Contacts of the helix formed by residues 58 - 73 (chain F) 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 F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54F SER 5.0 0.8 + - - -
55F VAL* 2.9 18.5 + - + +
57F HIS* 1.3 89.3 + - + +
59F TRP* 1.3 63.0 + - - +
60F ASN 3.4 2.7 - - - -
61F GLU* 3.4 33.9 + - - +
62F ILE* 3.2 22.5 + - - +
180F VAL* 3.7 22.4 - - + -
181F LYS* 3.4 34.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 59 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49F LEU* 4.0 22.0 - - + -
50F ASP 3.2 28.9 - - - -
51F LYS* 3.8 18.4 - - + -
55F VAL* 3.2 5.2 + - + +
56F LEU 3.7 4.2 + - - +
57F HIS 3.5 1.8 - - - -
58F HIS* 1.3 76.0 - - - +
60F ASN* 1.3 69.7 + - - +
62F ILE* 3.1 19.6 + - + -
63F TYR* 2.8 42.2 + - + +
84F VAL* 4.4 3.4 - - + -
109F LEU* 2.9 45.6 + - + -
110F GLN 4.2 7.3 + - - -
112F VAL* 3.5 37.5 + - + +
114F PRO* 3.6 25.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 60 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57F HIS 5.1 5.1 + - - +
58F HIS* 3.4 0.6 - - - +
59F TRP* 1.3 83.6 - - - +
61F GLU* 1.3 57.2 + - - +
63F TYR* 4.6 2.6 - - - +
64F TYR* 2.9 58.5 + - + +
110F GLN 5.4 2.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 61 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58F HIS* 3.4 28.9 + - + +
59F TRP 3.2 0.2 - - - -
60F ASN* 1.3 79.1 - - - +
62F ILE* 1.3 61.5 + - + +
64F TYR* 4.2 2.5 - - - +
65F PHE* 3.3 22.7 + - - +
180F VAL* 3.4 24.9 - - - +
181F LYS 4.8 0.9 + - - -
201F VAL* 3.5 32.5 - - + +
202F ASN* 6.1 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 62 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49F LEU* 4.0 15.9 - - + -
50F ASP* 3.5 25.1 - - + +
55F VAL* 4.2 19.1 - - + -
58F HIS 3.5 15.0 - - - +
59F TRP* 3.1 31.3 + - + +
61F GLU* 1.3 73.6 - - - +
63F TYR* 1.3 65.5 - - - +
65F PHE* 3.3 7.1 + - - +
66F VAL* 3.3 19.8 + - - +
148F LEU* 3.9 30.7 - - + +
180F VAL* 3.9 28.0 - - + -
201F VAL* 5.3 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 63 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49F LEU* 6.0 0.7 - - - -
59F TRP* 2.8 36.7 + - + +
60F ASN* 3.9 3.6 - - - +
62F ILE* 1.3 76.5 - - - +
64F TYR* 1.3 89.9 + + + +
66F VAL* 3.0 9.9 + - - +
67F GLU* 2.7 65.1 + - + +
71F HIS* 5.5 0.2 - - - -
106F LEU* 3.3 37.1 + - + +
109F LEU* 3.6 24.9 - - + -
110F GLN* 2.9 41.0 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 64 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60F ASN* 2.9 50.8 + - + +
61F GLU* 4.5 2.7 - - - +
63F TYR* 1.3 96.3 - + - +
65F PHE* 1.3 59.3 + - - +
66F VAL 3.3 0.2 - - - -
67F GLU* 3.3 29.8 - - - +
68F GLN* 2.9 41.2 + - + +
110F GLN* 5.3 3.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 65 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47F PHE* 4.3 2.7 - + - -
61F GLU 3.3 13.9 + - - +
62F ILE 3.3 10.4 + - - +
64F TYR* 1.3 77.4 - - - +
66F VAL* 1.3 66.0 + - + +
68F GLN* 3.7 10.1 + - - +
69F LEU* 3.3 48.3 + - + +
146F ILE* 4.0 6.5 - - + -
148F LEU* 3.7 36.1 - - + -
178F VAL* 3.9 19.3 - - + -
201F VAL* 4.4 18.2 - - + -
204F GLY* 3.3 10.1 - - - -
205F PHE* 3.3 38.5 - - + -
208F LEU* 4.2 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 66 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47F PHE* 3.9 23.6 - - + -
49F LEU* 3.6 33.9 - - + -
62F ILE 3.5 13.2 - - - +
63F TYR* 3.0 9.9 + - + +
65F PHE* 1.3 80.3 - - + +
67F GLU* 1.3 60.5 + - - +
69F LEU* 3.3 4.3 + - - +
70F ALA* 2.9 26.7 + - - +
82F PHE* 3.6 33.9 - - + -
106F LEU* 4.2 3.1 - - + -
109F LEU* 4.1 14.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 67 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63F TYR* 2.7 59.0 + - + +
64F TYR* 3.3 25.7 - - - +
66F VAL* 1.3 72.5 - - - +
68F GLN* 1.3 58.9 + - - +
70F ALA* 3.8 0.6 - - - +
71F HIS* 2.9 61.2 + - + +
106F LEU* 4.0 12.8 - - + +
110F GLN* 4.2 5.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 68 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64F TYR* 2.9 29.8 + - + +
65F PHE* 3.7 7.7 - - - +
67F GLU* 1.3 78.4 + - - +
69F LEU* 1.3 61.9 + - - +
71F HIS* 4.0 3.1 - - - +
72F LYS* 3.1 25.3 + - - +
205F PHE* 3.6 48.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 69 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45F LEU* 5.7 0.7 - - + -
47F PHE* 3.8 23.6 - - + -
65F PHE* 3.3 43.0 + - + +
66F VAL 3.3 7.0 + - - +
68F GLN* 1.3 75.9 - - - +
70F ALA* 1.3 66.3 + - - +
72F LYS* 3.2 2.4 + - - -
73F PHE* 3.0 33.6 + - + +
78F LEU* 6.2 0.2 - - - -
80F MET* 5.5 0.9 - - - -
146F ILE* 4.2 4.7 - - + -
205F PHE* 3.7 26.9 - - + +
208F LEU* 4.4 2.2 - - + -
209F GLN* 4.0 20.6 - - + +
212F ILE* 3.8 29.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 70 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47F PHE* 5.5 0.8 - - + -
66F VAL 2.9 17.7 + - - +
67F GLU 3.8 4.0 - - - +
69F LEU* 1.3 76.7 - - - +
71F HIS* 1.3 62.3 + - - +
73F PHE 3.2 22.0 - - - +
74F ILE* 3.9 5.0 - - - +
80F MET* 4.0 32.8 - - + +
82F PHE* 4.8 0.9 - - + -
99F ARG* 5.0 1.6 + - - -
102F ILE* 4.5 5.5 - - + +
106F LEU* 3.9 27.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 71 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67F GLU* 2.9 48.6 + - + +
68F GLN* 4.2 2.7 - - - +
70F ALA* 1.3 75.3 - - - +
72F LYS* 1.3 63.4 + - - +
74F ILE* 3.4 18.4 - - + +
102F ILE* 6.3 0.2 - - + -
103F ARG* 6.2 0.2 - - - -
106F LEU* 3.7 24.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 72 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68F GLN 3.1 19.2 + - - +
69F LEU* 3.2 4.9 + - - +
71F HIS* 1.3 79.6 - - - +
73F PHE* 1.3 78.0 + - + +
74F ILE* 3.8 4.5 + - - +
205F PHE* 4.7 15.9 - - + -
209F GLN* 4.9 13.0 - - + +
223F ACT 3.5 38.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 73 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69F LEU* 3.0 33.4 + - + +
70F ALA 3.2 11.0 - - - +
71F HIS 3.4 0.2 - - - -
72F LYS* 1.3 92.1 - - + +
74F ILE* 1.3 59.9 + - - +
75F SER* 3.4 3.4 - - - +
78F LEU* 3.6 20.6 - - + +
80F MET* 4.2 1.0 - - - +
99F ARG* 2.8 19.6 + - - -
209F GLN* 3.2 43.3 - - + -
212F ILE* 3.7 26.0 - - + -
213F HIS* 3.9 10.5 - - + -
216F LEU* 3.6 20.6 - - + -
223F ACT 3.5 35.0 - - + -
----------------------------------------------------------
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