Contacts of the helix formed by residues 32 - 47 (chain A) in PDB entry 2QKW
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
----------------------------------------------------------
30A ASN 4.6 2.6 + - - -
31A VAL* 1.3 76.3 - - - +
33A SER* 1.3 68.0 + - - +
34A SER* 3.4 24.7 - - - +
35A GLN* 3.0 31.1 + - - +
36A LEU* 2.8 32.7 + - - +
90A MET* 3.9 3.1 - - - +
74B GLU* 4.0 18.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 33 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A THR* 1.3 76.7 - - - +
34A SER* 1.3 61.1 + - - +
36A LEU* 3.4 6.6 - - - +
37A LEU* 2.8 31.7 + - - +
87A HIS* 3.5 23.5 - - - -
90A MET* 3.5 35.2 - - - +
91A THR* 4.5 7.6 + - - -
74B GLU* 5.1 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 34 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A THR* 3.4 17.3 - - - +
33A SER* 1.3 80.0 + - - +
35A GLN* 1.3 66.4 + - - +
37A LEU* 4.0 6.8 - - - +
38A SER* 3.1 24.1 + - - -
87A HIS* 5.5 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 35 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A ASN 4.1 4.9 + - - +
31A VAL* 3.4 20.0 - - + +
32A THR* 3.0 43.1 + - - +
34A SER* 1.3 83.6 + - - +
36A LEU* 1.3 63.1 + - - +
38A SER* 3.4 8.4 + - - -
39A VAL* 3.1 28.5 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
31A VAL* 4.6 1.1 - - + +
32A THR 2.8 16.3 + - - +
33A SER* 3.4 7.9 - - - +
34A SER 3.2 0.2 - - - -
35A GLN* 1.3 73.8 - - - +
37A LEU* 1.3 63.3 + - - +
39A VAL* 2.8 7.6 + - - +
40A ARG* 2.8 26.5 + - + -
83A ALA* 3.8 27.8 - - + +
86A GLN* 4.4 10.5 - - + -
87A HIS* 4.8 8.5 - - + +
90A MET* 3.9 25.1 - - - -
102A PRO* 3.8 29.4 - - + +
105A ASN* 4.4 2.7 - - + -
106A VAL* 4.2 14.1 - - + -
109A MET* 3.6 20.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 37 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A SER 2.8 19.5 + - - +
34A SER* 4.0 6.1 - - - +
36A LEU* 1.3 76.0 - - - +
38A SER* 1.3 57.3 + - - +
40A ARG* 3.3 10.6 + - + +
41A HIS* 3.0 65.9 + - + +
84A ASP* 6.0 1.1 - - - +
87A HIS* 3.5 36.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 38 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A SER 3.1 14.6 + - - -
35A GLN* 3.4 13.7 - - - -
36A LEU 3.1 0.4 - - - -
37A LEU* 1.3 80.4 - - - +
39A VAL* 1.3 57.3 + - - +
41A HIS* 3.7 5.4 + - - +
42A GLN* 3.2 30.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 39 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A GLN* 3.1 16.3 + - + +
36A LEU 2.8 7.6 + - - +
38A SER* 1.3 74.8 - - - +
40A ARG* 1.3 64.6 + - - +
42A GLN* 3.5 15.6 - - - +
43A LEU* 3.2 21.7 + - - +
106A VAL* 4.4 12.6 - - + +
109A MET* 3.8 25.6 - - + +
110A ARG* 3.8 53.6 - - + +
113A ILE* 4.7 2.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 40 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A LEU* 2.8 13.1 + - + +
37A LEU* 3.4 15.9 - - + +
39A VAL* 1.3 77.6 - - - +
41A HIS* 1.3 86.2 + - - +
43A LEU* 3.2 6.4 + - - +
44A ALA* 3.1 40.1 + - - +
80A LEU* 3.6 31.1 - - + +
83A ALA* 4.1 17.0 - - + -
84A ASP* 3.0 40.8 + - - +
109A MET* 3.6 14.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 41 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A LEU* 3.0 49.5 + - + +
38A SER* 4.1 5.2 - - - +
40A ARG* 1.3 101.3 + - - +
42A GLN* 1.3 60.1 + - - +
44A ALA* 3.3 5.2 + - - +
45A GLU* 2.9 33.9 + - - +
84A ASP* 5.9 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 42 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A SER* 3.2 21.0 + - - +
39A VAL* 3.5 23.5 - - - +
41A HIS* 1.3 79.6 - - - +
43A LEU* 1.3 58.0 + - - +
45A GLU* 3.6 4.8 + - - +
46A SER* 3.0 27.0 + - - -
110A ARG* 4.9 8.9 + - - +
113A ILE* 4.1 21.3 - - + +
----------------------------------------------------------
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 VAL 3.2 10.8 + - - +
40A ARG 3.2 6.9 + - - +
42A GLN* 1.3 77.1 - - - +
44A ALA* 1.3 55.1 + - - +
46A SER* 3.1 7.0 + - - +
47A ALA* 2.8 33.6 + - - +
76A THR* 3.7 27.4 - - + -
79A THR* 4.1 11.7 - - + -
80A LEU* 3.7 25.1 - - + -
109A MET* 3.5 26.7 - - + -
112A ALA* 3.7 24.2 - - + -
113A ILE* 3.9 19.7 - - + +
116A TRP* 4.2 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 44 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A ARG* 3.1 41.4 + - - +
41A HIS* 3.3 5.6 + - - +
43A LEU* 1.3 76.4 - - - +
45A GLU* 1.3 62.3 + - - +
46A SER 3.5 0.5 + - - -
47A ALA* 3.5 18.0 + - - +
80A LEU* 4.1 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 45 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A HIS 2.9 18.8 + - - +
42A GLN* 4.0 5.6 - - - +
44A ALA* 1.3 76.9 - - - +
46A SER* 1.3 58.8 + - - +
47A ALA 3.9 0.5 + - - -
48A GLY* 4.9 4.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 46 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A GLN* 3.0 18.7 + - - -
43A LEU* 3.1 12.3 + - - +
45A GLU* 1.3 75.9 - - - +
47A ALA* 1.3 56.7 + - - +
48A GLY 2.9 14.4 + - - +
113A ILE* 3.8 23.9 - - - +
116A TRP* 3.8 8.2 - - - +
120A ARG* 3.4 29.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 47 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A LEU 2.8 15.9 + - - +
44A ALA* 3.5 14.7 + - - +
45A GLU 3.5 1.7 - - - -
46A SER* 1.3 73.9 - - - +
48A GLY* 1.3 56.6 + - - +
73A TYR* 5.1 8.6 - - + -
76A THR* 4.0 13.7 - - + -
80A LEU* 5.5 1.8 - - + -
116A TRP* 3.6 40.5 - - + +
----------------------------------------------------------
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