Contacts of the helix formed by residues 76 - 90 (chain N) in PDB entry 2I2X
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 ALA 76 (chain N).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40N ILE* 3.7 15.2 - - + +
43N ILE* 3.6 46.9 - - + +
44N ALA* 4.3 1.9 + - - -
47N ILE* 4.4 0.5 - - - +
59N LEU* 5.0 0.4 - - + -
72N LEU* 3.3 26.9 + - + +
75N ASP* 1.3 81.1 - - - +
77N LEU* 1.3 61.2 + - + +
78N MET 3.6 0.6 - - - +
79N VAL* 4.9 0.2 - - - -
80N GLY* 3.4 21.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 77 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43N ILE* 3.7 24.2 - - + -
47N ILE* 3.7 18.1 - - + +
55N VAL* 3.8 16.2 - - + -
59N LEU* 4.0 12.1 - - + -
72N LEU 3.2 16.5 + - - +
73N ILE* 4.0 6.3 - - - +
76N ALA* 1.3 74.9 - - - +
78N MET* 1.3 61.7 + - + +
80N GLY 3.9 0.4 - - - -
81N MET* 3.0 26.7 + - - +
105N MET* 4.0 22.0 - - + +
108N GLY* 3.6 32.8 - - - +
109N ILE* 3.8 17.0 - - + +
112N CYS* 4.4 11.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 78 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73N ILE* 2.9 31.8 + - + +
74N ASP* 3.9 22.4 - - - +
77N LEU* 1.3 76.3 - - - +
79N VAL* 1.3 53.7 + - + +
81N MET* 3.3 5.2 + - - +
82N GLY* 2.7 30.0 + - - -
85N ILE* 5.2 2.8 - - + +
105N MET* 5.4 7.2 - - - +
109N ILE* 5.6 4.5 - - + -
123N LYS* 5.5 7.6 - - - -
148N ARG 5.6 0.9 - - - +
149N ALA 4.4 9.4 - - - +
150N ASN* 3.4 22.9 - - - +
151N GLY* 3.8 24.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 79 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35N PRO* 3.8 30.1 - - + -
40N ILE* 5.6 0.4 - - + -
74N ASP 3.3 21.1 - - - +
75N ASP* 3.4 22.4 - - - +
76N ALA* 4.9 0.4 - - - +
77N LEU 3.5 1.2 - - - +
78N MET* 1.3 72.5 - - + +
80N GLY* 1.3 64.4 + - - +
82N GLY* 3.1 11.2 + - - +
83N VAL* 3.3 15.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 80 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44N ALA* 3.8 29.9 - - - +
47N ILE* 3.8 15.0 - - - +
48N PHE* 5.7 0.5 - - - +
76N ALA 3.4 19.5 + - - -
77N LEU 4.0 1.1 - - - -
78N MET 3.3 0.6 - - - -
79N VAL* 1.3 80.7 - - - +
81N MET* 1.3 59.2 + - - +
83N VAL* 3.4 18.0 + - - +
84N VAL* 3.6 5.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 81 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47N ILE* 3.8 13.6 - - - +
77N LEU 3.0 20.1 + - - +
78N MET* 3.5 8.5 - - - +
79N VAL 3.3 0.2 - - - -
80N GLY* 1.3 73.1 - - - +
82N GLY* 1.3 59.5 + - - +
84N VAL* 3.0 15.8 + - + +
85N ILE* 2.8 35.3 + - + +
98N VAL* 3.7 11.4 - - + +
101N SER* 3.6 22.9 - - - +
102N ALA* 3.5 30.1 - - + +
105N MET* 4.0 18.6 - - - -
149N ALA* 3.4 42.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 82 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78N MET 2.7 18.8 + - - -
79N VAL* 3.1 7.3 + - - -
81N MET* 1.3 72.9 - - - +
83N VAL* 1.3 60.4 + - - +
85N ILE* 3.8 12.6 - - - +
86N ARG* 3.1 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 83 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30N ALA* 4.3 14.6 - - + +
33N LEU* 3.5 49.6 - - + +
34N TYR* 4.6 12.1 - - + +
35N PRO* 4.5 8.7 - - + -
48N PHE* 5.0 4.5 - - + -
79N VAL* 3.3 13.6 + - + +
80N GLY* 3.4 10.8 - - - +
81N MET 3.2 0.2 - - - -
82N GLY* 1.3 75.0 - - - +
84N VAL* 1.3 53.6 + - + +
86N ARG* 3.1 7.1 + - - +
87N LEU* 2.8 48.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 84 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47N ILE* 4.1 2.2 - - + -
48N PHE* 3.8 30.3 - - + -
80N GLY 3.6 9.4 + - - +
81N MET* 3.0 24.1 + - + +
83N VAL* 1.3 79.8 - - + +
85N ILE* 1.3 65.0 + - - +
86N ARG 3.2 0.2 + - - -
87N LEU* 3.4 1.9 + - - -
88N TYR* 3.1 22.9 + - - +
93N ILE* 3.6 12.7 - - + +
98N VAL* 3.9 22.2 - - + -
101N SER* 3.4 38.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 85 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78N MET* 5.2 3.6 - - + +
81N MET* 2.8 37.1 + - + +
82N GLY* 3.8 10.3 - - - +
84N VAL* 1.3 74.3 - - + +
86N ARG* 1.3 60.1 + - - +
88N TYR* 3.6 7.9 + - + +
89N ASP* 2.9 39.4 + - - +
98N VAL* 5.6 2.5 - - + -
146N LEU* 4.5 13.7 - - + -
149N ALA* 3.0 38.8 - - + +
150N ASN* 4.0 29.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 86 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33N LEU* 3.6 41.1 - - + +
82N GLY 3.1 19.1 + - - +
83N VAL* 3.1 4.8 + - - +
85N ILE* 1.3 76.6 - - - +
87N LEU* 1.3 65.6 + - - +
89N ASP* 3.1 19.5 + - - +
90N GLU* 2.7 40.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 87 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26N PRO 4.1 1.3 - - - +
29N ALA* 3.8 13.7 - - + +
30N ALA* 3.8 36.3 - - + +
33N LEU* 3.9 18.4 - - + -
48N PHE* 3.9 15.9 - - + -
83N VAL* 2.8 26.9 + - + +
84N VAL 3.9 1.6 - - - +
86N ARG* 1.3 73.5 - - - +
88N TYR* 1.3 59.1 + - - +
90N GLU* 3.5 19.0 + - - +
91N GLY 3.3 3.3 + - - -
92N VAL* 3.0 54.6 + - + -
93N ILE* 3.6 12.9 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 88 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236M LYS* 2.9 50.4 + - + +
237M ASN* 2.7 22.9 + - - -
84N VAL 3.1 17.1 + - - +
85N ILE* 3.7 8.1 - - + +
86N ARG 3.2 0.2 - - - -
87N LEU* 1.3 75.4 - - - +
89N ASP* 1.3 66.6 + - - +
91N GLY* 3.2 7.3 + - - -
93N ILE* 3.6 20.6 - - + +
94N PHE 3.8 8.3 - - - -
95N LEU* 3.4 33.0 - - + +
98N VAL* 3.8 19.7 - - + -
142N ILE* 5.4 3.1 - - - +
146N LEU* 4.8 23.3 - - + -
230N GLU* 5.1 4.9 + - - +
232N ALA* 4.8 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 89 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236M LYS* 3.4 16.2 + - - +
85N ILE* 2.9 33.6 + - - +
86N ARG* 3.1 12.7 + - - +
88N TYR* 1.3 80.1 - - - +
90N GLU* 1.3 61.4 + - + +
91N GLY* 3.2 1.4 + - - -
232N ALA* 4.8 15.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 90 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22N LYS* 3.5 32.9 + - - +
33N LEU* 5.1 0.9 - - - +
86N ARG* 2.7 50.0 + - - +
87N LEU* 3.8 18.4 - - - +
88N TYR 3.2 0.2 - - - -
89N ASP* 1.3 76.3 - - + +
91N GLY* 1.3 60.7 + - - +
92N VAL* 3.6 16.2 + - + +
----------------------------------------------------------
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