Contacts of the helix formed by residues 73 - 94 (chain B) in PDB entry 5HZZ
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 LEU 73 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B LEU* 3.9 23.1 - - + -
68B LEU* 4.8 6.1 - - + -
69B SER 3.8 8.5 - - - +
70B ALA* 3.0 20.5 + - + +
72B ASP* 1.3 78.0 - - - +
74B ALA* 1.3 65.2 + - - +
75B PRO* 3.4 1.1 - - - -
76B LEU* 3.2 5.6 + - - +
77B ALA* 2.9 22.0 + - - +
29D PRO* 4.8 0.9 - - + -
30D THR 3.8 36.1 - - - +
31D PRO* 4.1 2.7 - - + -
32D PRO* 3.8 21.5 - - + -
94D LEU* 4.3 13.9 - - + +
96D ILE* 4.0 26.5 - - + -
138D ILE* 4.1 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 74 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B GLY 3.2 13.0 + - - +
73B LEU* 1.3 76.7 - - - +
75B PRO* 1.3 64.5 - - + +
77B ALA 3.4 0.2 + - - -
78B HIS* 2.8 30.5 + - - +
134D VAL* 3.5 5.9 - - + +
135D ARG* 3.6 43.3 - - + +
138D ILE* 3.5 18.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 75 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B GLU* 3.5 28.7 - - - +
72B ASP* 3.6 17.0 - - - +
73B LEU 3.6 0.4 - - - -
74B ALA* 1.3 94.3 - - + +
76B LEU* 1.3 60.6 + - - +
78B HIS* 3.3 7.3 + - + +
79B GLU* 3.0 30.0 + - - +
135D ARG* 4.2 16.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 76 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B VAL* 4.1 8.7 - - + -
54B GLU* 3.8 22.3 + - + +
55B ILE* 3.7 28.3 - - + -
58B LEU* 3.7 29.2 - - + -
72B ASP 5.1 0.4 + - - -
73B LEU* 3.2 7.7 + - + +
75B PRO* 1.3 79.8 - - - +
77B ALA* 1.3 58.7 + - - +
79B GLU* 3.2 1.6 + - - -
80B LEU* 2.9 54.7 + - + +
37D LEU* 4.0 17.9 - - + -
90D ALA* 6.3 0.7 - - + -
94D LEU* 3.9 21.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 77 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B LEU 2.9 16.1 + - - +
74B ALA 3.7 3.6 - - - +
76B LEU* 1.3 77.4 - - - +
78B HIS* 1.3 64.7 + - - +
80B LEU* 3.4 3.0 + - - +
81B ALA* 3.0 23.7 + - - +
91D LEU* 3.7 25.3 - - + +
94D LEU* 5.2 0.8 - - - +
96D ILE* 4.0 21.5 - - + -
101D VAL* 3.7 6.2 - - + +
134D VAL* 3.9 13.5 - - + -
138D ILE* 4.2 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 78 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B ALA 2.8 18.1 + - - +
75B PRO* 3.4 8.7 - - + +
77B ALA* 1.3 75.4 - - - +
79B GLU* 1.3 67.3 + - - +
81B ALA* 3.1 4.5 + - - +
82B ASP* 2.9 48.8 + - - -
101D VAL* 4.6 2.0 - - - -
105D VAL* 4.0 10.4 - - + +
131D PRO* 6.4 0.2 - - + -
132D ALA* 3.9 32.2 + - + +
134D VAL* 3.6 22.2 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
47B ALA* 4.7 1.9 - - - +
50B GLU* 3.6 24.2 - - + +
51B VAL* 3.3 31.7 - - + +
54B GLU* 3.7 22.5 - - + +
75B PRO* 3.0 21.9 + - - +
76B LEU 3.2 2.4 + - - +
78B HIS* 1.3 82.3 + - - +
80B LEU* 1.3 65.1 + - - +
82B ASP* 3.3 5.5 + - - +
83B LEU 3.0 17.8 + - - -
201B MN 2.2 36.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 80 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B VAL* 3.8 25.8 - - + -
55B ILE* 5.8 0.7 - - + -
76B LEU* 2.9 44.1 + - + +
77B ALA 3.7 4.0 - - - +
79B GLU* 1.3 77.0 - - - +
81B ALA* 1.3 57.1 + - - +
83B LEU* 3.2 2.1 + - + -
84B LEU* 3.0 24.7 + - - +
44D LEU* 4.3 9.0 - - + -
87D THR* 3.3 29.7 - - + +
90D ALA* 4.0 27.6 - - + -
91D LEU* 3.8 33.0 - - + -
94D LEU* 4.2 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 81 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B ALA 3.0 13.8 + - - +
78B HIS 3.5 7.2 - - - +
80B LEU* 1.3 73.2 - - - +
82B ASP* 1.3 61.0 + - - +
84B LEU* 3.3 16.1 + - + +
85B TYR* 2.9 26.7 + - - +
91D LEU* 4.6 3.1 - - + +
98D ALA 5.6 0.2 - - - +
101D VAL* 3.6 22.7 - - + -
102D PHE* 4.2 16.5 - - - +
105D VAL* 3.9 16.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 82 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B ALA* 4.5 7.5 - - + +
78B HIS* 2.9 31.8 + - - +
79B GLU* 3.3 9.5 + - - +
81B ALA* 1.3 75.7 - - - +
83B LEU* 1.3 62.3 + - - +
85B TYR* 3.2 8.1 + - - +
86B VAL* 3.1 26.6 + - - +
201B MN 2.2 39.0 + - - +
105D VAL* 3.6 20.1 - - - +
109D ASN* 5.2 1.9 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
44B LEU* 4.2 9.2 - - + +
47B ALA* 3.9 20.5 - - + +
48B SER* 3.8 26.7 - - - +
51B VAL* 4.2 16.2 - - + -
79B GLU 3.0 12.9 + - - +
80B LEU* 3.2 8.7 + - + +
82B ASP* 1.3 74.4 - - - +
84B LEU* 1.3 61.7 + - - +
86B VAL* 3.3 10.0 + - + +
87B THR* 2.7 44.0 + - - +
44D LEU* 3.8 18.8 - - + -
48D SER* 5.8 0.2 - - - +
83D LEU* 4.5 9.0 - - + -
87D THR* 3.5 25.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 84 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B LEU 3.0 15.5 + - - +
81B ALA* 3.4 11.7 - - + +
83B LEU* 1.3 74.9 - - - +
85B TYR* 1.3 58.3 + - - +
87B THR* 4.4 3.4 - - - -
88B TYR* 2.8 39.0 + - + +
84D LEU* 3.9 19.7 - - + +
87D THR* 3.6 25.1 - - + -
88D TYR* 3.8 45.3 - - + +
91D LEU* 4.2 17.7 - - + -
98D ALA* 4.7 2.7 - - + -
102D PHE* 3.9 25.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 85 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B LEU* 3.7 27.2 - - + +
17B PHE* 3.4 38.9 - + - +
81B ALA 2.9 12.1 + - - +
82B ASP* 3.4 12.8 - - - +
83B LEU 3.1 0.6 - - - -
84B LEU* 1.3 76.3 - - - +
86B VAL* 1.3 63.3 + - + +
89B GLY* 2.8 24.3 + - - -
102D PHE* 3.5 29.8 - + - -
105D VAL* 3.8 14.6 - - + -
106D HIS* 2.7 41.9 + - - -
109D ASN* 3.5 29.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 86 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B ARG* 3.0 30.2 + - - +
43B LEU* 3.9 38.1 - - + +
44B LEU* 3.9 16.5 - - + +
47B ALA* 3.8 22.9 - - + -
82B ASP 3.1 13.1 + - - +
83B LEU* 3.4 12.3 - - + +
85B TYR* 1.3 78.7 - - + +
87B THR* 1.3 60.9 + - - +
89B GLY 3.6 0.7 - - - -
90B ALA* 3.0 14.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 87 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B LEU* 3.6 15.9 - - - +
83B LEU* 2.7 26.3 + - - +
84B LEU* 5.8 0.2 - - - -
86B VAL* 1.3 73.2 - - - +
88B TYR* 1.3 67.4 + - - +
89B GLY 3.1 0.9 - - - -
90B ALA* 3.1 13.5 + - - +
91B LEU* 3.2 15.2 + - - +
80D LEU* 3.5 42.3 - - + +
83D LEU* 3.7 17.4 - - + +
84D LEU* 3.5 23.6 - - + +
87D THR* 5.5 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 88 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B ASN* 3.5 18.9 + - + +
11B ALA* 3.7 27.5 + - + -
14B LEU* 3.7 19.1 - - + +
84B LEU* 2.8 29.2 + - + +
87B THR* 1.3 74.3 - - - +
89B GLY* 1.3 63.3 + - - +
91B LEU* 3.3 5.8 + - - +
92B ASP* 2.9 25.5 + - - +
98B ALA* 3.7 24.9 - - + -
99B ASP* 4.5 0.3 + - - -
10D ASN* 2.9 24.0 + - - -
84D LEU* 3.8 22.2 - - + +
88D TYR* 2.4 38.5 + + - -
102D PHE* 4.0 16.4 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 89 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B LEU* 3.6 17.7 - - - +
18B HIS* 3.6 7.1 - - - -
40B ARG* 3.4 16.2 - - - -
85B TYR 2.8 21.6 + - - -
86B VAL 3.5 0.2 + - - -
87B THR 3.1 0.6 - - - -
88B TYR* 1.3 76.5 - - - +
90B ALA* 1.3 61.3 + - - +
92B ASP 3.4 0.3 + - - -
93B GLN* 3.1 28.6 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
40B ARG* 3.4 34.3 - - + +
44B LEU* 5.2 4.9 - - + -
86B VAL 3.0 13.6 + - - +
87B THR* 3.1 7.8 + - - +
89B GLY* 1.3 74.1 - - - +
91B LEU* 1.3 64.9 + - - +
93B GLN* 3.3 4.5 + - - +
94B LEU* 3.1 30.3 + - + +
80D LEU* 4.2 20.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 91 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B THR 3.2 11.8 + - - +
88B TYR* 3.8 6.1 - - - +
90B ALA* 1.3 76.8 - - - +
92B ASP* 1.3 63.5 + - - +
94B LEU* 3.1 11.7 + - + +
96B ILE* 3.0 60.1 + - + +
98B ALA* 3.8 27.1 - - + -
101B VAL* 5.4 2.5 - - + -
77D ALA* 4.1 17.7 - - + +
80D LEU* 3.8 39.3 - - + -
81D ALA* 4.6 3.6 - - + +
84D LEU* 4.0 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 92 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B ALA 4.6 3.6 - - - +
14B LEU* 4.4 7.0 - - + -
15B HIS* 2.7 42.1 + - - +
18B HIS* 2.7 24.8 + - + +
25B THR* 2.6 31.0 + - - +
26B PRO 4.3 1.4 - - - +
88B TYR 2.9 16.6 + - - +
89B GLY 3.8 4.3 - - - +
91B LEU* 1.3 77.6 - - - +
93B GLN* 1.3 56.2 + - - +
95B GLY* 2.9 19.2 + - - +
96B ILE 4.5 5.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 93 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B HIS* 3.6 24.6 + - + -
23B ALA* 5.0 8.5 + - - +
25B THR* 3.8 17.8 - - + +
26B PRO* 3.8 14.0 - - - +
30B THR* 4.9 2.3 - - - +
32B PRO* 5.5 0.3 - - - +
36B LEU* 3.1 48.1 - - + +
39B LEU* 5.9 0.5 - - - +
40B ARG* 3.4 23.9 + - + +
89B GLY 3.1 18.9 + - - +
90B ALA* 3.3 6.0 + - - +
92B ASP* 1.3 76.3 - - - +
94B LEU* 1.3 61.8 + - + +
95B GLY 3.2 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 94 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B PRO* 3.4 2.8 - - - +
30B THR* 2.9 33.5 + - - +
32B PRO* 3.5 41.5 - - + -
36B LEU* 5.4 2.5 - - + -
37B LEU* 4.6 8.3 - - + -
90B ALA* 3.1 18.7 + - + +
91B LEU* 3.1 10.2 + - + +
93B GLN* 1.3 77.4 - - + +
95B GLY* 1.3 59.6 + - - +
96B ILE* 3.7 24.1 - - + +
73D LEU* 4.3 9.1 - - + +
76D LEU* 4.0 24.0 - - + -
77D ALA 5.7 0.7 - - - +
80D LEU* 4.1 15.5 - - + -
----------------------------------------------------------
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