Contacts of the helix formed by residues 51 - 71 (chain A) in PDB entry 2P02
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 HIS 51 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A CL 3.1 22.7 - - + +
2A SAM 3.1 35.4 + - - -
47A VAL* 3.6 32.7 - - + +
48A GLY 3.1 16.4 + - - +
50A GLY* 1.3 76.3 - - - +
52A PRO* 1.3 64.1 - - + +
53A ASP* 3.1 43.5 + - + +
54A LYS* 3.0 7.3 + - + -
55A ILE* 2.8 24.4 + - - +
201A ASP* 3.4 10.6 - - - +
202A SER 4.0 3.6 - - - +
203A LYS* 3.8 5.8 - - + +
280A ASP* 4.8 0.2 - - - -
287A LYS* 3.5 10.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 52 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A SAM 3.3 26.9 - - - +
50A GLY 3.8 4.0 - - - +
51A HIS* 1.3 85.8 - - + +
53A ASP* 1.3 60.9 + - - +
55A ILE* 3.4 14.9 + - + +
56A CYS* 3.3 26.2 + - - -
82A ALA* 4.5 1.0 - - - +
201A ASP* 3.9 12.3 - - - +
276A GLY 4.0 6.3 - - - +
277A PRO* 3.9 16.8 - - + -
280A ASP* 3.2 32.1 - - - +
281A ALA 4.4 2.0 - - - +
282A GLY* 3.6 11.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 53 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A CL 4.2 2.6 - - - +
51A HIS* 3.1 17.5 + - + +
52A PRO* 1.3 76.3 - - - +
54A LYS* 1.3 59.3 + - - +
56A CYS* 3.2 6.1 + - - +
57A ASP* 3.0 28.1 + - - +
280A ASP* 5.4 1.0 - - - +
281A ALA 3.9 5.6 - - - +
282A GLY* 3.3 6.6 - - - -
283A LEU* 3.0 33.6 + - - +
286A ARG* 3.5 25.2 + - + +
287A LYS* 2.8 40.0 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 54 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A VAL* 3.6 26.0 - - + +
48A GLY 3.5 23.3 - - - +
51A HIS* 3.0 6.1 + - - +
53A ASP* 1.3 77.1 - - - +
55A ILE* 1.3 65.1 + - - +
57A ASP* 2.8 28.1 + - - +
58A GLN* 2.9 37.1 + - - +
287A LYS* 3.9 16.8 - - + -
290A VAL* 4.2 12.1 - - - -
291A ASP* 2.8 30.3 + - - -
397A ALA* 2.8 34.2 + - - +
398A ALA* 4.4 11.7 - - + +
399A TYR 5.2 2.0 - - - +
400A GLY 5.7 0.2 - - - +
401A HIS* 4.9 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 55 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A GLU 3.7 12.8 - - - +
50A GLY* 3.4 20.0 - - - +
51A HIS 2.8 14.4 + - - +
52A PRO* 3.5 11.4 - - + +
53A ASP 3.3 0.2 - - - -
54A LYS* 1.3 76.2 - - - +
56A CYS* 1.3 58.0 + - - +
58A GLN* 3.3 7.9 + - - +
59A ILE* 2.9 49.1 + - + +
82A ALA* 5.0 2.9 - - + -
87A ILE* 4.5 11.4 - - + -
109A VAL* 4.6 7.4 - - + -
112A ILE* 4.1 15.0 - - + -
114A TYR* 3.9 16.4 - - + -
121A PHE* 6.0 2.9 - - + -
277A PRO* 3.8 28.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 56 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A PRO 3.5 6.7 - - - -
53A ASP 3.2 9.9 + - - +
55A ILE* 1.3 77.3 - - - +
57A ASP* 1.3 67.6 + - - +
59A ILE 3.3 0.2 + - - -
60A SER* 2.9 28.2 + - - -
80A THR* 3.3 35.2 + - - +
81A VAL 3.8 0.4 - - - -
82A ALA* 3.6 20.6 - - - -
282A GLY 3.4 27.4 - - - -
283A LEU 3.5 0.2 - - - -
284A THR* 3.4 21.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 57 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A ASP 3.0 18.6 + - - +
54A LYS* 2.8 41.1 + - - +
56A CYS* 1.3 75.1 - - - +
58A GLN* 1.3 57.3 + - - +
60A SER* 3.4 1.2 + - - -
61A ASP* 3.0 25.6 + - - +
284A THR* 3.5 6.8 - - - +
285A GLY* 2.9 29.9 + - - -
286A ARG 5.0 0.2 + - - -
287A LYS* 4.3 7.8 + - - +
291A ASP* 4.0 8.0 - - - +
305A SER* 3.4 30.5 + - - +
397A ALA* 3.9 4.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 58 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A GLU* 2.8 46.6 + - - +
54A LYS* 2.9 30.2 + - - +
55A ILE 3.7 3.4 - - - +
57A ASP* 1.3 75.4 - - - +
59A ILE* 1.3 58.1 + - + +
61A ASP 3.4 1.4 + - - -
62A ALA* 2.8 29.2 + - - +
108A ALA* 5.1 1.8 - - + -
111A HIS* 5.0 5.2 - - - -
112A ILE* 3.6 25.3 - - + +
394A GLN* 3.7 24.9 + - + +
397A ALA* 3.8 26.5 - - + +
398A ALA* 4.2 10.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 59 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A ILE* 2.9 42.0 + - + +
56A CYS 3.9 3.1 - - - +
58A GLN* 1.3 73.1 - - + +
60A SER* 1.3 67.0 + - - +
62A ALA* 3.1 7.7 + - + +
63A VAL* 2.9 25.5 + - + +
80A THR* 3.6 17.7 - - + +
87A ILE* 3.7 27.4 - - + -
89A LEU* 3.8 18.4 - - + -
105A VAL* 3.9 20.0 - - + +
108A ALA* 4.0 19.1 - - + -
109A VAL* 3.9 12.8 - - + -
112A ILE* 5.5 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 60 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A CYS 2.9 12.3 + - - -
57A ASP 3.6 4.9 - - - -
59A ILE* 1.3 76.4 - - - +
61A ASP* 1.3 58.4 + - - +
63A VAL* 3.4 7.8 + - - +
64A LEU 3.0 21.0 + - - -
78A CYS* 2.7 30.8 + - - +
80A THR* 2.9 13.7 + - - -
284A THR* 2.8 23.7 + - - -
305A SER 4.0 3.6 - - - -
306A GLY* 3.6 22.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 61 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A ASP 3.0 11.3 + - - +
58A GLN 4.0 1.1 - - - +
60A SER* 1.3 74.0 - - - +
62A ALA* 1.3 58.5 + - - +
64A LEU* 3.6 7.1 - - - +
65A ASP* 2.9 33.6 + - - -
305A SER* 2.8 26.0 + - - -
306A GLY 2.8 11.4 + - - -
314A ARG* 2.8 41.7 + - - -
393A TYR* 3.4 22.6 - - + +
394A GLN* 3.7 11.2 - - - +
397A ALA* 3.5 7.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 62 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A GLN 2.8 20.9 + - - +
59A ILE* 3.1 9.6 + - - +
61A ASP* 1.3 71.3 - - - +
63A VAL* 1.3 57.8 + - - +
65A ASP* 3.5 4.0 + - - +
66A ALA* 3.0 28.9 + - - +
104A VAL* 3.7 18.5 - - + +
108A ALA* 4.2 9.4 - - + -
394A GLN* 3.5 29.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 63 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A ILE* 2.9 22.4 + - + +
60A SER 3.6 7.6 - - - +
62A ALA* 1.3 73.2 - - - +
64A LEU* 1.3 66.2 + - - +
66A ALA* 3.2 4.0 + - - +
67A HIS* 3.1 25.0 + - + -
76A VAL* 4.9 0.4 - - + -
78A CYS* 3.8 23.1 - - + -
89A LEU* 4.1 22.7 - - + -
93A ILE* 3.9 14.6 - - + -
99A VAL* 5.4 0.7 - - + -
101A TYR* 3.8 27.1 - - + -
104A VAL* 4.1 16.8 - - + -
105A VAL* 4.9 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 64 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A SER 3.0 14.7 + - - +
61A ASP* 3.4 12.3 + - - +
63A VAL* 1.3 75.4 - - - +
65A ASP* 1.3 58.1 + - - +
67A HIS* 3.2 5.2 + - - +
68A LEU* 2.9 51.3 + - + +
76A VAL* 3.7 38.3 - - + +
306A GLY* 4.6 1.6 - - - -
307A LYS 3.3 23.3 - - - +
308A ASP* 3.9 16.2 - - + +
314A ARG* 3.4 20.2 - - - +
393A TYR* 3.4 19.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 65 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A ASP 2.9 18.3 + - - +
62A ALA* 3.8 5.4 - - - +
64A LEU* 1.3 72.7 - - - +
66A ALA* 1.3 63.5 + - - +
68A LEU* 3.2 1.9 + - - +
69A GLN* 2.9 38.5 + - - +
391A PRO* 3.1 35.3 - - + +
392A ILE 3.9 0.5 - - - -
393A TYR* 2.9 29.7 + - - +
394A GLN* 2.9 31.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 66 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A ALA 3.0 18.7 + - - +
63A VAL 3.2 4.9 + - - +
65A ASP* 1.3 76.9 - - - +
67A HIS* 1.3 64.4 + - - +
69A GLN* 3.6 25.3 + - - +
70A GLN* 3.8 11.5 + - - +
99A VAL* 4.0 20.4 - - + +
104A VAL* 3.9 25.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 67 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A VAL* 3.1 35.6 + - + +
64A LEU 3.6 7.0 - - - +
66A ALA* 1.3 78.2 - - - +
68A LEU* 1.3 58.3 + - - +
70A GLN* 3.1 5.7 + - - +
71A ASP* 2.8 29.0 + - - +
74A ALA* 3.9 14.4 - - + -
76A VAL* 4.1 7.2 - - + -
93A ILE* 3.6 25.4 - - + +
95A SER* 2.8 26.8 + - - -
97A ALA* 3.5 16.1 - - + +
99A VAL* 3.6 21.0 - - + +
101A TYR* 2.9 28.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 68 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A LEU* 2.9 34.7 + - + +
65A ASP 3.2 3.8 + - - +
67A HIS* 1.3 75.7 - - - +
69A GLN* 1.3 63.1 + - - +
70A GLN 3.3 0.7 + - - -
71A ASP 3.5 13.7 + - - +
72A PRO* 3.5 41.6 - - - +
74A ALA* 4.4 14.4 - - + +
308A ASP* 5.2 4.3 - - + -
309A TYR* 6.5 0.4 - - + -
388A LEU 4.6 1.6 - - - +
389A LYS* 3.8 26.4 - - - +
390A LYS 4.2 3.4 - - - +
391A PRO* 4.1 11.6 - - + +
393A TYR* 3.6 37.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 69 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A ASP* 2.9 34.0 + - - +
66A ALA* 3.7 16.6 - - - +
67A HIS 3.2 0.2 - - - -
68A LEU* 1.3 77.1 - - - +
70A GLN* 1.3 63.4 + - + +
72A PRO* 5.5 0.7 - - - +
391A PRO* 3.9 23.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 70 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A ALA* 3.8 12.6 + - - +
67A HIS 3.1 2.0 + - - -
69A GLN* 1.3 84.1 - - + +
71A ASP* 1.3 57.9 + - - +
72A PRO* 4.0 7.3 - - - +
96A ARG* 4.8 1.9 - - - +
97A ALA* 3.4 18.9 - - + +
98A ALA* 2.9 47.6 + - - +
99A VAL* 4.2 4.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 71 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A HIS 2.8 16.0 + - - +
68A LEU* 3.5 5.7 - - - -
70A GLN* 1.3 74.4 - - - +
72A PRO* 1.3 66.6 - - - +
73A ASP* 2.9 11.3 + - - -
74A ALA* 3.0 26.5 + - - +
95A SER* 3.6 18.4 - - - +
96A ARG* 2.8 66.1 + - + +
97A ALA 4.1 4.3 - - - +
----------------------------------------------------------
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