Contacts of the helix formed by residues 63 - 82 (chain A) in PDB entry 3ESF
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 LYS 63 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A THR 4.8 5.4 - - - +
62A GLU* 1.3 85.4 + - - +
64A GLY* 1.3 68.3 + - - +
65A PRO 3.9 0.2 - - - -
66A ILE* 4.0 6.1 + - - +
67A PHE* 3.7 11.3 + - + -
17D ALA* 3.2 17.9 + - - +
18D LYS* 3.7 8.5 - - - +
19D GLY* 3.4 35.2 - - - +
171D TYR* 3.6 31.7 + - - +
177D ALA* 6.0 1.6 - - - +
181D THR* 3.8 9.9 - - - +
184D ASN* 6.3 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 64 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A LYS* 1.3 74.9 - - - +
65A PRO* 1.4 78.0 - - - +
67A PHE* 3.0 15.1 + - - +
68A ASN* 3.1 20.5 + - - +
16D ALA* 3.5 13.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 65 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A LYS 4.4 0.2 - - - +
64A GLY* 1.4 81.8 - - - +
66A ILE* 1.3 68.6 + - + +
68A ASN* 3.2 15.1 + - + +
69A LEU* 3.2 26.7 + - + +
16D ALA* 4.5 7.4 - - + +
17D ALA* 4.4 19.3 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
40A LEU* 3.9 11.7 - - + -
43A ALA* 3.6 28.7 - - + -
50A LEU* 3.9 31.6 - - + -
58A ILE* 4.0 11.2 - - + +
62A GLU* 4.6 12.6 - - + +
63A LYS 4.0 6.6 + - - +
64A GLY 3.1 1.2 + - - -
65A PRO* 1.3 78.0 - - + +
67A PHE* 1.3 65.7 + - - +
69A LEU* 3.3 18.7 + - + +
70A ALA* 3.2 17.7 + - - +
17D ALA* 6.3 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 67 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A ILE* 4.4 9.9 - - - -
59A ILE* 3.3 42.0 - - + -
62A GLU* 3.5 25.6 - - - +
63A LYS* 3.7 12.8 + - + -
64A GLY 3.0 10.3 + - - +
66A ILE* 1.3 78.9 - - - +
68A ASN* 1.3 73.6 + - - +
70A ALA* 3.3 0.9 + - - +
71A ALA* 2.8 49.9 + - + +
145A ALA 3.7 13.9 - - - -
146A GLY* 4.6 3.1 - - - -
147A CYS 4.5 7.4 - - - -
150A THR* 3.5 22.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 68 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A GLY* 3.1 18.5 + - - +
65A PRO* 3.2 15.5 + - + +
67A PHE* 1.3 90.1 - - - +
69A LEU* 1.3 58.5 + - + +
72A GLN* 2.9 37.0 + - - +
144A ASP* 6.0 0.2 - - - +
145A ALA* 3.7 12.8 + - - +
121B PHE* 3.7 49.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 69 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A TYR* 3.9 33.0 - - + +
39A LYS* 3.8 34.5 - - + +
40A LEU* 3.6 34.1 - - + +
65A PRO* 3.3 16.4 - - + +
66A ILE* 3.5 24.5 - - + +
67A PHE 3.2 0.4 - - - -
68A ASN* 1.3 76.6 - - + +
70A ALA* 1.3 64.4 + - - +
72A GLN* 3.5 1.9 + - - +
73A ILE* 3.0 30.6 + - - +
121B PHE* 5.9 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 70 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A LEU* 4.5 4.6 - - + +
55A VAL* 3.2 27.6 - - + +
58A ILE* 3.4 45.5 - - + -
59A ILE* 3.9 4.5 - - + -
66A ILE 3.2 5.3 + - - +
67A PHE 4.0 0.9 - - - +
69A LEU* 1.3 77.8 - - - +
71A ALA* 1.3 62.9 + - - +
73A ILE* 3.1 9.2 + - - +
74A PHE* 3.0 19.9 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
59A ILE* 3.7 14.6 - - + +
67A PHE* 2.8 42.8 + - + +
68A ASN 3.9 2.7 - - - +
70A ALA* 1.3 72.3 - - - +
72A GLN* 1.3 56.1 + - - +
74A PHE* 3.4 1.7 + - - +
75A ASN* 2.9 36.6 + - - +
145A ALA* 3.0 25.6 - - + +
147A CYS* 4.3 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 72 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A HIS* 4.5 0.2 - - - -
36A TYR* 2.9 50.7 + - + -
68A ASN 2.9 22.5 + - - +
71A ALA* 1.3 72.8 - - - +
73A ILE* 1.3 66.1 + - - +
75A ASN* 3.5 1.9 + - - -
76A HIS* 2.6 49.5 + - - -
125A TRP* 3.1 25.8 + - - -
145A ALA* 3.4 23.7 - - + -
163A TRP* 3.4 25.8 - - - +
121B PHE* 3.9 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 73 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A PHE* 5.5 2.2 - - + -
4A SER 4.9 2.9 - - - +
5A ILE* 3.5 24.2 - - + -
33A HIS* 3.3 10.5 + - + +
36A TYR* 3.7 16.8 - - + +
37A VAL* 3.9 30.3 - - + +
40A LEU* 3.7 28.7 - - + -
55A VAL* 4.1 18.4 - - + -
69A LEU 3.0 22.7 + - - +
70A ALA* 3.1 8.0 + - - +
72A GLN* 1.3 76.4 - - - +
74A PHE* 1.3 62.0 + - - +
77A ASN* 3.1 35.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 74 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A VAL* 3.9 8.3 - - + -
56A GLU* 3.4 36.3 - - + -
59A ILE* 3.4 22.7 - - + -
70A ALA 3.0 6.9 + - - +
71A ALA 3.8 0.7 - - - +
73A ILE* 1.3 76.8 - - - +
75A ASN* 1.3 69.9 + - - +
77A ASN* 3.3 10.8 + - + +
78A PHE* 2.9 48.9 + + + +
127A TRP* 4.4 9.6 - + - -
147A CYS* 3.7 16.8 - - - -
149A LEU* 3.7 20.9 - - + -
156A PRO* 4.1 18.6 - - + -
----------------------------------------------------------
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 ALA 2.9 24.3 + - - +
72A GLN* 3.5 8.9 + - - +
74A PHE* 1.3 76.8 - - - +
76A HIS* 1.3 57.8 + - - +
78A PHE* 3.4 2.5 + - - +
79A TYR* 2.9 27.7 + - - +
125A TRP* 3.3 45.4 - - + +
127A TRP* 3.3 29.2 - - - -
145A ALA 3.6 6.1 + - - -
146A GLY 3.3 21.4 + - - -
147A CYS* 3.5 15.2 - - - -
159A THR* 3.8 1.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 76 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A HIS* 3.2 20.1 + + - -
32A HIS* 5.0 0.6 - - - +
33A HIS* 3.4 40.8 - + + +
36A TYR* 3.6 16.0 - + - -
72A GLN* 2.6 53.4 + - - +
75A ASN* 1.3 72.8 - - - +
77A ASN* 1.3 67.2 + - - +
79A TYR* 3.4 8.9 - + - +
80A TRP* 3.0 32.0 + + - +
125A TRP* 3.5 12.0 - + - -
161A ASP* 3.3 3.5 + - - -
165A HIS* 3.8 1.4 + - - -
198A FE 2.2 30.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A SER 5.4 0.6 + - - -
5A ILE* 3.6 2.0 - - - +
6A PRO* 3.5 35.5 - - + +
33A HIS* 2.9 25.7 + - - -
55A VAL* 5.9 0.8 - - - +
73A ILE* 3.1 31.9 + - - +
74A PHE* 3.5 12.6 - - + +
76A HIS* 1.3 76.5 - - - +
78A PHE* 1.3 63.6 + - - +
80A TRP* 3.5 5.9 + - - +
81A GLU* 3.2 27.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A PHE* 2.9 37.5 + + + +
75A ASN* 3.6 5.2 - - - +
77A ASN* 1.3 76.4 - - - +
79A TYR* 1.3 56.3 + - - +
81A GLU* 3.4 6.6 + - + +
82A SER* 2.7 39.0 + - - -
127A TRP* 3.6 17.9 - + + -
156A PRO* 3.3 39.7 - - + -
157A ILE 3.4 30.5 - - - -
158A LEU* 3.5 9.2 - - - -
159A THR* 3.9 4.5 - - + -
190A HIS* 3.6 20.1 - + - -
194A GLN* 3.8 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A ILE* 4.4 4.3 - - - +
28A HIS* 3.5 28.6 + + - -
75A ASN 2.9 17.9 + - - +
76A HIS* 3.4 8.5 - + - +
77A ASN 3.3 0.2 - - - -
78A PHE* 1.3 73.4 - - - +
80A TRP* 1.3 93.6 + + - +
82A SER* 3.1 15.8 + - - -
83A MET* 3.6 32.9 + - + +
125A TRP* 3.9 4.7 - - + -
159A THR* 3.5 22.3 - - + +
160A CYS* 4.1 4.3 - - - -
161A ASP* 3.4 34.8 - - + -
166A ALA* 4.2 6.6 + - - +
178A TYR* 2.6 32.1 + - - -
182A PHE* 4.6 2.2 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A PRO 5.9 0.2 - - - -
7A PRO 6.0 0.2 - - - -
8A LEU* 3.5 16.6 - - + -
9A PRO* 3.6 22.4 - - + +
10A TRP* 3.3 38.0 + + + -
20A ILE* 5.7 2.2 - - + -
25A VAL* 4.4 17.5 - - + -
28A HIS* 3.4 40.6 - + + -
29A TYR* 3.4 31.9 - + + -
33A HIS* 3.1 31.4 + + - -
76A HIS* 3.0 24.4 + + + +
77A ASN* 4.0 5.2 - - - +
79A TYR* 1.3 90.6 - + - +
81A GLU* 1.3 57.6 + - - +
83A MET* 3.1 36.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A PRO* 6.1 0.9 - - - +
9A PRO* 3.5 29.9 - - + +
77A ASN 3.2 14.5 + - - +
78A PHE* 3.7 6.1 - - - +
80A TRP* 1.3 72.4 - - - +
82A SER* 1.3 56.8 + - - +
83A MET 3.1 6.5 - - - -
187A ASN* 3.0 33.8 + - - -
190A HIS* 3.2 36.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A PHE* 2.7 25.5 + - - -
79A TYR 3.1 9.1 + - - -
81A GLU* 1.3 75.7 - - - +
83A MET* 1.3 59.6 + - - +
158A LEU* 3.6 24.0 - - - +
159A THR 3.1 39.6 + - - -
182A PHE* 4.1 3.7 - - - -
186A VAL* 3.5 8.3 - - - +
187A ASN* 2.9 21.5 + - - -
190A HIS* 4.0 4.3 - - - -
----------------------------------------------------------
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