Contacts of the helix formed by residues 66 - 88 (chain B) in PDB entry 3DOY
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 PRO 66 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A MET* 3.9 15.9 - - + -
72A GLU* 5.3 1.3 - - - +
54B VAL* 3.6 32.1 - - + -
55B PHE* 5.1 0.9 - - + -
58B HIS* 3.7 32.3 - - + +
64B ILE 3.3 5.8 - - - +
65B PHE* 1.3 91.1 - - + +
67B GLY* 1.3 60.7 + - - +
68B VAL* 4.4 4.5 - - + -
69B LEU* 3.0 40.2 + - + +
70B ILE* 3.2 12.0 + - - +
1002B CL 3.9 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 67 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A GLU* 5.6 0.2 + - - -
101A PHE* 5.2 0.4 - - - -
65B PHE 3.3 1.4 + - - -
66B PRO* 1.3 73.5 - - - +
68B VAL* 1.3 60.5 + - - +
70B ILE* 3.2 20.2 + - - +
71B VAL* 3.3 7.1 + - - +
109B PHE* 3.1 42.2 - - - -
1002B CL 3.1 20.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 68 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A MET* 5.0 0.2 - - + -
68A VAL* 3.6 44.3 - - + +
69A LEU* 4.4 5.2 - - + -
71A VAL* 4.4 6.3 - - + -
72A GLU* 3.4 23.8 - - + +
101A PHE* 3.3 34.7 - - + -
104A ILE* 4.5 5.2 - - + -
66B PRO* 4.4 6.1 - - + -
67B GLY* 1.3 76.5 - - - +
69B LEU* 1.3 73.3 + - + +
70B ILE 3.2 0.2 - - - -
71B VAL* 3.4 11.8 + - - +
72B GLU* 3.0 20.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 69 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A MET* 5.0 4.3 - - - -
68A VAL* 4.4 13.0 - - + -
69A LEU* 4.5 11.0 - - + -
27B MET* 4.7 12.6 - - - -
29B LEU* 3.6 28.0 - - + +
54B VAL* 3.8 34.5 - - + -
65B PHE* 3.7 24.3 - - + -
66B PRO* 3.0 26.7 + - + +
68B VAL* 1.3 88.1 - - + +
70B ILE* 1.3 64.0 + - - +
72B GLU* 3.7 2.5 - - + -
73B GLY* 3.1 16.8 + - - -
121B TYR* 4.6 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 70 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B PHE* 3.7 20.4 - - + +
66B PRO 3.2 10.9 + - - +
67B GLY* 3.2 20.6 + - - +
69B LEU* 1.3 77.0 - - - +
71B VAL* 1.3 65.0 + - + +
73B GLY* 3.3 2.6 + - - -
74B MET* 3.1 24.2 + - - +
109B PHE* 4.8 10.5 - - + -
111B ILE 5.3 2.7 - - - +
113B VAL* 3.6 31.2 - - + +
119B LEU* 4.0 14.1 - - + -
121B TYR* 3.7 3.0 - - + -
139B ALA* 3.5 30.7 - - + -
146B VAL* 4.9 4.5 - - + +
147B ALA* 4.2 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 71 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A VAL* 4.5 5.4 - - + -
104A ILE* 5.5 2.9 - - + -
67B GLY 3.3 15.2 + - - +
68B VAL* 3.5 11.4 - - - +
70B ILE* 1.3 75.2 - - + +
72B GLU* 1.3 60.4 - - - +
74B MET* 3.0 12.6 + - + +
75B ALA* 2.8 26.9 + - - +
104B ILE* 4.0 37.5 - - + -
107B VAL* 4.1 16.4 - - + -
109B PHE* 4.1 16.8 - - + -
147B ALA* 6.3 0.4 - - + -
149B ALA* 4.9 8.7 - - + -
151B LEU* 4.4 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 72 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A HIS* 4.6 5.7 + - - -
66A PRO* 5.5 0.8 - - - +
67A GLY 5.7 0.5 + - - -
68A VAL* 3.6 26.8 + - + +
23B HIS* 3.9 12.1 + - - -
27B MET* 3.8 21.0 - - + +
29B LEU* 3.6 15.3 - - + -
68B VAL 3.0 17.4 + - - +
69B LEU* 3.7 8.1 - - + +
70B ILE 3.3 0.2 - - - -
71B VAL* 1.3 75.8 - - - +
73B GLY* 1.3 57.9 + - - +
75B ALA* 3.2 10.8 + - - +
76B GLN* 2.9 64.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 73 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B LEU* 4.2 12.8 - - - +
30B VAL* 3.9 2.8 - - - +
69B LEU 3.1 9.3 + - - -
70B ILE 3.3 1.5 + - - -
71B VAL 3.1 0.8 - - - -
72B GLU* 1.3 80.2 - - - +
74B MET* 1.3 58.4 + - - +
76B GLN* 3.6 3.3 + - - -
77B SER* 3.0 27.2 + - - -
121B TYR* 3.5 32.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 74 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B ILE* 3.1 18.1 + - - +
71B VAL* 3.0 13.3 + - + +
73B GLY* 1.3 73.8 - - - +
75B ALA* 1.3 61.0 + - - +
77B SER* 3.3 2.6 + - - -
78B GLY* 2.9 24.6 + - - -
121B TYR* 3.6 17.5 - - + -
123B LEU* 3.7 37.5 - - + +
135B VAL* 5.2 0.3 - - - +
137B GLY 3.6 11.2 - - - +
138B THR* 3.5 36.1 - - - +
139B ALA* 4.1 16.8 - - + -
147B ALA* 5.1 2.5 - - - -
148B GLU* 4.9 2.2 - - - -
149B ALA* 4.0 25.6 - - + +
151B LEU* 4.5 7.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 75 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B VAL* 2.8 9.9 + - + +
72B GLU* 3.4 19.7 - - - +
74B MET* 1.3 76.6 - - - +
76B GLN* 1.3 52.8 + - + +
78B GLY 3.1 1.0 + - - -
79B GLY 2.7 32.6 + - - -
101B PHE* 3.2 35.4 - - + -
104B ILE* 5.9 1.8 - - + -
135B VAL* 6.0 0.2 - - - -
151B LEU* 3.4 24.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 76 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B LEU* 4.0 16.1 - - + +
23B HIS* 3.3 21.2 - - + +
27B MET 2.8 22.3 - - - +
28B LEU* 3.8 12.3 - - - +
29B LEU* 2.8 33.3 + - - +
30B VAL* 3.7 19.6 - - + +
72B GLU* 2.9 47.1 + - - +
73B GLY 3.9 0.2 - - - +
75B ALA* 1.3 75.7 - - + +
77B SER* 1.3 57.4 + - - +
79B GLY* 3.8 1.6 - - - +
80B PHE* 2.9 28.6 + - - +
101B PHE* 5.3 0.4 - - - -
2009B BEN 5.6 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 77 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B VAL* 3.8 9.8 - - - +
42B ILE* 3.5 23.9 - - - +
44B ALA* 4.0 6.7 - - - +
73B GLY 3.0 19.0 + - - -
74B MET 3.6 4.9 - - - -
75B ALA 3.2 0.2 - - - -
76B GLN* 1.3 77.4 - - - +
78B GLY* 1.3 57.6 + - - +
80B PHE* 3.1 9.6 + - - +
81B LEU* 2.9 24.1 + - - +
121B TYR* 3.1 31.8 - - - +
123B LEU* 4.2 5.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 78 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B MET 2.9 14.9 + - - -
75B ALA 3.5 2.7 - - - -
77B SER* 1.3 77.1 - - - +
79B GLY* 1.3 57.0 + - - +
81B LEU* 3.2 8.6 + - - +
82B ALA* 2.9 29.5 + - - +
101B PHE* 4.9 2.9 - - - -
123B LEU* 4.3 7.6 - - - +
135B VAL* 4.2 28.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 79 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B ALA 2.7 19.1 + - - -
76B GLN 3.8 2.0 - - - -
78B GLY* 1.3 69.4 - - - +
80B PHE* 1.3 65.2 + - - +
82B ALA* 3.8 3.8 - - - +
83B PHE* 3.0 26.7 + - - +
99B VAL* 4.0 28.6 - - - +
101B PHE* 4.2 4.8 - - - -
153B ALA* 5.5 0.4 - - - -
2009B BEN 4.5 10.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 80 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B PHE* 4.2 20.2 - + + -
16B HIS 5.2 0.4 - - - -
17B ILE* 4.2 15.0 - - + -
20B ILE* 3.5 38.1 - - + -
21B LEU* 4.2 21.0 - - + +
33B ILE* 3.2 36.6 - - + -
36B LEU* 4.0 13.7 - - + -
42B ILE* 4.2 8.3 - - + -
76B GLN 2.9 14.5 + - - +
77B SER* 3.1 12.3 + - - +
79B GLY* 1.3 76.7 - - - +
81B LEU* 1.3 60.1 + - - +
83B PHE* 4.0 3.3 - - - +
84B THR* 2.8 54.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 81 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B LEU* 3.6 17.3 - - + -
37B GLN 3.8 13.7 - - - +
40B GLN 4.7 1.3 - - - +
41B LYS* 3.4 37.9 - - - +
42B ILE* 3.9 15.5 - - + -
77B SER 2.9 12.6 + - - +
78B GLY 3.3 7.2 - - - +
80B PHE* 1.3 75.6 - - - +
82B ALA* 1.3 65.7 + - - +
83B PHE 3.3 0.2 + - - -
84B THR* 3.3 4.4 + - - -
85B SER* 2.8 36.2 + - - +
123B LEU* 4.3 6.3 - - + +
124B GLU 4.6 0.4 - - - -
125B VAL* 3.7 31.0 - - + +
135B VAL* 4.5 11.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 82 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B GLY 2.9 18.0 + - - +
79B GLY* 3.8 7.2 - - - +
81B LEU* 1.3 75.4 - - - +
83B PHE* 1.3 65.0 + - - +
85B SER* 3.4 8.8 + - - -
86B LEU* 3.4 17.5 + - - +
99B VAL* 5.4 2.7 - - + -
133B TRP* 4.0 36.8 - - + -
135B VAL* 5.8 1.1 - - + -
153B ALA* 5.7 3.4 - - + -
155B ILE* 3.9 21.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 83 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B ILE* 3.6 22.4 - - + -
79B GLY 3.0 18.8 + - - +
80B PHE* 4.0 2.9 - - - +
82B ALA* 1.3 76.7 - - - +
84B THR* 1.3 60.1 + - + +
86B LEU 3.2 2.4 + - - -
87B TRP* 3.0 71.9 + + + -
88B GLY 3.7 19.1 - - - -
90B ASP 3.8 7.6 - - - -
93B ILE* 4.1 5.6 - - + -
94B ALA* 3.3 46.0 - - + -
97B LYS* 4.2 7.4 - - + -
99B VAL* 4.9 4.9 - - + -
155B ILE* 4.4 3.0 - - - +
2009B BEN 3.5 26.2 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 84 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B PHE* 5.4 3.6 - - + -
20B ILE* 4.6 3.8 - - + -
36B LEU* 3.3 25.5 - - + +
38B ALA* 5.4 0.9 - - - +
80B PHE* 2.8 48.9 + - + +
81B LEU* 3.3 6.6 + - - -
83B PHE* 1.3 83.9 - - + +
85B SER* 1.3 62.8 + - - +
88B GLY* 2.6 50.3 + - - +
89B PHE* 4.7 2.5 - - - +
2007B BEN 4.3 3.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 85 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B ALA* 3.6 18.3 - - - +
39B ASN* 2.8 46.9 + - - +
81B LEU* 2.8 31.3 + - - +
82B ALA 3.5 5.8 - - - -
83B PHE 3.2 0.2 - - - -
84B THR* 1.3 78.5 + - - +
86B LEU* 1.3 62.9 + - - +
133B TRP* 3.8 10.1 - - - -
2007B BEN 4.6 7.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 86 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B ASN* 5.2 2.0 - - - +
82B ALA 3.7 7.2 - - - +
83B PHE 3.2 1.6 + - - +
84B THR 3.2 0.2 - - - -
85B SER* 1.3 80.7 - - - +
87B TRP* 1.3 93.3 + - + +
128B HIS* 6.3 0.2 - - + -
130B GLY 5.3 1.1 - - - +
131B MET* 4.1 18.8 - - + -
133B TRP* 3.7 30.1 - - + +
155B ILE* 3.7 30.1 - - + -
2007B BEN 4.4 6.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 87 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B PHE* 3.0 64.9 + + + +
86B LEU* 1.3 107.7 + - + +
88B GLY* 1.3 64.9 + - - +
90B ASP* 3.6 11.2 - - + +
93B ILE* 3.9 24.7 - - + +
97B LYS* 3.6 33.7 - - + +
131B MET* 4.2 11.9 - - + -
155B ILE* 3.7 28.9 - - + -
2007B BEN 3.0 26.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 88 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B PHE* 3.7 15.9 - - - -
84B THR* 2.6 41.1 + - - +
87B TRP* 1.3 76.3 - - - +
89B PHE* 1.3 58.6 + - - -
90B ASP 2.9 7.4 + - - -
2007B BEN 3.4 19.8 - - - -
----------------------------------------------------------
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