - - + -
322F LYS 3.7 2.2 + - - -
323F PRO* 1.3 72.2 - - - +
325F PHE* 1.3 64.5 + - - +
327F ALA* 3.0 14.2 + - + +
328F LEU* 3.1 27.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 325 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249F GLN 4.2 1.3 - - - -
250F PRO* 3.5 33.4 - - + -
257F ASN* 3.3 31.2 - - - -
261F LEU* 4.0 13.0 - - + +
323F PRO* 3.0 19.1 + - + -
324F LEU* 1.3 78.6 - - - +
326F GLN* 1.3 68.2 + - - +
328F LEU 3.9 0.6 - - - -
329F ILE* 2.9 43.7 + - + +
349F LEU* 3.9 22.0 - - + +
352F LEU* 3.1 52.3 - - + -
353F CYS* 4.1 8.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 326 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322F LYS* 3.8 26.9 - - + -
323F PRO* 2.9 20.1 + - + +
325F PHE* 1.3 83.3 - - + +
327F ALA* 1.3 64.1 + - - +
329F ILE* 3.7 12.4 + - - +
330F ASP* 3.1 57.2 + - - +
333F ARG* 5.3 3.4 - - - +
353F CYS* 4.4 17.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 327 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305F ILE* 4.5 4.9 - - + -
319F PRO* 4.1 31.6 - - + -
322F LYS* 4.2 19.3 - - + +
323F PRO 3.4 3.9 + - - +
324F LEU* 3.0 12.6 + - + +
326F GLN* 1.3 80.5 - - - +
328F LEU* 1.3 57.1 + - - +
330F ASP* 3.2 4.7 + - - +
331F GLY 2.9 24.3 + - - -
337F TYR* 3.7 9.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 328 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261F LEU* 3.8 27.4 - - + -
265F HIS* 4.2 7.0 - - + -
291F TYR* 4.3 14.4 - - + +
293F PHE* 3.7 35.7 - - + -
305F ILE* 3.5 29.6 - - + -
324F LEU* 3.1 16.8 + - + +
326F GLN 3.4 0.2 - - - -
327F ALA* 1.3 72.8 - - - +
329F ILE* 1.3 61.6 + - - +
331F GLY 3.7 0.7 - - - -
332F PHE* 2.8 30.7 + - - +
337F TYR* 3.9 16.4 - - + +
349F LEU* 3.8 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 329 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325F PHE* 2.9 35.7 + - + +
326F GLN* 4.0 16.4 - - - +
327F ALA 3.4 0.2 - - - -
328F LEU* 1.3 75.5 - - - +
330F ASP* 1.3 58.4 + - - +
332F PHE* 3.8 6.1 - - + +
333F ARG* 3.0 59.8 + - + +
349F LEU* 3.8 40.4 - - + +
350F THR* 4.0 13.9 - - + +
353F CYS* 4.4 9.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 330 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322F LYS* 4.1 13.9 - - - +
326F GLN* 3.1 48.6 + - - +
327F ALA* 3.2 5.7 + - - +
328F LEU 3.1 0.8 - - - -
329F ILE* 1.3 77.4 - - - +
331F GLY* 1.3 61.0 + - - +
332F PHE 3.1 1.3 - - - -
333F ARG* 3.2 13.5 + - - +
334F GLU* 2.9 34.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 331 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327F ALA 2.9 10.5 + - - -
328F LEU 3.7 0.9 - - - -
330F ASP* 1.3 74.1 - - - +
332F PHE* 1.3 62.6 + - - +
334F GLU* 3.8 6.5 - - - -
335F GLY 3.1 2.1 + - - -
336F PHE* 2.7 33.4 + - - -
337F TYR* 3.0 32.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 332 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328F LEU 2.8 19.3 + - - +
329F ILE* 3.9 7.9 - - + +
330F ASP 3.1 0.4 - - - -
331F GLY* 1.3 77.6 - - - +
333F ARG* 1.3 73.6 + - + +
335F GLY* 3.0 15.8 + - - -
337F TYR 3.2 25.3 + - - +
338F LEU* 3.9 22.5 - - + +
346F ASN* 3.5 33.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 333 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326F GLN* 5.3 3.4 - - - +
329F ILE* 3.0 40.9 + - + +
330F ASP* 3.2 14.2 + - - +
332F PHE* 1.3 85.8 - - + +
334F GLU* 1.3 62.4 + - - +
350F THR* 4.0 18.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 334 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330F ASP* 2.9 19.8 + - - +
331F GLY* 4.0 6.1 - - - +
333F ARG* 1.3 83.5 - - - +
335F GLY* 1.3 57.6 + - - +
336F PHE* 3.7 29.8 - - + -
----------------------------------------------------------
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