Contacts of the helix formed by residues 70 - 86 (chain A) in PDB entry 2H8C
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 ASN 70 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A ARG* 1.3 78.9 + - - +
71A LEU* 1.3 68.9 + - - +
72A ASP* 3.6 19.4 + - - +
73A ASN* 3.4 31.2 + - - +
74A LEU* 3.7 10.5 + - - +
90B ASP* 5.4 0.6 + - - -
91B ASP* 4.4 17.2 + - - -
92B ALA* 4.8 10.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 71 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A CYS* 3.9 14.4 - - + -
63A MET* 3.8 15.9 - - + -
69A ARG 3.9 3.2 + - - +
70A ASN* 1.3 71.8 - - - +
72A ASP* 1.3 54.6 + - - +
74A LEU* 2.7 53.9 + - + +
75A GLN* 3.2 4.7 + - - +
99A VAL* 3.9 17.0 - - + +
101A LYS* 4.2 14.1 - - + +
94B VAL 3.5 19.5 - - - +
95B VAL* 3.3 29.6 - - - +
96B ASP 4.2 1.6 - - - +
97B TYR* 3.8 22.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 72 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A ASN* 3.6 14.0 + - - +
71A LEU* 1.3 78.5 - - - +
73A ASN* 1.3 90.8 + - - +
74A LEU 3.3 0.2 - - - -
75A GLN* 3.4 8.1 + - - +
76A LYS* 2.8 28.9 + - - +
75B GLN* 3.0 41.0 + - - +
76B LYS* 5.1 8.0 - - - +
79B PHE* 4.8 5.1 - - + -
97B TYR* 3.2 17.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 73 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ASN* 3.6 42.2 + - + +
70A ASN* 3.6 26.6 + - - +
71A LEU 3.0 0.6 + - - -
72A ASP* 1.3 94.6 + - - +
74A LEU* 1.3 68.4 + - + +
76A LYS* 3.3 7.8 + - - +
77A ALA* 3.0 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 74 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A TRP* 3.2 48.5 - - + +
11A PRO* 3.7 22.7 - - + -
59A ILE* 5.0 1.8 - - - -
61A CYS* 3.4 34.8 - - + -
63A MET* 3.6 14.6 - - + -
69A ARG* 5.5 2.7 - - + -
70A ASN 3.7 9.4 - - - +
71A LEU* 2.7 23.7 + - + +
73A ASN* 1.3 74.2 - - + +
75A GLN* 1.3 54.6 + - - +
77A ALA* 4.1 0.5 - - - +
78A ALA* 2.9 31.8 + - - +
110A LEU* 4.0 10.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 75 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A ILE* 4.3 11.8 - - + +
71A LEU 3.2 4.8 + - - -
72A ASP* 3.4 14.5 - - - +
74A LEU* 1.3 73.7 - - - +
76A LYS* 1.3 73.8 + - - +
77A ALA 3.1 1.8 - - - -
79A PHE* 2.9 55.7 + - + +
97A TYR* 3.5 30.6 + - + -
99A VAL* 3.9 21.5 - - + +
72B ASP* 3.4 35.1 + - - +
75B GLN* 4.4 3.8 - - - +
97B TYR* 3.9 6.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 76 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ASN* 2.9 33.2 + - - +
18A TYR* 3.3 38.1 - - + +
72A ASP 2.8 21.1 + - - +
73A ASN* 3.7 10.3 - - - +
75A GLN* 1.3 85.2 - - - +
77A ALA* 1.3 58.1 + - + +
79A PHE* 4.1 1.9 - - - +
80A ASP* 3.2 25.5 + - - +
72B ASP* 5.0 8.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A PRO* 3.9 26.2 - - + -
12A PRO 5.2 2.2 - - - +
17A TYR* 4.0 26.3 + - + -
18A TYR* 6.3 0.2 - - + -
34A TYR* 4.2 2.3 - - - -
73A ASN 3.0 16.2 + - - +
74A LEU 4.1 0.9 - - - +
76A LYS* 1.3 80.5 - - + +
78A ALA* 1.3 65.5 + - - +
80A ASP* 3.3 6.1 + - - +
81A ALA* 3.0 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A LEU* 4.8 5.5 - - + +
34A TYR* 5.0 1.8 - - - -
59A ILE* 4.1 20.2 - - + -
74A LEU 2.9 20.1 + - - +
75A GLN 3.8 2.0 - - - +
77A ALA* 1.3 77.4 - - - +
79A PHE* 1.3 62.6 + - - +
81A ALA* 3.4 4.2 + - - +
82A LEU* 3.2 30.6 + - - +
110A LEU* 4.0 20.1 - - + +
112A LEU* 4.4 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A ILE* 3.5 28.5 - - + -
59A ILE* 3.6 28.0 - - + -
75A GLN* 2.9 40.0 + - + +
76A LYS 4.1 2.2 - - - +
78A ALA* 1.3 76.6 - - - +
80A ASP* 1.3 64.0 + - - +
82A LEU* 3.1 4.4 + - + +
83A THR* 2.9 27.8 + - - -
88A TRP* 3.9 16.0 - + + -
91A ASP* 3.7 30.1 - - + +
94A VAL* 3.7 26.7 - - + -
97A TYR* 3.8 23.1 - + - -
72B ASP* 5.3 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A TYR* 2.7 31.1 + - + -
18A TYR* 4.9 6.7 - - - +
35A ARG* 2.4 42.0 + - - -
76A LYS 3.2 18.8 + - - +
77A ALA* 3.3 7.4 + - - +
79A PHE* 1.3 78.3 - - - +
81A ALA* 1.3 63.1 + - - +
83A THR* 3.5 5.8 + - - -
84A LYS* 3.0 27.4 + - - +
91A ASP* 5.1 2.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A LEU* 5.5 0.7 - - + -
17A TYR* 4.3 1.6 - - - +
34A TYR* 3.7 16.8 - - + -
35A ARG* 4.5 8.7 - - - +
38A VAL* 3.5 34.5 - - + +
77A ALA 3.0 16.3 + - - +
78A ALA* 3.9 4.0 - - - +
79A PHE 3.3 0.2 - - - -
80A ASP* 1.3 80.9 - - - +
82A LEU* 1.3 58.1 + - + +
84A LYS* 3.6 6.2 + - - +
85A ALA* 2.9 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A ILE* 4.6 3.1 - - + -
8A LEU* 4.2 12.1 - - + -
38A VAL* 4.1 10.1 - - + -
42A ILE* 4.1 21.3 - - + -
57A ILE* 6.3 0.7 - - + -
78A ALA* 3.2 17.2 + - + +
79A PHE* 3.1 5.2 + - + +
81A ALA* 1.3 74.1 - - - +
83A THR* 1.3 67.6 + - - +
85A ALA* 2.9 13.5 + - - +
86A GLY 2.9 10.4 + - - -
87A PHE* 3.2 40.5 + - + -
88A TRP* 4.1 27.6 - - + -
112A LEU* 3.2 31.0 - - + -
114A ILE* 5.3 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A PHE 2.9 17.0 + - - -
80A ASP* 3.6 6.3 - - - -
82A LEU* 1.3 74.3 - - - +
84A LYS* 1.3 70.6 + - + +
86A GLY* 2.9 21.1 + - - -
88A TRP* 2.8 36.8 + - - +
89A LEU 4.0 18.5 - - - +
90A ASP* 4.9 2.9 - - - -
91A ASP* 3.8 15.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A ARG* 3.2 59.0 - - + +
39A ALA* 5.8 0.8 - - - +
80A ASP* 3.0 16.6 + - - +
81A ALA* 3.6 5.8 - - - +
83A THR* 1.3 88.3 - - - +
85A ALA* 1.3 62.0 + - - +
86A GLY* 3.1 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A ARG 5.7 0.2 + - - -
38A VAL* 3.9 7.9 - - + -
39A ALA* 3.9 24.1 - - - +
42A ILE* 3.7 31.4 - - + +
43A LYS* 5.7 3.7 - - - +
48A ASP* 3.7 18.5 - - - +
81A ALA 2.9 18.4 + - - +
82A LEU* 2.9 6.1 + - - +
84A LYS* 1.3 74.9 - - - +
86A GLY* 1.3 60.6 + - - +
87A PHE 3.2 1.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A ASP* 3.6 9.5 - - - +
50A GLY* 2.8 35.5 + - - -
82A LEU 2.9 3.4 + - - -
83A THR 2.9 13.2 + - - -
84A LYS 3.0 2.3 - - - -
85A ALA* 1.3 78.8 - - - +
87A PHE* 1.3 53.9 + - - +
88A TRP 3.5 6.3 - - - -
89A LEU* 5.4 2.9 - - - +
----------------------------------------------------------
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