Contacts of the helix formed by residues 63 - 76 (chain A) in PDB entry 4BT9
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 63 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A GLY 3.3 7.9 + - - +
60A PHE 3.2 11.8 - - - +
61A VAL 4.4 2.3 - - - +
62A GLY* 1.3 81.4 - - - +
64A PRO* 1.3 74.4 - - + +
65A VAL 3.3 1.3 - - - +
66A ASN* 3.1 26.8 + - - +
67A ALA 4.3 0.9 + - - -
126B LEU* 5.6 5.8 - - + -
130B THR* 3.6 36.8 + - + +
131B ILE* 4.6 5.7 + - - +
134B GLY* 3.5 35.1 + - - -
135B ASN* 4.1 9.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 64 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A VAL 5.3 2.0 - - - +
62A GLY 3.9 6.7 - - - +
63A HIS* 1.3 88.1 - - + +
65A VAL* 1.3 64.8 + - - +
66A ASN 3.0 3.2 + - - -
67A ALA* 3.4 9.3 + - + +
68A PHE* 3.3 20.1 + - - +
3B GLY* 5.9 1.3 - - - -
4B PHE 6.2 0.7 - - - +
113B ALA 4.8 1.4 - - - +
116B ALA* 4.7 2.5 - - + -
117B LEU* 3.6 32.9 - - + +
120B LEU* 3.8 30.3 - - + -
126B LEU* 5.2 3.6 - - + -
131B ILE* 4.1 22.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 65 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A HIS* 4.6 1.1 + - - +
64A PRO* 1.3 80.2 - - - +
66A ASN* 1.3 71.5 + - - +
68A PHE* 3.5 1.0 + - + +
69A LYS* 2.9 34.6 + - + +
117B LEU* 3.8 12.0 - - + +
131B ILE* 3.2 33.7 + - + +
132B SER* 4.4 7.2 - - - +
134B GLY* 3.7 22.0 - - - +
144B PHE* 4.6 8.3 - - + -
145B LEU* 3.6 38.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 66 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A PHE* 3.0 65.4 + - + +
63A HIS* 3.1 14.8 + - - +
64A PRO 3.0 1.0 - - - -
65A VAL* 1.3 84.7 - - - +
67A ALA* 1.3 61.1 + - - +
69A LYS* 3.4 4.0 + - - +
70A LEU* 3.0 31.0 + - - +
135B ASN* 2.9 29.7 + - - +
144B PHE* 4.7 11.4 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
60A PHE 5.0 0.4 + - - -
61A VAL 6.1 1.1 - - - +
63A HIS 4.3 1.0 + - - +
64A PRO* 3.4 10.7 + - + +
66A ASN* 1.3 75.3 - - - +
68A PHE* 1.3 66.7 + - - +
70A LEU* 3.9 1.0 - - - +
71A MET* 3.0 30.3 + - - +
4B PHE* 3.8 29.8 - - + +
5B PHE* 3.5 35.9 - - + -
113B ALA* 3.9 3.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 68 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A PRO 3.3 14.7 + - - +
65A VAL 3.8 2.9 - - - +
66A ASN 3.3 0.6 - - - -
67A ALA* 1.3 80.8 - - - +
69A LYS* 1.3 71.2 + - + +
71A MET* 4.0 1.0 - - - +
72A LYS* 3.2 30.0 + - + +
110B GLN* 4.1 16.4 - - + -
113B ALA* 3.7 14.7 - - - +
114B ALA* 3.8 33.9 - - + -
117B LEU* 4.1 17.7 - - + -
145B LEU* 4.3 9.6 - - + -
149B ASP* 4.3 25.4 - - + -
152B GLU* 4.2 23.3 - - + -
153B LEU* 3.9 25.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 69 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A VAL* 2.9 27.9 + - + +
66A ASN 4.0 2.0 - - - +
68A PHE* 1.3 80.7 - - + +
70A LEU* 1.3 57.1 + - - +
72A LYS* 3.9 7.3 - - + +
73A ARG* 2.9 34.3 + - - +
77A GLU* 5.5 4.8 + - - -
144B PHE* 3.2 65.5 + - + -
145B LEU* 3.7 11.0 - - + -
146B THR* 4.4 9.3 - - - +
149B ASP* 2.7 36.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 70 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A PHE* 4.4 9.0 - - + -
66A ASN 3.0 17.9 + - - +
67A ALA 3.9 3.1 - - - +
69A LYS* 1.3 74.4 - - - +
71A MET* 1.3 75.4 + - + +
73A ARG* 3.3 31.8 + - - +
74A LEU* 3.1 39.3 + - + +
5B PHE* 3.9 24.5 - - + -
11B MET* 4.6 1.3 - - + -
14B LEU* 4.2 15.5 - - + +
15B ILE* 3.8 23.8 - - + -
18B GLU* 3.5 13.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 71 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A ALA 3.0 21.9 + - - +
68A PHE 4.0 2.9 - - - +
70A LEU* 1.3 92.4 - - + +
72A LYS* 1.3 58.3 + - - +
74A LEU* 4.1 0.9 - - - +
75A ASN* 2.9 34.3 + - - +
4B PHE* 3.7 18.2 - - + -
5B PHE* 4.0 13.0 - - + -
14B LEU* 3.7 28.7 - - + -
105B PRO* 3.5 32.0 - - + +
106B ASN 5.6 0.2 - - - +
109B ASP* 3.7 17.9 - - - +
110B GLN* 3.8 20.9 - - - +
113B ALA* 3.8 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 72 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A PHE* 3.2 24.4 + - + +
69A LYS* 3.9 9.4 - - + +
71A MET* 1.3 78.6 - - - +
73A ARG* 1.3 59.6 + - - +
76A THR* 2.8 48.1 + - + -
77A GLU* 3.3 2.4 + - + +
110B GLN* 3.5 28.2 - - + +
148B GLU* 2.9 28.2 + - - -
149B ASP* 2.6 33.6 + - - +
152B GLU* 2.7 35.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 73 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A LEU* 3.8 16.4 - - + +
49A LEU* 3.8 39.0 + - - +
50A THR* 4.7 1.0 - - - +
60A PHE* 5.5 3.8 - - - -
69A LYS* 2.9 30.1 + - - +
70A LEU* 3.3 21.6 - - - +
71A MET 3.3 0.2 - - - -
72A LYS* 1.3 78.0 - - - +
74A LEU* 1.3 58.3 + - + +
77A GLU* 3.0 35.1 + - + +
78A TRP* 2.9 37.3 + - + -
15B ILE* 4.3 8.3 - - - +
18B GLU* 2.7 43.1 + - - +
144B PHE* 4.0 16.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 74 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A LEU* 3.1 40.8 + - + +
73A ARG* 1.3 77.5 - - - +
75A ASN* 1.3 61.8 + - - +
78A TRP* 3.9 24.8 - - + +
79A SER* 5.1 1.0 + - - -
14B LEU* 4.2 23.3 - - + +
17B THR* 5.8 1.1 - - + -
18B GLU* 4.1 20.6 - - + +
101B ARG* 4.9 2.8 + - - -
104B PHE* 3.2 50.8 - - + -
105B PRO* 3.7 33.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 75 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A MET 2.9 20.2 + - - +
74A LEU* 1.3 80.5 - - - +
76A THR* 1.3 62.0 + - - +
79A SER* 4.0 12.1 + - - -
101B ARG* 5.9 0.2 + - - -
104B PHE* 5.2 0.7 - - - -
105B PRO* 3.7 11.8 - - + +
106B ASN* 3.6 26.8 + - - +
107B ASP* 2.7 37.3 + - - +
110B GLN* 3.0 20.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 76 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A LYS* 2.8 31.4 + - + -
74A LEU 3.4 0.4 - - - -
75A ASN* 1.3 80.1 + - - +
77A GLU* 1.3 65.5 + - - +
78A TRP 3.3 1.3 - - - -
79A SER* 3.1 16.7 + - - -
80A GLU* 3.3 26.7 + - + +
110B GLN* 3.3 20.5 + - - -
148B GLU* 5.9 1.1 - - - +
----------------------------------------------------------
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