Contacts of the helix formed by residues 70 - 89 (chain B) in PDB entry 4ZWJ
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 THR 70 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B LYS 5.4 0.4 - - - +
67B LYS 4.0 7.9 - - - +
68B LEU 2.7 14.3 + - - -
69B ARG* 1.3 79.5 - - - +
71B PRO* 1.3 66.8 - - + +
72B LEU 3.2 2.3 + - - -
73B ASN* 2.7 38.1 + - - +
74B TYR* 3.2 14.5 + - - -
2070B GLN* 5.3 4.7 - - + -
2073B ILE* 3.4 40.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 71 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B THR* 1.3 88.7 - - + +
72B LEU* 1.3 62.3 + - + +
74B TYR* 3.0 33.9 + - + +
75B ILE 3.8 2.1 + - - -
134B GLU* 4.7 0.7 - - - +
148B PHE* 3.5 30.6 - - + +
149B GLY* 3.3 38.4 - - - +
150B GLU* 3.8 6.1 - - + +
153B ALA* 3.4 10.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 72 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B THR* 2.9 3.8 + - - +
71B PRO* 1.3 77.5 - - + +
73B ASN* 1.3 69.3 + - - +
75B ILE* 3.3 24.1 - - - +
76B LEU* 3.8 6.9 + - - +
131B LEU* 4.7 4.1 - - + +
134B GLU* 3.6 32.8 - - + +
135B ARG* 5.0 8.3 - - + +
138B VAL* 4.2 32.5 - - + -
145B ASN* 5.0 4.9 - - - +
148B PHE* 3.9 16.2 - - + -
2073B ILE* 3.6 30.7 - - + -
2074B ASP* 5.3 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 73 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B LEU* 2.8 30.9 + - - +
70B THR* 2.7 23.9 + - - +
72B LEU* 1.3 79.6 - - - +
74B TYR* 1.3 52.3 + - - -
75B ILE 3.2 0.2 - - - -
76B LEU* 3.1 15.1 + - - +
77B LEU* 2.8 43.9 + - + +
310B ASN* 5.8 0.5 + - - -
312B GLN* 3.6 18.0 + - - +
313B PHE* 3.5 34.1 - - + -
2073B ILE* 5.0 5.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 74 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B ARG* 4.4 11.4 + - + +
70B THR* 3.2 35.0 - - - -
71B PRO* 3.0 17.5 + - + +
73B ASN* 1.3 77.0 - - - +
75B ILE* 1.3 56.9 + - - +
77B LEU* 3.3 17.4 + - + +
78B ASN* 3.0 26.5 + - - +
150B GLU* 4.3 30.6 + - + +
153B ALA* 3.9 18.2 - - + -
154B ILE* 4.4 22.9 - - + -
157B VAL* 3.8 11.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 75 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B PRO 3.8 1.4 + - - -
72B LEU 3.3 15.6 + - - +
74B TYR* 1.3 80.5 - - - +
76B LEU* 1.3 65.6 + - + +
78B ASN* 3.3 4.5 + - - +
79B LEU* 3.1 19.9 + - - +
127B SER* 3.4 30.0 + - - +
130B VAL* 3.5 29.8 - - + -
131B LEU* 3.7 22.4 - - + -
134B GLU* 3.3 24.7 - - - +
153B ALA* 5.5 1.0 + - - +
156B GLY 4.1 2.9 - - - +
157B VAL* 4.0 19.7 - - + +
160B THR* 3.7 17.3 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
58B THR* 5.1 1.0 - - - +
72B LEU 4.1 8.3 - - - +
73B ASN* 3.1 26.9 + - + +
75B ILE* 1.3 85.0 - - + +
77B LEU* 1.3 60.1 + - - +
79B LEU* 3.4 12.9 + - + +
80B ALA* 3.3 17.0 + - - +
131B LEU* 3.6 34.3 - - + -
135B ARG* 4.2 8.3 - - - +
306B TYR* 4.0 15.3 - - + +
307B ILE* 3.9 30.9 - - + +
310B ASN* 4.0 23.6 - - - +
313B PHE* 4.3 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 77 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B THR* 4.3 10.1 - - + +
59B LEU* 3.7 22.9 - - + +
62B THR* 3.3 43.7 - - + +
69B ARG* 5.4 4.3 - - + -
73B ASN* 2.8 33.2 + - + +
74B TYR* 3.5 20.4 - - + +
75B ILE 3.3 0.2 - - - -
76B LEU* 1.3 70.3 - - - +
78B ASN* 1.3 65.9 + - - +
80B ALA* 3.1 7.6 + - - +
81B VAL* 3.1 27.1 + - + +
313B PHE* 5.1 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 78 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B TYR 3.0 13.4 + - - +
75B ILE* 3.3 11.1 + - - +
77B LEU* 1.3 76.0 - - - +
79B LEU* 1.3 58.1 + - - +
81B VAL* 3.4 9.0 + - - +
82B ALA* 3.0 27.2 + - - +
123B ILE* 3.6 5.1 - - - +
127B SER* 3.2 17.6 + - - -
157B VAL* 3.6 29.6 - - + +
160B THR* 3.4 27.7 + - - +
161B TRP* 2.9 25.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 79 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B ILE 3.1 12.7 + - - +
76B LEU* 3.4 15.0 - - + +
77B LEU 3.2 0.4 - - - -
78B ASN* 1.3 77.9 - - - +
80B ALA* 1.3 60.2 + - - +
82B ALA* 3.4 4.5 + - - +
83B ASP* 3.0 41.0 + - - +
124B ALA* 3.6 43.3 - - + +
127B SER* 4.0 9.6 + - - -
128B LEU* 3.9 26.0 - - + -
302B ASN* 4.8 13.0 - - + +
303B PRO* 5.2 0.7 - - + -
306B TYR* 4.0 23.3 - - + -
307B ILE* 4.7 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 80 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B ASN* 3.6 33.5 - - - +
58B THR* 4.1 20.2 - - + +
59B LEU* 4.1 8.7 - - + -
76B LEU 3.3 9.3 + - - +
77B LEU 3.1 10.4 + - - +
79B LEU* 1.3 79.6 - - - +
81B VAL* 1.3 61.4 + - - +
83B ASP* 3.5 1.1 + - - -
84B LEU* 3.1 29.4 + - - +
307B ILE* 5.8 4.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 81 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B LEU* 4.0 22.2 - - + -
77B LEU 3.1 15.3 + - - +
78B ASN* 3.7 12.6 - - - +
80B ALA* 1.3 73.4 - - - +
82B ALA* 1.3 64.8 + - - +
84B LEU* 3.3 11.3 + - + +
85B PHE* 3.2 46.9 + - + -
123B ILE* 6.4 0.9 - - + -
161B TRP* 4.9 14.4 - - + -
----------------------------------------------------------
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 ASN 3.0 16.6 + - - +
79B LEU 3.6 5.8 - - - +
81B VAL* 1.3 79.3 - - - +
83B ASP* 1.3 61.0 + - - +
85B PHE* 3.3 9.8 + - - +
86B MET* 3.3 16.3 + - - +
120B GLY* 3.4 34.3 - - - +
123B ILE* 3.5 23.8 - - + -
124B ALA* 3.6 11.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 83 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B ASN* 3.2 26.9 - - - +
79B LEU* 3.0 28.3 + - - +
80B ALA 3.9 0.2 - - - +
82B ALA* 1.3 74.3 - - - +
84B LEU* 1.3 63.2 + - - +
86B MET* 3.2 14.5 + - - +
87B VAL* 3.1 26.0 + - - +
124B ALA* 4.0 16.5 - - - +
298B ALA 4.9 0.5 - - - +
299B ALA* 3.9 28.4 - - + +
302B ASN* 5.0 1.6 - - - +
303B PRO* 3.4 23.5 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
51B GLY 5.0 0.2 - - - +
52B PHE* 3.8 37.2 - - + +
55B ASN* 3.7 22.4 - - + +
56B PHE* 3.9 14.6 - - + +
59B LEU* 3.4 32.1 - - + -
80B ALA 3.1 17.9 + - - +
81B VAL* 3.5 11.0 - - + +
82B ALA 3.3 0.4 - - - -
83B ASP* 1.3 77.5 - - - +
85B PHE* 1.3 57.7 + - + +
87B VAL* 3.2 3.2 + - - +
88B LEU* 3.0 43.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 85 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B VAL* 3.2 44.4 + - + -
82B ALA* 3.3 12.5 + - - +
84B LEU* 1.3 76.3 - - + +
86B MET* 1.3 59.1 + - - +
88B LEU* 5.1 5.8 - - + -
89B GLY* 2.9 32.6 + - - +
90B GLY 3.4 1.2 + - - -
116B PHE* 4.3 26.8 - + + +
119B LEU* 5.1 13.7 - - + -
120B GLY* 4.3 9.2 - - - +
123B ILE* 5.1 13.9 - - + -
161B TRP* 5.4 7.9 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 86 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B ALA 3.3 10.7 + - - +
83B ASP* 3.2 19.4 + - - +
85B PHE* 1.3 78.1 - - - +
87B VAL* 1.3 57.0 + - - +
90B GLY* 3.2 8.3 + - - +
91B PHE* 3.0 51.5 + - + -
116B PHE 5.0 2.7 - - - -
117B ALA* 4.4 12.6 - - + +
120B GLY* 3.7 28.9 - - - +
121B GLY* 3.9 11.4 - - - +
124B ALA* 5.2 1.3 - - - -
295B ALA* 4.3 14.6 - - + +
296B LYS* 4.4 6.3 - - + -
299B ALA* 3.8 27.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 87 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B LEU 4.5 1.1 - - - +
48B ILE* 4.3 24.2 - - + -
51B GLY* 4.0 29.6 - - - +
52B PHE* 4.0 26.7 - - + +
55B ASN* 4.9 0.9 - - - +
83B ASP 3.1 15.4 + - - +
84B LEU* 3.2 9.2 + - - +
86B MET* 1.3 74.8 - - - +
88B LEU* 1.3 70.3 + - + +
91B PHE* 3.2 22.9 + - + -
92B THR* 3.2 29.0 + - + +
299B ALA* 6.0 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 88 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B PHE* 4.6 26.7 - - + -
84B LEU* 3.0 29.1 + - + +
85B PHE* 5.1 6.1 - - + -
87B VAL* 1.3 81.1 - - + +
89B GLY* 1.3 61.7 + - - +
92B THR* 2.6 28.3 + - + -
93B SER* 4.6 2.6 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
85B PHE* 2.9 16.8 + - - +
88B LEU* 1.3 79.0 - - - +
90B GLY* 1.3 59.8 + - - +
93B SER* 3.7 10.3 + - - -
113B GLN* 3.4 23.6 - - - +
116B PHE* 4.1 28.3 - - - -
----------------------------------------------------------
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