Contacts of the helix formed by residues 65 - 81 (chain A) in PDB entry 3HSJ
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 65 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A SER 3.8 1.2 + - - -
64A LEU* 1.3 75.4 - - - +
66A PRO* 1.3 76.7 - - + +
67A GLU* 3.8 21.8 - - - +
68A GLU* 2.9 26.2 + - - +
69A LEU* 2.9 19.4 + - - +
101A PHE* 4.0 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 66 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A ALA* 1.3 87.4 - - + +
67A GLU* 1.3 66.3 + - - +
69A LEU* 3.2 4.0 + - - +
70A LEU* 3.0 26.7 + - - +
98A ILE* 4.2 3.3 - - + +
101A PHE* 3.7 40.4 - - + -
104A GLU* 4.5 8.1 - - - +
106A ILE* 3.6 33.9 - - + -
111A LEU* 3.9 13.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 67 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A ALA* 3.8 17.2 - - + +
66A PRO* 1.3 90.6 - - - +
68A GLU* 1.3 64.3 - - + +
70A LEU* 3.4 10.6 + - + +
71A ASN* 3.0 33.4 + - - +
110A ARG* 3.5 16.0 + - + +
111A LEU* 4.3 8.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 68 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A GLU* 5.3 1.0 - - - +
64A LEU* 3.7 23.3 - - + +
65A ALA* 2.9 37.4 + - + +
67A GLU* 1.3 82.9 - - + +
69A LEU* 1.3 65.1 + - - +
71A ASN* 3.2 23.8 + - - +
72A HIS* 3.2 23.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 69 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A ALA* 3.7 30.3 - - + -
5A ILE* 4.4 5.6 - - + -
28A ILE* 4.1 16.4 - - + -
60A LEU* 3.7 25.4 - - + -
62A THR* 4.5 4.0 - - + +
64A LEU* 4.1 20.1 - - + +
65A ALA 2.9 11.5 + - - +
66A PRO* 3.5 9.9 - - + +
68A GLU* 1.3 77.0 - - - +
70A LEU* 1.3 62.5 + - - +
72A HIS* 3.0 4.3 + - - +
73A THR* 2.9 27.3 + - + -
98A ILE* 3.9 24.0 - - + -
101A PHE* 4.0 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 70 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A PRO 3.0 13.2 + - - +
67A GLU* 3.5 9.4 - - + +
68A GLU 3.3 0.2 - - - -
69A LEU* 1.3 77.1 - - - +
71A ASN* 1.3 63.3 + - - +
73A THR* 3.2 14.4 + - - +
74A GLN* 2.9 46.0 + - + +
96A LEU 6.1 0.4 - - - +
98A ILE* 3.8 15.8 - - + +
110A ARG* 3.6 50.0 - - + +
111A LEU* 4.2 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 71 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A GLU* 3.0 19.9 + - - +
68A GLU* 3.3 20.9 - - - +
69A LEU 3.2 0.2 - - - -
70A LEU* 1.3 74.4 - - - +
72A HIS* 1.3 62.8 + - + +
74A GLN* 3.7 3.6 - - - +
75A ARG* 2.9 27.9 + - - +
110A ARG* 2.6 43.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 72 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A ILE* 3.7 24.5 - - + -
29A PRO* 3.3 33.0 - - + +
64A LEU* 3.8 21.2 - - + +
68A GLU* 3.2 23.0 + - + +
69A LEU 3.0 7.6 + - - +
71A ASN* 1.3 81.9 - - + +
73A THR* 1.3 60.9 + - - +
75A ARG* 3.0 32.5 + - - +
76A ILE* 2.9 35.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 73 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ILE* 4.2 25.4 - - + -
25A LEU* 4.4 13.7 - - + -
28A ILE* 4.9 0.4 - - + -
69A LEU* 2.9 22.2 + - + +
70A LEU* 3.2 27.7 + - - +
72A HIS* 1.3 75.5 - - - +
74A GLN* 1.3 61.7 + - - +
76A ILE* 3.4 1.4 + - - -
77A GLU* 3.0 29.6 + - - +
96A LEU* 3.8 31.7 + - + +
98A ILE* 4.3 9.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 74 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A LEU* 2.9 42.0 + - + +
71A ASN* 3.7 4.0 - - - +
73A THR* 1.3 74.9 + - - +
75A ARG* 1.3 65.1 + - - +
77A GLU* 3.2 15.2 + - - +
78A LEU* 3.0 32.5 + - + +
110A ARG* 2.8 36.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 75 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ALA* 5.0 5.3 + - - +
27A ASP 5.6 0.8 + - - -
28A ILE* 4.2 9.7 - - - +
29A PRO* 5.0 1.0 - - - +
71A ASN 2.9 19.3 + - - +
72A HIS* 3.0 39.4 + - - +
74A GLN* 1.3 76.5 - - - +
76A ILE* 1.3 81.8 + - - +
78A LEU* 3.1 11.5 + - - +
79A GLN* 2.9 68.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 76 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ALA* 4.5 5.4 - - - +
24A ALA* 3.8 41.1 - - + +
25A LEU* 3.9 12.3 - - + +
28A ILE* 4.0 20.4 - - + -
72A HIS 2.9 20.8 + - - +
74A GLN 3.3 0.2 - - - -
75A ARG* 1.3 93.4 - - - +
77A GLU* 1.3 58.2 + - - +
79A GLN* 4.4 6.5 - - - +
80A GLN* 2.8 49.5 + - + +
94A LEU* 4.5 4.0 - - + -
96A LEU* 3.5 21.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A THR 3.0 18.5 + - - +
74A GLN* 3.5 19.5 - - - +
76A ILE* 1.3 78.1 - - - +
78A LEU* 1.3 56.4 + - + +
81A GLY* 3.0 24.3 + - - -
92A ARG* 3.1 35.3 + - - +
94A LEU* 3.4 22.5 - - + +
95A ASP* 3.5 9.4 - - - +
96A LEU* 2.9 45.4 + - + +
97A ASP* 4.9 2.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A GLN* 3.0 23.0 + - + +
75A ARG* 3.5 11.2 - - - +
77A GLU* 1.3 77.0 - - + +
79A GLN* 1.3 64.7 + - + +
81A GLY 3.4 11.1 - - - +
92A ARG* 3.7 25.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A ARG* 2.9 63.4 + - + +
76A ILE* 4.0 4.4 - - - +
78A LEU* 1.3 80.1 - - + +
80A GLN* 1.3 75.3 + - - +
81A GLY 3.7 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LEU* 5.9 0.3 - - - +
17A GLN* 3.5 25.3 + - - +
20A ALA* 3.8 29.7 - - - +
21A ALA* 4.7 6.5 - - + +
24A ALA* 4.8 7.1 - - + +
76A ILE* 2.8 38.8 + - + +
79A GLN* 1.3 88.6 + - + +
81A GLY* 1.3 57.8 + - - +
93A THR* 4.7 0.5 + - - -
94A LEU* 3.5 24.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A GLU 3.0 22.2 + - - +
78A LEU 3.4 10.7 - - - +
79A GLN 3.7 0.5 - - - -
80A GLN* 1.3 79.4 - - - +
82A ARG* 1.3 66.1 + - - +
92A ARG* 3.3 4.5 + - - -
93A THR* 3.3 13.5 - - - -
94A LEU* 4.2 9.4 - - - -
----------------------------------------------------------
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