Contacts of the helix formed by residues 49 - 68 (chain A) in PDB entry 2P6U
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 49 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A MET* 4.3 4.2 - - - +
48A PRO* 1.3 86.3 - - - +
50A ALA* 1.3 67.3 + - + +
51A ALA* 3.0 31.5 + - + +
52A GLY 4.4 0.9 + - - -
53A LYS* 3.4 11.8 + - - +
201A TRP 5.8 0.4 - - - -
202A ARG* 3.6 33.3 + - - +
203A PRO* 4.8 4.0 - - + -
368A GLY* 3.9 19.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 50 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A PRO 3.6 2.6 + - - -
49A THR* 1.3 75.2 - - + +
51A ALA* 1.3 68.3 + - - +
53A LYS* 3.1 16.5 + - - +
54A THR* 3.0 23.5 + - - +
84A LYS* 5.8 0.2 - - - -
708A PO4 3.1 46.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 51 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A LEU 5.0 2.2 - - - +
49A THR* 3.0 25.9 - - + +
50A ALA* 1.3 82.0 - - - +
52A GLY* 1.3 62.7 + - - +
54A THR* 3.2 9.7 + - - -
55A LEU* 3.7 7.6 + - - +
203A PRO* 3.9 23.3 - - + -
703A PO4 4.2 6.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 52 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A LEU 3.9 19.6 + - - -
27A PHE* 4.3 0.8 - - - +
28A PRO* 4.3 5.4 - - - -
47A MET* 4.3 7.6 - - - -
49A THR 4.4 1.8 + - - -
51A ALA* 1.3 77.3 - - - +
53A LYS* 1.3 66.6 + - - +
55A LEU* 3.4 3.4 + - - +
56A LEU* 3.3 26.5 + - - +
201A TRP* 4.3 19.2 - - - -
203A PRO* 5.0 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 53 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A LEU* 3.8 16.9 - - + +
47A MET* 3.2 48.0 + - + +
48A PRO 3.6 6.3 + - - -
49A THR 3.4 20.0 + - - +
50A ALA* 3.2 25.4 - - - +
52A GLY* 1.3 78.3 - - - +
54A THR* 1.3 63.2 + - - +
56A LEU* 3.5 4.5 + - - +
57A ALA* 3.3 18.9 + - - +
145A ASP* 5.2 1.1 - - - -
146A GLU* 6.2 0.7 - - - +
148A HIS* 6.2 1.1 - - - -
178A LEU* 4.0 28.9 - - + +
179A SER* 3.2 37.8 - - - +
180A ALA* 4.2 2.2 - - - +
708A PO4 4.7 7.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 54 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A ALA* 3.0 17.4 + - - +
51A ALA 3.2 1.7 + - - -
53A LYS* 1.3 73.8 - - - +
55A LEU* 1.3 59.4 + - - +
57A ALA* 3.2 6.7 + - - +
58A GLU* 2.8 52.0 + - + +
73A TYR* 3.9 18.5 + - + +
84A LYS* 4.0 17.7 + - + -
87A SER* 5.3 1.1 - - - +
88A PHE* 4.2 12.8 - - + -
178A LEU* 4.8 4.4 - - - +
703A PO4 3.6 12.3 - - - +
708A PO4 4.2 6.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 55 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A SER* 4.0 5.4 - - - -
15A VAL* 4.7 9.6 - - + -
26A LEU* 3.0 45.1 - - + +
27A PHE* 4.0 7.0 - - + -
51A ALA 3.7 5.0 + - - +
52A GLY 3.4 6.9 + - - +
54A THR* 1.3 77.0 - - - +
56A LEU* 1.3 58.5 + - - +
58A GLU* 3.5 12.7 - - - +
59A MET* 2.9 55.2 + - + +
91A TRP* 4.0 17.5 - - + -
703A PO4 3.5 26.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 56 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A PHE* 4.2 21.8 - - + -
28A PRO* 3.6 18.8 - - + -
33A ALA* 3.6 21.8 - - + -
34A VAL* 4.3 11.0 - - + +
37A VAL* 3.6 23.6 - - + +
45A LEU* 3.7 18.8 - - + -
47A MET* 3.4 31.4 - - + -
52A GLY 3.3 8.6 + - - +
53A LYS 3.7 7.6 - - - +
54A THR 3.2 0.6 - - - -
55A LEU* 1.3 76.0 - - - +
57A ALA* 1.3 61.4 + - - +
59A MET* 3.4 10.0 + - - +
60A ALA* 2.9 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 57 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A LEU* 4.9 1.1 - - - +
53A LYS 3.3 4.4 + - - +
54A THR* 3.2 9.3 + - - +
56A LEU* 1.3 80.1 - - - +
58A GLU* 1.3 56.5 + - - +
60A ALA* 2.8 27.7 - - - +
61A MET* 2.8 21.8 + - + +
73A TYR* 4.5 2.2 - - + -
143A VAL* 4.2 13.8 - - + +
176A ILE* 5.1 3.6 - - + -
178A LEU* 3.7 37.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 58 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A THR* 2.8 41.0 + - + +
55A LEU* 3.5 8.3 - - - +
57A ALA* 1.3 73.1 - - - +
59A MET* 1.3 54.2 + - - +
61A MET* 2.9 13.8 + - + +
62A VAL* 2.7 38.5 + - - +
88A PHE* 3.6 32.9 - - + -
90A LYS* 3.2 7.0 - - - -
91A TRP* 2.7 39.5 + - + +
117A ILE* 5.2 1.2 - - + +
703A PO4 2.6 34.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 59 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A ALA* 3.8 17.7 - - - +
10A ILE* 3.9 19.5 - - + +
11A SER* 3.3 24.9 - - - -
27A PHE* 3.6 24.9 - - + -
34A VAL* 5.4 0.2 - - - -
37A VAL* 4.4 8.7 - - + -
38A PHE* 4.3 14.3 - - + -
55A LEU* 2.9 53.5 + - + +
56A LEU* 3.5 11.2 - - - +
58A GLU* 1.3 71.0 - - - +
60A ALA* 1.3 70.2 + - - +
62A VAL* 3.0 9.2 + - - +
63A ARG* 2.8 26.6 + - - +
91A TRP* 5.0 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 60 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A VAL* 3.7 20.8 - - + +
56A LEU 2.9 14.9 + - - +
57A ALA* 2.8 17.0 - - - +
59A MET* 1.3 79.2 - - - +
61A MET* 1.3 55.0 + - + +
63A ARG* 3.4 8.9 + - - +
64A GLU* 3.0 25.1 + - - +
141A CYS* 5.5 1.9 - - - -
143A VAL* 5.5 0.2 - - + -
174A ARG* 4.6 4.4 + - - +
176A ILE* 3.5 31.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 61 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A ALA* 2.8 22.7 + - + +
58A GLU* 2.9 19.9 + - + +
60A ALA* 1.3 73.9 - - - +
62A VAL* 1.3 67.6 + - - +
64A GLU* 3.0 3.6 + - - +
65A ALA* 2.7 25.7 + - - +
71A SER* 3.3 32.1 + - - +
73A TYR* 3.3 39.7 - - + -
88A PHE* 3.9 13.2 - - + -
96A LEU* 4.8 0.9 - - - -
117A ILE* 3.5 42.0 - - + -
141A CYS* 5.2 1.3 - - - -
143A VAL* 4.3 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 62 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ILE* 3.9 27.6 - - + -
58A GLU 2.7 22.4 + - - +
59A MET* 3.0 9.6 + - - +
61A MET* 1.3 72.4 - - + +
63A ARG* 1.3 63.8 + - - +
65A ALA* 3.3 3.3 + - - +
66A ILE* 3.1 35.7 + - + +
91A TRP* 3.4 51.6 - - + +
94A ILE* 4.7 11.4 - - + -
96A LEU* 4.1 15.2 - - + +
117A ILE* 5.7 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 63 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ILE* 5.6 1.8 - - - +
37A VAL 4.6 1.6 - - - -
38A PHE* 3.2 60.7 + - + +
39A SER 4.2 2.4 + - - -
40A GLY* 3.6 19.3 - - - -
59A MET 2.8 16.3 + - - +
60A ALA* 3.5 5.3 + - - +
62A VAL* 1.3 77.9 - - - +
64A GLU* 1.3 81.3 + - - +
66A ILE* 2.9 22.1 + - - +
67A LYS* 2.9 52.2 + - + +
174A ARG* 3.3 24.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 64 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A ALA 3.0 11.2 + - - +
61A MET 3.0 7.9 + - - +
63A ARG* 1.3 87.7 + - - +
65A ALA* 1.3 54.4 + - - +
67A LYS* 3.2 29.3 + - - +
68A GLY 3.2 4.9 + - - -
69A GLY* 2.7 35.7 + - - -
70A LYS 4.1 1.8 - - - +
71A SER* 3.9 13.2 - - - +
140A SER* 2.4 38.9 + - - +
141A CYS* 3.8 23.9 - - + +
174A ARG* 4.7 9.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 65 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A MET 2.7 15.4 + - - +
62A VAL 3.3 10.8 - - - +
64A GLU* 1.3 73.3 - - - +
66A ILE* 1.3 55.4 + - - +
68A GLY* 2.6 28.4 + - - -
69A GLY 4.0 11.7 - - - +
70A LYS* 5.9 0.2 - - - +
71A SER* 5.2 0.6 + - - +
96A LEU* 3.6 31.0 - - + -
116A ASP* 4.3 17.7 - - + +
117A ILE* 6.1 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 66 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A LEU* 6.4 0.2 - - + -
10A ILE* 4.7 12.3 - - + -
62A VAL* 3.2 28.9 - - + +
63A ARG* 2.9 10.4 + - - +
65A ALA* 1.3 76.8 - - + +
67A LYS* 1.3 61.2 + - + +
68A GLY* 3.1 1.6 + - - -
94A ILE* 5.3 11.7 - - + -
96A LEU* 5.5 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 67 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A GLY* 5.4 1.4 - - - -
63A ARG* 2.9 59.6 + - + +
64A GLU* 3.3 32.8 + - - +
65A ALA 3.1 0.2 - - - -
66A ILE* 1.3 76.0 - - + +
68A GLY* 1.3 59.6 + - - +
69A GLY 4.5 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 68 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A ALA 2.6 14.4 + - - -
66A ILE 2.9 2.1 - - - -
67A LYS* 1.3 80.8 - - - +
69A GLY* 1.3 61.6 + - - +
----------------------------------------------------------
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