Contacts of the helix formed by residues 76 - 97 (chain B) in PDB entry 2LUC
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 ASP 76 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A MET* 5.9 0.2 - - - +
21B PHE* 3.4 5.8 - - - -
32B TYR 4.5 0.4 - - - -
33B THR* 3.3 16.9 - - + +
70B ASN* 5.6 4.0 - - + +
75B LEU* 1.3 74.1 - - - +
77B PHE* 1.3 75.4 + - + +
78B SER* 2.6 28.6 + - - -
79B GLU* 2.7 44.7 + - - +
80B PHE* 2.7 30.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 77 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A MET* 4.6 12.3 - - + -
92A HIS* 3.2 43.4 + + + -
96A LEU* 3.5 37.5 - - + -
21B PHE* 3.3 22.4 - + - -
22B GLN* 4.0 2.9 - - - -
31B ASN 3.8 16.8 - - - -
32B TYR* 3.6 23.3 - - + -
76B ASP* 1.3 89.3 - - + +
78B SER* 1.3 59.4 + - - +
80B PHE* 3.6 3.5 + - - +
81B LEU* 2.9 31.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 78 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A MET* 3.3 30.9 - - - -
76B ASP* 2.6 23.7 + - - -
77B PHE* 1.3 76.7 - - - +
79B GLU* 1.3 56.4 + - - +
81B LEU* 3.1 7.6 + - - +
82B ASN* 2.7 42.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 79 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B THR* 4.5 0.7 - - - +
67B LEU* 3.2 26.0 - - - +
68B ASP* 3.2 5.9 - - - -
69B THR* 2.6 41.2 + - + -
70B ASN* 2.7 28.4 + - - +
74B GLN 3.6 7.4 - - - +
75B LEU* 3.7 10.5 - - + -
76B ASP* 2.7 50.9 + - - +
78B SER* 1.3 74.4 - - - +
80B PHE* 1.3 64.8 + - - +
82B ASN* 3.3 11.9 - - - +
83B LEU* 3.1 17.3 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
92A HIS* 5.5 1.1 - - - -
17B LEU* 3.9 18.2 - - + -
20B VAL* 3.4 22.9 - - + -
21B PHE* 3.4 36.1 - + + -
34B LEU* 3.8 17.3 - - + -
39B PHE* 4.5 1.8 - + - -
42B PHE* 3.2 32.3 - + - -
75B LEU* 4.0 8.4 - - + +
76B ASP 2.7 19.3 + - - +
77B PHE 3.8 2.5 - - - +
79B GLU* 1.3 73.1 - - - +
81B LEU* 1.3 67.6 + - + +
83B LEU* 2.9 25.1 - - + +
84B ILE* 2.9 47.1 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
81A LEU 5.5 2.6 - - - +
84A ILE* 5.3 1.8 - - + +
85A GLY* 3.4 30.3 - - - +
88A ALA* 3.3 28.3 - - + -
89A MET* 3.8 11.7 - - + -
92A HIS* 4.7 6.5 - - + +
17B LEU* 3.4 35.7 - - + -
77B PHE 2.9 22.9 - - - +
78B SER* 3.1 7.9 + - - +
80B PHE* 1.3 87.2 - - + +
82B ASN* 1.3 62.1 + - - +
83B LEU 3.1 0.2 - - - -
84B ILE* 3.2 7.1 + - + +
85B GLY* 2.8 25.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 82 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A ASN* 5.7 1.0 - - - +
67B LEU* 3.8 23.4 + - + +
69B THR* 5.0 8.7 - - - +
78B SER* 2.7 25.7 + - - +
79B GLU* 3.3 20.1 - - - +
81B LEU* 1.3 73.3 - - - +
83B LEU* 1.3 60.7 + - - +
85B GLY* 3.1 10.8 + - - -
86B GLY* 3.1 10.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 83 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B PHE* 3.5 32.5 - - + -
43B MET* 4.6 0.7 - - + -
47B LEU* 4.0 7.9 - - + -
63B MET* 3.6 31.4 - - + +
67B LEU* 3.3 27.5 - - + +
79B GLU 3.1 2.0 + - - +
80B PHE* 2.9 37.0 - - + +
82B ASN* 1.3 77.3 - - - +
84B ILE* 1.3 52.5 + - + +
86B GLY* 2.8 6.3 + - - -
87B LEU* 2.8 57.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 84 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A THR* 3.1 26.9 - - - +
13A CYS* 4.3 2.9 - - - -
14A ILE* 4.1 15.3 - - + -
17A LEU* 4.6 11.0 - - + -
81A LEU* 5.6 1.3 - - + -
84A ILE* 5.4 3.1 - - + -
17B LEU* 3.5 34.8 - - + -
80B PHE* 2.9 38.4 + - + +
81B LEU* 3.4 15.9 - - + +
83B LEU* 1.3 75.1 - - - +
85B GLY* 1.3 56.0 + - - +
87B LEU* 3.6 15.6 - - + +
88B ALA* 2.8 29.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 85 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A SER* 6.4 0.2 - - - -
81A LEU* 3.4 23.2 - - - +
81B LEU 2.8 14.3 + - - -
82B ASN* 3.1 6.3 + - - -
83B LEU 3.0 0.6 - - - -
84B ILE* 1.3 77.9 - - - +
86B GLY* 1.3 55.9 + - - +
89B MET* 2.9 42.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 86 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B PHE* 6.3 0.4 - - - -
63B MET* 6.6 0.2 - - - -
66B LYS* 5.8 5.8 - - - -
82B ASN 3.1 8.1 + - - -
83B LEU* 2.8 10.4 + - - -
85B GLY* 1.3 69.9 - - - +
87B LEU* 1.3 59.3 + - - +
89B MET* 3.4 16.0 + - - +
90B ALA* 3.0 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 87 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ILE* 3.4 15.7 - - + -
43B MET* 5.1 0.2 - - + -
47B LEU* 3.4 46.9 - - + -
50B PHE* 4.0 37.7 - - + -
63B MET* 5.2 1.3 - - + -
83B LEU* 2.8 37.5 + - + +
84B ILE* 3.6 18.6 - - + +
86B GLY* 1.3 74.0 - - - +
88B ALA* 1.3 65.2 + - - +
90B ALA* 3.0 8.7 + - - +
91B CYS* 3.0 22.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 88 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ILE* 3.2 27.5 - - + +
17A LEU* 4.7 3.8 - - + -
81A LEU* 3.3 30.1 - - + -
84B ILE 2.8 22.2 + - - +
87B LEU* 1.3 73.9 - - - +
89B MET* 1.3 53.5 + - - +
91B CYS* 3.3 1.4 + - - +
92B HIS* 2.7 47.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 89 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A PHE* 4.6 7.6 - - + -
78A SER* 3.3 37.0 - - - +
81A LEU* 3.8 13.2 - - + -
85B GLY* 2.9 30.9 + - - +
86B GLY* 3.7 16.4 - - - +
88B ALA* 1.3 76.9 - - - +
90B ALA* 1.3 57.2 + - - +
92B HIS* 3.7 6.5 - - - +
93B ASP* 2.8 30.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 90 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B PHE* 4.6 21.5 - - + -
86B GLY 3.0 14.6 + - - +
87B LEU* 3.0 11.2 + - - +
89B MET* 1.3 78.0 - - - +
91B CYS* 1.3 52.5 + - - +
93B ASP* 3.4 7.9 + - - +
94B SER* 2.7 34.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 91 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ILE* 4.0 9.9 - - + -
15A GLU* 4.1 20.6 - - - -
18A ILE* 3.4 22.9 - - + -
87B LEU 3.0 14.1 + - - +
88B ALA 3.9 2.0 - - - +
90B ALA* 1.3 73.1 - - - +
92B HIS* 1.3 66.7 + - - +
94B SER* 3.1 12.9 - - - -
95B PHE* 3.0 38.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 92 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A LEU* 4.0 7.8 + - - +
18A ILE* 3.3 44.6 + - + +
21A PHE* 3.6 27.0 - + - +
22A GLN* 2.7 24.5 + - - -
77A PHE* 3.2 28.9 + + + +
80A PHE* 5.4 0.6 - - - -
81A LEU* 4.7 9.1 - - + +
88B ALA* 2.7 41.3 + - + +
89B MET* 3.7 9.0 - - - +
91B CYS* 1.3 72.5 - - - +
93B ASP* 1.3 50.6 + - - +
95B PHE* 2.8 5.6 + - - +
96B LEU* 2.7 40.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 93 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B MET 2.8 19.9 + - - +
90B ALA* 3.5 8.7 - - - +
92B HIS* 1.3 76.3 - - - +
94B SER* 1.3 56.9 + - - +
96B LEU* 4.1 8.3 - - - +
97B LYS* 2.8 58.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 94 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B ALA 2.7 20.5 + - - -
91B CYS* 3.1 17.7 - - - -
93B ASP* 1.3 78.0 + - - +
95B PHE* 1.3 59.4 + - - +
97B LYS* 3.2 8.2 + - - +
98B ALA* 3.0 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 95 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A GLU* 4.8 11.9 - - + -
18A ILE* 3.7 27.6 - - + -
22A GLN* 4.1 20.4 - - - +
91B CYS* 3.0 33.1 + - - -
92B HIS 2.8 8.8 + - - +
94B SER* 1.3 74.9 - - - +
96B LEU* 1.3 62.0 + - - +
98B ALA* 2.9 7.4 + - + -
99B VAL* 2.6 55.9 + - + +
100B PRO* 3.0 10.3 - - + -
102B GLN* 3.8 26.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 96 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A GLN* 3.9 6.3 - - - +
31A ASN 5.5 0.7 - - - +
32A TYR* 3.8 18.2 - - + -
77A PHE* 3.5 38.4 - - + -
92B HIS 2.7 32.5 + - - +
93B ASP* 3.2 10.3 + - - +
95B PHE* 1.3 72.9 - - - +
97B LYS* 1.3 75.4 + - + +
98B ALA 3.2 1.1 + - - -
100B PRO* 3.6 36.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 97 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B ASP* 2.8 48.1 + - - +
94B SER* 3.3 7.0 - - - +
95B PHE 3.1 0.2 - - - -
96B LEU* 1.3 94.5 + - - +
98B ALA* 1.3 58.6 + - - +
----------------------------------------------------------
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