Contacts of the helix formed by residues 58 - 73 (chain E) in PDB entry 3N2N
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 58 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54E SER 4.6 5.2 - - - -
55E VAL* 2.9 10.8 + - + +
57E HIS* 1.3 99.2 + + + +
59E TRP* 1.3 64.7 + - - +
60E ASN* 3.3 2.7 - - - -
61E GLU* 3.2 38.5 + - - +
62E ILE* 3.2 22.5 + - - +
180E VAL* 4.3 18.6 - - + -
181E LYS* 3.5 52.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 59 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49E LEU* 4.2 14.4 - - + -
50E ASP 3.3 28.5 - - - -
51E LYS* 3.9 14.8 - - + -
55E VAL* 3.1 5.2 + - + +
56E LEU 4.1 4.6 + - - +
57E HIS 3.8 0.6 - - - -
58E HIS* 1.3 78.9 - - - +
60E ASN* 1.3 61.6 + - - +
62E ILE* 3.1 21.9 + - + -
63E TYR* 2.7 47.1 + - + +
84E VAL* 4.4 4.9 - - + -
109E LEU* 3.1 49.1 + - + -
110E GLN 4.2 7.9 + - - -
112E VAL* 3.4 38.1 + - + +
114E PRO* 3.6 24.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 60 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57E HIS 5.7 4.5 + - - +
58E HIS* 3.3 1.2 - - - -
59E TRP* 1.3 82.7 - - - +
61E GLU* 1.3 58.1 + - + +
63E TYR* 4.5 4.4 - - - +
64E TYR* 2.9 53.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 61 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57E HIS 5.5 1.6 - - - +
58E HIS* 3.2 38.6 + - - +
59E TRP 3.2 0.2 - - - -
60E ASN* 1.3 78.0 - - + +
62E ILE* 1.3 62.3 + - - +
64E TYR* 4.1 2.7 - - - +
65E PHE* 3.1 24.4 + - - +
180E VAL* 4.1 7.2 - - + +
181E LYS 5.0 0.7 + - - -
201E VAL* 3.6 36.7 - - + +
202E ASN* 4.9 10.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 62 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49E LEU* 3.9 27.6 - - + -
50E ASP* 3.5 25.4 - - + +
55E VAL* 4.3 16.6 - - + -
58E HIS 3.2 12.3 + - - +
59E TRP* 3.1 29.0 + - + +
61E GLU* 1.3 73.4 - - - +
63E TYR* 1.3 66.8 + - - +
65E PHE* 3.4 9.4 + - - +
66E VAL* 3.2 20.3 + - - +
148E LEU* 3.9 21.5 - - + +
180E VAL* 4.0 26.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 63 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49E LEU* 6.2 0.4 - - - -
59E TRP* 2.7 37.9 + - + +
60E ASN* 3.9 4.3 - - - +
62E ILE* 1.3 74.5 - - - +
64E TYR* 1.3 81.4 + + - +
66E VAL* 3.0 8.5 + - - +
67E GLU* 2.7 68.5 + - + +
106E LEU* 3.2 45.1 + - + +
107E GLU* 5.3 0.2 - - - -
109E LEU* 3.8 24.2 - - + -
110E GLN* 3.7 32.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 64 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60E ASN* 2.9 41.9 + - + +
61E GLU* 4.3 3.4 - - - +
63E TYR* 1.3 89.6 - + - +
65E PHE* 1.3 60.2 + - - +
67E GLU* 3.2 33.3 + - - -
68E GLN* 2.8 55.3 + - + +
110E GLN* 5.8 2.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 65 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47E PHE* 4.2 4.3 - + - -
61E GLU 3.1 16.0 + - - +
62E ILE* 3.4 11.7 - - - +
64E TYR* 1.3 77.0 - - - +
66E VAL* 1.3 64.1 + - + +
68E GLN* 3.9 8.4 - - - +
69E LEU* 3.3 46.3 + - + +
146E ILE* 4.0 7.9 - - + -
148E LEU* 3.8 31.4 - - + -
178E VAL* 3.9 10.8 - - + -
201E VAL* 4.1 19.5 - - + -
204E GLY* 3.5 9.0 - - - -
205E PHE* 3.4 38.4 - - + -
208E LEU* 3.6 25.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 66 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47E PHE* 3.8 22.7 - - + -
49E LEU* 3.6 33.4 - - + -
62E ILE 3.2 14.8 + - - +
63E TYR* 3.0 8.1 + - - +
65E PHE* 1.3 80.7 - - + +
67E GLU* 1.3 60.8 + - - +
69E LEU* 3.3 3.6 + - - +
70E ALA* 2.9 27.0 + - - +
82E PHE* 3.6 32.8 - - + -
106E LEU* 3.9 6.3 - - + -
109E LEU* 3.9 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 67 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63E TYR* 2.7 61.9 + - + +
64E TYR* 3.2 27.3 + - - +
66E VAL* 1.3 72.8 - - - +
68E GLN* 1.3 59.7 + - - +
70E ALA* 3.4 0.6 + - - -
71E HIS* 2.9 66.3 + - + +
106E LEU* 4.0 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 68 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64E TYR* 2.8 49.9 + - + +
65E PHE* 3.9 4.2 - - - +
67E GLU* 1.3 77.8 - - - +
69E LEU* 1.3 58.2 + - - +
71E HIS* 3.9 3.4 - - - +
72E LYS* 3.0 30.7 + - - +
205E PHE* 3.5 45.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 69 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45E LEU* 5.6 0.9 - - + -
47E PHE* 3.8 23.1 - - + -
65E PHE* 3.3 44.7 + - + +
66E VAL 3.3 4.6 + - - +
68E GLN* 1.3 76.9 - - - +
70E ALA* 1.3 65.3 + - - +
72E LYS* 3.2 0.9 + - - -
73E PHE* 3.0 45.0 + - + +
78E LEU* 6.1 0.2 - - - -
80E MET* 5.2 1.3 - - - +
146E ILE* 4.3 4.7 - - + -
205E PHE* 3.7 25.8 - - + +
208E LEU* 4.8 1.8 - - + -
209E GLN* 4.0 13.5 - - - +
212E ILE* 3.8 29.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 70 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47E PHE* 5.4 0.2 - - - -
66E VAL 2.9 16.8 + - - +
67E GLU 3.8 0.7 - - - +
69E LEU* 1.3 76.0 - - - +
71E HIS* 1.3 64.2 + - - +
73E PHE 3.2 19.1 - - - +
74E ILE* 3.8 6.9 - - - +
80E MET* 3.9 32.5 - - + +
82E PHE* 4.9 0.4 - - + -
99E ARG* 5.0 1.6 + - - -
102E ILE* 4.4 7.0 - - + +
106E LEU* 3.8 29.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 71 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67E GLU* 2.9 46.1 + - + +
68E GLN* 4.1 4.5 - - - +
70E ALA* 1.3 77.0 - - - +
72E LYS* 1.3 60.8 + - - +
74E ILE* 3.5 17.3 - - + +
102E ILE* 6.3 0.2 - - + -
106E LEU* 3.6 27.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 72 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68E GLN 3.0 19.6 + - - +
69E LEU* 3.2 5.1 + - - +
71E HIS* 1.3 77.7 - - - +
73E PHE* 1.3 83.6 + - + +
74E ILE* 3.8 3.9 + - - +
205E PHE* 4.8 10.0 - - + -
209E GLN* 3.2 34.2 + - + +
222E ACT 3.6 32.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 73 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69E LEU* 3.0 46.6 + - + +
70E ALA 3.2 10.5 - - - +
72E LYS* 1.3 95.9 - - + +
74E ILE* 1.3 59.2 + - - +
75E SER* 3.4 3.1 - - - +
78E LEU* 3.6 21.0 - - + +
80E MET* 4.2 1.4 - - - +
99E ARG* 2.8 19.2 + - - -
209E GLN* 3.3 29.6 - - + -
212E ILE* 3.7 24.9 - - + -
213E HIS* 3.9 10.3 - - + -
216E LEU* 3.6 22.4 - - + -
222E ACT 3.6 33.2 - - + -
----------------------------------------------------------
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