Contacts of the helix formed by residues 320 - 328 (chain A) in PDB entry 4Y05
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 320 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A ARG* 3.6 2.9 - - - +
318A THR 3.5 5.4 + - - -
319A ALA* 1.3 76.9 - - - +
321A ASN* 1.3 64.8 + - - +
322A GLU* 3.5 17.1 + - - +
323A VAL* 3.1 27.4 + - - +
324A VAL* 3.1 20.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 321 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A ARG* 2.8 35.1 + - - +
320A SER* 1.3 73.1 - - - +
322A GLU* 1.3 53.0 + - - +
324A VAL* 3.3 4.0 + - - +
325A TYR* 2.8 35.9 + - - +
356A HIS* 3.0 39.8 + - - -
357A THR* 4.3 6.7 - - - +
360A GLY* 4.4 2.6 - - - -
361A ASP 4.9 1.2 - - - +
370A SER* 5.8 1.0 - - - -
371A LYS 2.8 30.4 + - - +
372A GLY 3.0 11.3 - - - +
373A ILE* 4.9 3.1 - - + +
376A MET* 4.2 4.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 322 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A MET* 3.7 26.3 - - + +
320A SER* 3.5 13.5 + - - +
321A ASN* 1.3 78.2 - - - +
323A VAL* 1.3 61.6 + - - +
325A TYR* 3.7 4.0 - - + +
326A ARG* 3.2 22.5 + - - +
376A MET* 3.4 27.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 323 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A LEU* 4.3 14.6 - - + +
249A THR 5.7 2.0 - - - -
250A MET* 3.6 32.5 - - + -
315A PHE* 4.1 11.4 - - + -
319A ALA* 4.0 19.1 - - + -
320A SER* 3.1 26.7 + - - +
322A GLU* 1.3 75.6 - - - +
324A VAL* 1.3 68.2 + - - +
326A ARG* 3.5 5.0 + - - +
327A PHE* 3.2 31.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 324 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A ARG* 3.6 30.5 - - - +
315A PHE* 3.8 37.4 - - + -
319A ALA* 4.4 3.1 - - + -
320A SER 3.1 13.1 + - - +
321A ASN* 3.6 8.3 - - - +
323A VAL* 1.3 76.1 - - - +
325A TYR* 1.3 56.8 + - - +
327A PHE* 3.2 9.9 + - - -
328A THR* 2.8 25.9 + - - +
357A THR* 4.3 13.5 - - + -
373A ILE* 4.4 2.5 - - + -
562A ILE* 4.1 30.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 325 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A ASN 2.8 20.9 + - - +
322A GLU 3.7 5.2 - - - +
324A VAL* 1.3 73.2 - - - +
326A ARG* 1.3 66.0 + - + +
327A PHE 3.1 1.2 + - - -
328A THR* 3.1 10.6 + - - -
329A ALA* 3.3 19.8 + - + -
330A ALA* 3.0 50.4 + - + -
333A VAL* 3.6 8.1 - - - +
373A ILE* 4.1 15.3 - - + -
376A MET* 3.2 50.9 + - + -
377A ALA* 3.4 23.0 - - + -
380A ASP* 2.6 34.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 326 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A MET* 2.9 47.7 + - + +
251A THR* 5.0 2.8 + - - +
252A ASP 2.4 31.5 + - - +
253A PRO* 5.2 1.2 - - - +
254A ILE* 3.6 29.9 - - + +
322A GLU 3.2 11.9 + - - +
323A VAL 3.5 11.2 - - - +
325A TYR* 1.3 81.3 - - - +
327A PHE* 1.3 77.3 + - + +
330A ALA* 3.7 8.5 - - + +
331A PRO* 3.3 18.2 - - - +
705A SO4 2.8 49.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 327 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A LEU* 3.8 27.8 - - + -
249A THR 3.4 25.1 - - - -
250A MET* 4.7 1.8 - - - -
252A ASP* 3.4 22.4 - - + -
253A PRO 4.0 10.8 - - - -
254A ILE* 4.3 10.5 - - - +
255A GLU 5.2 3.0 + - - +
260A CYS* 4.0 6.1 - - - -
313A PHE* 3.5 45.3 - + + -
315A PHE* 3.9 17.3 - + + -
323A VAL* 3.2 25.4 - - + -
324A VAL 3.2 2.4 + - - -
325A TYR 3.2 0.4 - - - -
326A ARG* 1.3 111.3 - - + +
328A THR* 1.3 62.8 + - - +
331A PRO* 4.2 8.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 328 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A CYS* 5.0 1.8 - - - +
262A CYS* 3.6 28.3 - - - -
315A PHE* 4.1 9.4 - - + -
324A VAL* 2.8 26.3 + - + +
325A TYR* 3.1 6.6 + - - -
326A ARG 3.5 0.2 - - - -
327A PHE* 1.3 80.8 - - - +
329A ALA* 1.3 70.2 + - - -
330A ALA 3.5 0.2 - - - -
331A PRO* 3.4 13.7 - - - +
332A LEU* 3.7 13.7 - - - +
344A CYS* 5.0 0.4 - - - -
373A ILE* 4.0 3.3 - - - +
560A CYS* 3.4 25.9 - - - +
562A ILE* 3.9 24.4 - - + +
----------------------------------------------------------
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