Contacts of the helix formed by residues 63 - 80 (chain A) in PDB entry 2L33
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 ASN 63 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A PHE* 3.6 20.9 - - + -
61A GLY 3.1 2.0 + - - -
62A SER* 1.3 88.0 + - - +
64A LYS* 1.3 67.8 + - - +
65A LYS* 3.3 11.6 + - - +
66A VAL* 2.9 45.2 + - - +
67A ALA* 2.8 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 64 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A LEU* 3.2 23.6 - - + +
37A GLU* 2.6 28.4 + - - -
46A PHE* 3.6 20.2 - - + -
48A MET* 3.3 28.9 - - + +
63A ASN* 1.3 75.0 - - - +
65A LYS* 1.3 64.9 + - + +
67A ALA 3.2 0.3 + - - -
68A LYS* 2.8 34.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 65 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A VAL* 4.5 4.3 - - - +
63A ASN* 3.3 8.1 + - - +
64A LYS* 1.3 81.7 - - + +
66A VAL* 1.3 59.0 + - + +
68A LYS* 3.4 22.4 - - + +
69A ALA* 3.1 24.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 66 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A HIS* 6.4 2.0 - - + -
11A MET* 5.3 6.3 - - + -
61A GLY* 4.0 8.5 - - - -
62A SER* 4.0 6.1 - - - +
63A ASN* 2.9 39.3 + - - +
65A LYS* 1.3 74.5 - - + +
67A ALA* 1.3 65.6 + - - +
69A ALA* 3.1 17.4 + - + +
70A TYR* 3.2 41.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 67 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A PHE* 3.4 27.8 - - + +
48A MET* 3.5 17.5 - - + -
59A GLY 3.6 11.9 - - - +
60A ALA 4.1 1.3 - - - -
61A GLY* 3.5 11.6 - - - +
63A ASN 2.8 19.0 + - - +
64A LYS 3.4 4.3 - - - +
66A VAL* 1.3 73.3 - - - +
68A LYS* 1.3 60.5 + - - +
70A TYR 3.3 0.9 + - - -
71A ALA* 2.9 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 68 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A VAL* 3.9 24.9 - - + +
32A TYR* 3.7 38.8 - - + +
48A MET* 3.7 33.0 - - + +
64A LYS* 2.8 22.0 + - + +
65A LYS* 3.4 24.1 - - + +
67A ALA* 1.3 76.4 - - - +
69A ALA* 1.3 56.5 + - - +
71A ALA* 3.3 4.1 + - - +
72A ALA* 2.8 31.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 69 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A MET* 4.7 16.2 - - + +
18A ASN* 4.7 4.3 - - - +
19A PRO* 3.5 25.3 - - + +
20A VAL* 3.8 8.5 - - + +
65A LYS 3.1 13.1 + - - +
66A VAL* 3.1 15.5 + - + +
68A LYS* 1.3 75.9 - - - +
70A TYR* 1.3 56.4 + - - +
72A ALA 3.3 1.4 + - - -
73A LEU* 2.9 34.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 70 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A MET* 3.0 41.6 - - + -
59A GLY* 4.1 3.5 - - - -
60A ALA 3.1 35.7 - - - +
61A GLY* 4.2 2.2 - - - -
66A VAL* 3.2 41.4 + - + +
67A ALA 3.9 4.3 - - - +
69A ALA* 1.3 74.4 - - - +
71A ALA* 1.3 60.8 + - - +
73A LEU* 3.7 11.9 - - + +
74A ALA* 2.8 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 71 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A TYR* 5.8 0.2 - - + -
48A MET* 3.5 26.5 - - + +
49A GLU 4.8 0.2 - - - -
50A VAL* 3.3 23.7 - - + +
57A PHE* 3.9 9.0 - - - +
58A GLN 4.2 2.9 - - - -
59A GLY* 3.5 12.7 - - - +
67A ALA 2.9 17.9 + - - +
68A LYS* 3.6 8.7 - - - +
70A TYR* 1.3 76.2 - - - +
72A ALA* 1.3 62.8 + - - +
74A ALA* 3.3 16.0 + - - +
75A ALA 3.4 3.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 72 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A PRO* 3.6 31.0 - - + +
20A VAL* 4.0 4.7 - - - +
23A LEU* 3.8 22.6 - - + +
32A TYR* 4.6 3.8 - - + +
50A VAL* 4.1 2.2 - - - +
68A LYS 2.8 17.7 + - - +
69A ALA 3.5 4.5 - - - +
71A ALA* 1.3 74.1 - - - +
73A LEU* 1.3 60.4 + - - +
75A ALA* 3.0 6.4 + - - +
76A LEU* 2.8 31.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 73 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A MET* 4.0 20.0 - - + -
12A LEU 3.8 15.5 - - - +
13A THR* 3.2 36.8 - - - +
14A LYS 4.9 0.7 - - - +
19A PRO* 3.7 7.6 - - + -
69A ALA 2.9 21.9 + - - +
70A TYR* 3.7 13.7 - - + +
72A ALA* 1.3 74.7 - - - +
74A ALA* 1.3 58.0 + - - +
76A LEU* 3.9 9.2 - - + -
77A GLU* 2.9 47.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 74 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A PHE* 4.0 22.3 - - + -
58A GLN 4.5 9.4 - - - +
59A GLY* 5.6 0.2 - - - -
70A TYR 2.8 14.2 + - - +
71A ALA* 3.3 14.4 - - - +
72A ALA 3.2 0.2 - - - -
73A LEU* 1.3 78.0 - - - +
75A ALA* 1.3 59.5 + - - +
77A GLU* 4.5 3.3 - - - +
78A LYS* 3.6 18.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 75 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A LEU* 4.4 6.7 - - + -
50A VAL* 4.6 0.9 - - + -
52A VAL* 3.8 25.4 - - + -
57A PHE* 3.6 33.6 - - + -
71A ALA 3.4 5.6 + - - +
72A ALA 3.0 8.6 + - - +
74A ALA* 1.3 77.9 - - - +
76A LEU* 1.3 55.7 + - - +
78A LYS* 3.1 3.1 + - - +
79A LEU* 2.8 41.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 76 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A THR* 3.7 12.1 - - - +
14A LYS* 6.4 1.8 - - + -
19A PRO* 3.9 21.8 - - + +
22A GLU* 3.3 27.1 - - - +
23A LEU* 3.6 30.7 - - + -
26A LYS* 4.4 7.4 - - + -
72A ALA 2.8 23.7 + - - +
73A LEU* 3.3 17.0 + - + +
75A ALA* 1.3 72.4 - - - +
77A GLU* 1.3 61.2 + - + +
80A PHE* 2.8 58.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A LYS* 2.7 37.4 + - - -
73A LEU* 2.9 30.4 + - + +
74A ALA* 4.5 3.8 - - - +
76A LEU* 1.3 78.0 - - + +
78A LYS* 1.3 56.8 + - - +
81A PRO* 3.4 25.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A GLN* 3.8 21.3 - - - +
57A PHE* 4.0 20.2 - - + -
74A ALA 3.6 13.0 + - - +
75A ALA 3.1 7.9 + - - +
76A LEU 3.0 0.6 - - - -
77A GLU* 1.3 80.1 - - - +
79A LEU* 1.3 81.0 + - + +
81A PRO* 3.9 7.7 - - - +
91A LYS* 2.7 49.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A ARG* 5.9 1.3 - - - +
52A VAL* 3.5 26.9 - - + +
53A ASP* 3.4 24.9 - - - +
55A GLN* 3.5 26.5 - - - +
57A PHE* 4.6 7.2 - - + -
75A ALA* 2.8 21.3 + - + +
78A LYS* 1.3 93.0 - - + +
80A PHE* 1.3 80.4 + - + +
81A PRO* 3.3 10.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A LYS* 4.9 9.4 - - - +
15A HIS* 6.2 0.3 - - - -
23A LEU* 4.4 9.2 - - + -
26A LYS* 3.9 39.3 - - + -
27A ARG* 3.5 57.0 - - + -
76A LEU* 2.8 43.5 + - + +
79A LEU* 1.3 97.4 - - + +
81A PRO* 1.4 61.4 - - - +
82A ASP* 3.3 7.3 + - - +
----------------------------------------------------------
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