Contacts of the helix formed by residues 42 - 61 (chain B) in PDB entry 2V32
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 42 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A PRO* 3.8 19.5 - - + -
212A TYR* 3.6 3.8 - - - -
39B ARG* 2.7 43.6 + - + -
40B ASP 3.8 2.0 - - - +
41B PHE* 1.3 84.8 - - - +
43B PRO* 1.4 65.3 - - - +
45B SER* 3.1 6.8 + - - -
46B THR* 2.6 36.0 + - - -
80B TRP* 4.3 0.2 - - - +
1220B BEZ 2.9 33.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 43 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A MET* 3.6 33.7 - - + -
185A VAL 3.6 22.2 - - - +
187A PRO* 4.0 13.5 - - + -
212A TYR* 3.4 26.6 - - + +
213A LEU* 4.0 12.4 - - + +
214A ARG 4.3 1.6 - - - +
42B THR* 1.4 80.5 - - - +
44B VAL* 1.3 64.5 + - - +
46B THR* 3.0 12.6 + - - -
47B THR* 3.1 16.3 + - - +
1220B BEZ 3.2 18.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 44 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A ALA* 3.5 26.7 - - + -
173A THR 3.5 24.5 - - - +
174A PRO* 4.1 3.4 - - + -
184A MET* 3.8 16.3 - - + +
43B PRO* 1.3 70.9 - - - +
45B SER* 1.3 57.3 + - - +
47B THR* 2.6 26.2 + - - -
48B GLU* 2.8 17.4 + - + +
128B ARG* 3.7 16.6 - - - +
147B ALA 4.8 0.9 - - - +
150B GLY* 3.5 20.9 - - - +
1220B BEZ 3.0 24.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 45 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B HIS* 3.5 16.6 - - - +
38B PRO* 3.7 5.4 - - - +
39B ARG 3.7 3.5 + - - -
42B THR* 3.1 24.1 + - - -
43B PRO 3.3 0.2 - - - -
44B VAL* 1.3 74.3 - - - +
46B THR* 1.3 58.0 + - - +
48B GLU* 4.0 4.5 - - - -
49B LEU* 3.0 33.8 + - - +
80B TRP* 3.7 18.9 - - - -
128B ARG* 3.0 22.1 + - - +
1220B BEZ 3.0 6.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 46 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A TYR* 3.4 17.4 - - - +
213A LEU* 4.0 11.4 - - + -
42B THR 2.6 23.4 + - - -
43B PRO 3.0 6.3 + - - -
45B SER* 1.3 74.8 - - - +
47B THR* 1.3 59.4 + - - +
49B LEU* 4.4 0.2 - - - +
50B GLY* 2.8 29.1 + - - -
80B TRP* 3.0 23.0 + - - +
83B ASP* 4.1 4.5 - - + +
84B VAL* 4.0 24.5 - - - +
87B LEU* 3.7 21.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 47 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A PRO* 3.4 19.1 - - + +
175A ALA* 3.0 31.1 + - - +
184A MET* 4.5 12.8 - - + -
215A TYR* 5.1 6.1 - - + +
43B PRO 3.1 13.7 + - - +
44B VAL 2.6 18.2 + - - -
46B THR* 1.3 76.9 - - - +
48B GLU* 1.3 54.1 + - - +
50B GLY* 3.7 0.7 - - - -
51B ARG* 2.8 30.1 + - - +
87B LEU* 3.7 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 48 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A ALA* 3.8 19.7 - - + -
37B HIS* 4.6 0.7 - - - +
44B VAL* 2.8 27.5 + - + +
45B SER* 3.9 5.4 - - - +
47B THR* 1.3 74.2 + - - +
49B LEU* 1.3 61.8 + - + +
51B ARG* 3.1 4.4 + - - +
52B VAL* 3.0 31.7 + - - +
128B ARG* 2.9 28.1 + - - -
150B GLY* 3.4 1.9 - - - -
151B ARG* 2.6 71.9 + - - +
153B PHE* 3.9 11.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 49 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B PHE* 3.8 23.1 - - + -
37B HIS* 3.9 31.2 - - + +
45B SER 3.0 21.9 + - - +
48B GLU* 1.3 78.1 - - + +
50B GLY* 1.3 63.9 + - - +
52B VAL* 3.4 3.6 + - - +
53B ILE* 3.2 18.0 + - - +
68B ALA* 4.3 4.9 - - + -
80B TRP* 3.7 24.9 - - + -
84B VAL* 3.7 17.9 - - + -
94B MET* 4.9 0.7 - - + -
96B TYR* 2.9 40.9 + - + +
98B ILE* 4.2 12.1 - - + -
151B ARG* 5.0 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 50 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B THR 2.8 19.9 + - - -
47B THR* 3.7 1.3 - - - -
49B LEU* 1.3 76.5 - - - +
51B ARG* 1.3 60.7 + - - +
53B ILE 3.5 1.0 + - - -
54B GLN* 3.3 20.5 + - - +
84B VAL* 3.7 11.6 - - - +
87B LEU* 4.9 2.7 - - - -
88B SER* 3.4 33.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 51 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A ALA* 4.3 8.7 - - + -
176A ASP* 3.3 26.8 + - - +
47B THR 2.8 18.8 + - - +
48B GLU 3.1 6.7 + - - +
50B GLY* 1.3 75.2 - - - +
52B VAL* 1.3 64.2 + - - +
54B GLN* 3.1 50.1 + - - +
55B LEU* 3.1 49.2 + - + +
153B PHE* 4.4 12.1 - - + +
154B SER* 4.4 13.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 52 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B PHE* 3.9 16.6 - - + -
48B GLU 3.0 15.4 + - - +
49B LEU 3.4 6.9 + - - +
51B ARG* 1.3 75.3 - - - +
53B ILE* 1.3 57.9 + - - +
55B LEU* 3.2 8.3 + - - +
56B GLU* 2.9 27.4 + - - +
59B PHE* 4.6 3.4 - - + -
66B LEU* 3.6 32.8 - - + -
96B TYR* 3.5 21.5 - - + -
153B PHE* 3.7 37.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 53 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B LEU 3.2 10.5 + - - +
50B GLY 3.5 7.4 - - - +
52B VAL* 1.3 72.8 - - - +
54B GLN* 1.3 66.3 + - - +
55B LEU 3.1 0.9 + - - -
56B GLU* 3.1 19.4 + - + +
84B VAL* 3.6 29.2 - - + +
85B LYS* 4.3 8.1 - - + -
88B SER* 3.7 24.9 - - - +
90B VAL* 3.7 26.4 - - + +
94B MET* 3.9 17.3 - - - -
95B PRO* 3.8 29.6 - - + -
96B TYR* 3.9 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 54 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B GLY 3.3 10.9 + - - +
51B ARG* 3.1 47.7 + - - +
53B ILE* 1.3 77.5 - - - +
55B LEU* 1.3 61.8 + - - +
56B GLU 3.8 0.2 + - - -
57B GLY 4.8 1.7 + - - -
58B ASP* 4.1 6.4 - - - +
87B LEU 4.4 3.8 + - - -
88B SER* 2.8 32.8 + - - +
90B VAL* 4.4 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 55 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B ARG* 3.1 57.3 + - + +
52B VAL* 3.2 3.8 + - - +
53B ILE 3.1 0.6 - - - -
54B GLN* 1.3 79.6 - - - +
56B GLU* 1.3 66.4 + - - +
57B GLY 3.1 3.1 - - - -
58B ASP* 3.0 35.3 + - + +
59B PHE* 3.1 29.2 + - + -
153B PHE* 3.7 30.5 - - + +
154B SER* 4.9 0.9 - - - +
157B LEU* 4.4 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 56 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B VAL 2.9 11.8 + - - +
53B ILE* 3.1 18.4 + - + +
55B LEU* 1.3 76.5 - - - +
57B GLY* 1.3 72.0 + - - +
59B PHE* 3.3 8.8 + - - +
60B LYS* 2.9 55.7 + - - +
66B LEU* 4.4 8.2 - - + +
90B VAL* 6.6 0.7 - - + -
95B PRO* 3.9 35.5 - - + +
96B TYR* 5.6 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 57 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B GLN 4.8 2.4 + - - -
55B LEU 3.1 0.8 - - - -
56B GLU* 1.3 93.2 - - - +
58B ASP* 1.3 63.7 + - - +
60B LYS* 3.6 8.0 - - - +
61B LYS* 3.1 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 58 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B GLN 4.1 4.3 - - - +
55B LEU* 3.3 34.4 - - - +
57B GLY* 1.3 76.8 - - - +
59B PHE* 1.3 60.0 + - - +
61B LYS* 3.3 29.5 + - - +
62B ARG* 2.8 36.4 + - - +
157B LEU* 4.0 20.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 59 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B VAL* 4.6 1.6 - - + -
52B VAL* 4.6 7.0 - - + -
55B LEU* 3.1 44.2 + - + -
56B GLU 3.6 5.6 - - - +
58B ASP* 1.3 75.4 - - - +
60B LYS* 1.3 65.8 + - - +
62B ARG* 3.0 14.1 + - - +
64B VAL* 3.1 43.3 + - + +
66B LEU* 3.5 47.8 - - + -
153B PHE* 4.5 15.7 - + - -
156B ILE* 4.0 16.6 - - + -
157B LEU* 4.0 21.1 - - + -
160B ILE* 3.8 24.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 60 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B GLU* 2.9 43.0 + - - +
57B GLY* 3.6 7.4 - - - +
59B PHE* 1.3 75.7 - - - +
61B LYS* 1.3 61.2 + - - +
62B ARG 3.0 0.2 - - - -
63B GLY* 3.1 14.7 + - - +
64B VAL 4.2 5.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 61 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B GLY 3.1 21.3 + - - +
58B ASP* 3.3 28.4 + - - +
60B LYS* 1.3 77.3 - - - +
62B ARG* 1.4 90.4 + - + +
63B GLY 3.4 0.4 + - - -
----------------------------------------------------------
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