Contacts of the helix formed by residues 32 - 44 (chain A) in PDB entry 3QNQ
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 THR 32 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A GLY 4.7 0.7 - - - +
29A LEU* 2.8 28.3 + - + +
31A LEU* 1.3 77.5 - - - +
33A MET* 1.3 68.4 + - - +
34A PRO 3.7 0.2 - - - -
35A PHE* 3.3 17.1 + - - +
36A LEU* 3.4 17.7 + - - +
80A MET* 3.9 23.1 - - + +
83A ILE* 3.7 19.1 - - + -
84A ALA* 3.5 34.1 - - + +
264A LEU* 5.0 11.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 33 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A LEU 4.1 3.4 - - - +
30A VAL* 3.6 28.3 - - + +
32A THR* 1.3 82.6 + - - +
34A PRO* 1.3 76.0 - - + +
35A PHE 2.8 2.1 + - - -
36A LEU* 3.0 15.0 + - - +
37A ILE* 3.2 20.5 + - + +
382A TRP* 4.9 8.1 - - + -
183B SER* 5.0 2.7 - - - +
184B PHE* 5.6 2.9 - - - -
1E NAG 3.3 61.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 34 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A VAL 3.6 10.8 - - - +
31A LEU 4.0 6.7 - - - +
32A THR 3.9 1.1 - - - -
33A MET* 1.3 96.6 - - + +
35A PHE* 1.3 57.0 + - - +
37A ILE* 3.4 17.4 + - + +
38A ILE* 3.0 34.4 + - + +
600A ZDM 3.8 32.8 - - + -
183B SER* 4.0 28.0 - - - +
187B LEU* 3.5 17.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 35 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A LEU* 3.1 29.2 - - + -
32A THR* 3.5 7.4 - - - +
33A MET 2.8 5.7 + - - -
34A PRO* 1.3 73.3 - - - +
36A LEU* 1.3 57.1 + - + +
38A ILE* 2.7 16.7 + - + +
39A GLY 2.6 33.8 + - - -
76A THR* 3.6 20.2 - - + +
83A ILE* 3.7 26.0 - - + -
600A ZDM 4.1 21.1 - - + -
105B ALA* 4.0 12.6 - - + -
106B LEU* 4.0 40.2 - - + -
109B VAL* 3.6 34.3 - - + -
194B VAL* 5.5 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 36 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A THR* 3.5 20.6 - - - +
33A MET* 3.0 5.5 + - - +
35A PHE* 1.3 76.0 - - + +
37A ILE* 1.3 60.5 + - + +
39A GLY* 4.2 1.6 - - - +
40A SER* 2.8 36.4 + - - -
76A THR* 4.2 3.8 - - - +
77A PHE* 4.1 32.1 - - + +
80A MET* 3.9 38.4 - - + -
83A ILE* 6.5 0.7 - - + -
264A LEU* 4.5 14.6 - - + -
267A MET* 4.5 18.8 - - - -
379A ALA* 3.8 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 37 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A MET* 3.2 15.9 + - + +
34A PRO* 3.4 23.8 - - + +
35A PHE 3.1 0.4 - - - -
36A LEU* 1.3 78.1 - - + +
38A ILE* 1.3 61.0 + - - +
40A SER* 3.8 1.9 - - - -
41A ILE* 3.3 32.4 + - + +
379A ALA* 3.9 9.4 - - + +
381A THR* 3.1 46.4 - - + +
184B PHE* 4.5 8.3 - - + -
187B LEU* 3.5 34.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 38 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A PRO* 3.0 21.3 + - + +
35A PHE* 2.7 20.3 + - + +
37A ILE* 1.3 74.5 - - - +
39A GLY* 1.3 67.7 + - - +
41A ILE* 3.1 14.4 + - - +
42A PHE* 3.3 16.8 - - + -
72A PRO* 5.5 1.1 - - + -
76A THR* 4.9 5.6 - - + -
600A ZDM 6.3 1.1 - - + -
106B LEU* 5.4 0.2 - - + -
187B LEU* 3.9 14.8 - - + +
190B GLY* 3.5 12.6 - - - +
191B PHE* 3.2 47.3 - - + +
194B VAL* 3.3 35.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 39 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A PHE 2.6 15.5 + - - -
36A LEU 3.9 1.1 - - - -
38A ILE* 1.3 74.9 - - - +
40A SER* 1.3 56.2 + - - +
42A PHE* 3.2 11.7 + - - +
43A LEU* 3.1 21.1 + - - +
72A PRO 4.2 7.2 - - - -
73A VAL* 3.7 6.5 - - - +
76A THR* 3.4 28.0 + - - +
77A PHE* 3.8 8.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 40 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A LEU 2.8 26.0 + - - -
37A ILE 3.8 2.5 - - - -
38A ILE 3.1 0.2 - - - -
39A GLY* 1.3 72.0 - - - +
41A ILE* 1.3 60.2 + - - +
43A LEU* 3.9 7.6 - - - -
44A ILE* 2.8 37.2 + - - +
77A PHE* 3.1 11.4 - - - -
378A ALA* 3.5 5.9 - - - -
379A ALA* 2.7 43.6 + - - -
380A VAL* 5.0 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 41 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ILE* 3.3 23.8 + - + +
38A ILE* 3.1 9.5 + - + +
40A SER* 1.3 77.1 - - - +
42A PHE* 1.3 61.4 + - + +
44A ILE* 3.6 14.4 - - + +
45A ILE* 3.2 35.4 + - + +
187B LEU* 6.2 1.3 - - + -
191B PHE* 3.5 42.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 42 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A ILE* 3.3 30.5 - - + -
39A GLY 3.2 6.8 + - - +
41A ILE* 1.3 77.0 - - + +
43A LEU* 1.3 69.0 + - - +
45A ILE* 2.9 19.1 + - + +
46A SER* 3.0 14.4 + - - -
69A LEU* 3.7 35.3 - - + +
72A PRO* 3.3 42.8 - - + -
73A VAL* 4.3 0.9 - - + -
191B PHE* 4.2 15.5 - + - -
194B VAL* 4.3 4.7 - - + -
195B THR* 4.0 23.8 - - + -
198B TRP* 3.9 29.2 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 43 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A GLY 3.1 13.8 + - - +
40A SER* 3.5 12.1 - - - +
42A PHE* 1.3 79.1 - - - +
44A ILE* 1.3 61.9 + - + +
45A ILE 3.0 3.3 + - - -
46A SER* 3.1 6.6 + - - +
47A THR* 3.0 39.5 - - + +
69A LEU 4.8 1.1 - - - -
73A VAL* 3.8 16.6 - - + +
77A PHE* 5.0 2.7 - - + -
271A ARG* 4.2 16.8 - - + -
274A PHE* 4.2 15.3 - - + -
275A GLN* 3.6 41.7 - - + +
377A GLY 5.6 0.2 - - - -
378A ALA* 4.0 25.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 44 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A SER* 2.8 23.4 + - - +
41A ILE* 3.6 19.3 - - + +
43A LEU* 1.3 72.4 - - + +
45A ILE* 1.3 61.0 + - + +
47A THR* 3.7 10.5 + - - +
48A LEU* 3.2 28.5 + - + +
376A SER* 5.1 0.7 - - - +
378A ALA* 3.1 33.4 - - + -
380A VAL* 5.6 10.8 - - + -
392A LEU* 4.4 42.3 - - + +
395A GLY* 5.8 3.1 - - - -
----------------------------------------------------------
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