Contacts of the helix formed by residues 321 - 332 (chain A) in PDB entry 2GC5
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 ILE 321 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A ALA* 5.1 7.6 - - + +
316A HIS 5.3 1.6 - - - +
317A ASN 3.0 14.3 + - - +
318A PRO* 3.6 21.5 - - + +
320A GLY* 1.3 79.2 - - - +
322A ASN* 1.3 64.3 + - - +
323A GLY 3.2 1.1 - - - -
324A LEU* 3.4 20.0 - - + +
325A ILE* 3.0 37.6 + - + +
351A MET* 3.8 33.2 - - + +
354A ARG* 5.3 2.0 - - + -
355A LEU* 3.7 37.2 - - + -
410A THR* 5.6 1.8 - - + -
411A GLY* 5.6 4.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 322 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A PRO 2.5 32.5 + - - -
319A ASP* 3.7 17.2 + - - +
321A ILE* 1.3 80.5 - - - +
323A GLY* 1.3 57.2 + - - +
324A LEU 3.3 0.2 - - - -
325A ILE* 3.8 13.2 - - - +
326A THR* 3.4 27.0 + - - +
354A ARG* 4.6 15.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 323 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A ASP* 6.0 1.8 - - - -
260A TYR* 6.1 3.1 - - - -
319A ASP* 3.2 17.5 + - - -
320A GLY* 4.2 3.1 - - - -
322A ASN* 1.3 73.2 - - - +
324A LEU* 1.3 60.3 + - - +
326A THR* 3.0 12.3 + - - -
327A ALA* 3.0 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 324 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A LEU* 4.0 21.3 - - + -
313A ASP* 4.0 20.0 - - + +
315A ALA* 4.1 3.6 - - + -
320A GLY 3.3 21.4 + - - +
321A ILE* 3.4 25.8 - - + +
323A GLY* 1.3 74.9 - - - +
325A ILE* 1.3 55.0 + - - +
327A ALA* 3.1 5.5 + - - +
328A LEU* 2.7 61.1 + - + +
355A LEU* 5.0 5.6 - - + -
408A VAL* 4.8 1.3 - - + -
410A THR* 3.2 39.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 325 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A ILE* 3.0 20.9 + - + +
322A ASN* 3.8 15.7 - - - +
323A GLY 3.4 0.2 - - - -
324A LEU* 1.3 74.8 - - - +
326A THR* 1.3 59.7 + - + +
328A LEU* 3.4 1.9 + - - +
329A LYS* 2.9 43.1 + - + +
354A ARG* 3.5 39.9 - - + +
355A LEU* 3.9 11.9 - - + -
358A ALA* 3.6 22.4 - - + -
359A PHE* 3.9 23.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 326 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A ASN 3.4 12.0 + - - +
323A GLY* 3.0 24.6 + - - -
325A ILE* 1.3 76.6 - - + +
327A ALA* 1.3 64.1 + - - +
329A LYS* 3.6 14.8 + - - +
330A GLN* 3.1 37.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 327 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A VAL* 4.3 9.0 - - + +
258A GLY* 5.5 5.8 - - - -
301A LEU* 3.6 28.9 - - + -
323A GLY 3.0 20.3 + - - +
324A LEU* 3.1 7.4 + - - +
326A THR* 1.3 76.8 + - - +
328A LEU* 1.3 56.9 + - - +
330A GLN* 3.1 15.9 + - - +
331A LEU* 3.0 33.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 328 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A LEU* 3.8 21.3 - - + -
311A VAL* 5.3 0.7 - - + -
324A LEU* 2.7 44.6 + - + +
327A ALA* 1.3 73.4 - - - +
329A LYS* 1.3 53.1 + - - +
331A LEU* 3.2 2.7 + - + +
332A PHE* 2.8 56.8 + - + +
336A ILE* 4.2 6.1 - - + -
338A VAL* 4.5 4.9 - - + -
355A LEU* 5.9 0.2 - - + -
359A PHE* 3.6 36.6 - - + -
408A VAL* 3.6 38.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 329 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A ILE* 2.9 32.9 + - + +
326A THR* 3.8 15.5 - - - +
328A LEU* 1.3 75.8 - - - +
330A GLN* 1.3 60.8 + - + +
332A PHE 3.2 19.1 - - - +
358A ALA* 5.5 8.3 - - + +
359A PHE* 4.7 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 330 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A LEU* 3.4 38.3 - - + +
257A VAL* 5.1 6.8 - - + +
258A GLY* 6.4 0.2 - - - -
259A ASP 6.2 0.4 - - - +
326A THR* 3.1 28.5 + - - +
327A ALA* 3.1 14.0 + - - +
329A LYS* 1.3 75.4 - - + +
331A LEU* 1.3 64.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 331 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A LEU* 4.5 14.8 - - + -
235A GLY 4.6 7.0 - - - +
236A TRP* 4.0 48.4 - - + +
257A VAL* 4.4 19.3 - - + -
301A LEU* 4.1 29.2 - - + -
327A ALA 3.0 20.7 + - - +
328A LEU* 3.2 8.0 + - + +
330A GLN* 1.3 80.2 - - - +
332A PHE* 1.3 75.4 + - + +
333A SER 4.4 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 332 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A TRP* 3.6 27.8 - + - -
309A LEU* 4.0 32.8 - - + -
311A VAL* 4.2 5.8 - - + -
328A LEU* 2.8 50.3 + - + +
329A LYS* 3.2 20.9 - - - +
330A GLN 3.6 0.2 - - - -
331A LEU* 1.3 87.0 - - + +
333A SER* 1.3 59.8 + - - +
334A GLN* 4.1 13.7 - - + +
336A ILE* 3.9 31.0 - - + -
359A PHE* 6.4 0.2 - - + -
406A PRO* 4.1 15.0 - - + -
408A VAL* 4.3 7.6 - - + -
----------------------------------------------------------
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