Contacts of the helix formed by residues 326 - 333 (chain D) in PDB entry 2QC8
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 326 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C ASN* 6.0 1.3 - - - +
76C ASP* 3.7 11.4 - - - +
255D ASN* 5.1 0.2 - - - +
324D ARG* 3.5 28.4 - - - +
325D ILE* 1.3 86.0 - - - +
327D ARG* 1.3 66.8 + - - +
328D THR* 4.5 7.4 - - - +
329D VAL* 2.9 24.0 + - + +
330D GLY* 3.0 9.5 + - - -
336D TYR* 3.6 49.6 - - + +
337D PHE* 4.4 1.8 - - - -
338D GLU* 4.6 5.2 - - + +
501D ADP 6.1 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 327 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C ASN* 6.4 0.4 - - - -
74C ASN* 2.6 33.3 + - - -
76C ASP* 3.0 55.0 + - + +
78C TYR* 3.4 36.1 - - + +
104C TYR* 3.5 34.0 + - - +
316D VAL* 4.1 18.4 - - + +
317D ALA* 3.4 17.8 - - + +
325D ILE 3.4 2.0 + - - -
326D PRO* 1.3 69.2 - - - +
328D THR* 1.3 57.1 + - - +
330D GLY* 3.0 2.8 + - - -
331D GLN* 2.9 43.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 328 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C ASN* 4.3 15.0 + - - +
76C ASP* 4.9 0.4 + - - -
78C TYR* 5.6 7.2 - - - -
326D PRO* 4.5 6.3 - - - +
327D ARG* 1.3 78.5 - - - +
329D VAL* 1.3 67.7 + - + +
331D GLN* 3.4 5.5 + - - +
332D GLU* 2.9 50.8 + - - +
334D LYS 5.7 0.4 - - - +
336D TYR* 5.9 5.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 329 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267D LEU* 4.5 4.2 - - + +
270D ILE* 3.5 22.4 - - + -
325D ILE* 4.0 11.2 - - + -
326D PRO* 2.9 26.5 + - + +
328D THR* 1.3 75.8 - - + +
330D GLY* 1.3 66.5 + - - +
333D LYS* 2.8 22.9 + - - -
334D LYS 3.1 24.0 - - - +
335D GLY* 4.2 0.9 - - - -
336D TYR* 3.4 50.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 330 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267D LEU* 4.3 11.9 - - - +
316D VAL* 5.0 11.0 - - - -
325D ILE* 3.9 12.0 - - - +
326D PRO 3.0 12.4 + - - -
327D ARG* 3.0 4.9 + - - -
329D VAL* 1.3 77.5 - - - +
331D GLN* 1.3 63.6 + - - +
333D LYS* 3.5 16.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 331 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C TYR* 4.2 18.7 + - - +
106C ARG* 5.0 7.8 + - - +
327D ARG* 2.9 33.8 + - + +
328D THR* 3.7 6.5 - - - +
330D GLY* 1.3 75.6 - - - +
332D GLU* 1.3 65.5 + - + +
333D LYS* 3.5 11.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 332 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264D GLU* 4.6 8.1 - - - +
265D ASN 5.5 0.3 + - - -
328D THR* 2.9 34.1 + - + +
331D GLN* 1.3 79.9 - - + +
333D LYS* 1.3 70.1 + - - +
334D LYS* 3.2 39.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 333 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265D ASN* 3.2 31.4 - - - +
266D GLY 3.1 9.5 + - - -
267D LEU* 3.0 40.2 + - + +
329D VAL 2.8 10.7 + - - -
330D GLY 3.7 13.2 - - - +
331D GLN 3.3 11.2 - - - +
332D GLU* 1.3 76.2 - - - +
334D LYS* 1.3 60.7 + - - +
----------------------------------------------------------
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