Contacts of the helix formed by residues 67 - 84 (chain A) in PDB entry 1A8H
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 PRO 67 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A VAL* 5.5 1.3 - - + +
57A TYR* 3.9 30.7 - - + -
60A ALA* 3.9 16.2 - - + -
61A GLN* 6.3 1.3 - - + -
65A GLU 3.5 4.9 - - - +
66A ASP* 1.3 93.9 - - - +
68A LYS* 1.3 62.2 + - - +
70A PHE* 3.2 3.3 + - - +
71A VAL* 3.1 28.2 + - - +
212A TRP* 3.7 36.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 68 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A ASP* 3.2 15.1 + - - +
67A PRO* 1.3 77.7 - - - +
69A ALA* 1.3 63.6 + - - +
71A VAL* 3.4 7.0 - - + +
72A ASP* 2.8 65.4 + - - +
94A ARG* 4.5 4.6 - - - +
96A THR* 4.5 26.4 + - - +
212A TRP* 3.8 14.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 69 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A GLU* 3.5 22.8 - - + +
66A ASP* 2.9 29.0 + - + +
68A LYS* 1.3 76.3 - - - +
70A PHE* 1.3 61.4 + - - +
72A ASP* 3.5 9.4 - - - +
73A ARG* 3.3 17.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 70 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A VAL* 6.2 0.2 - - + -
15A ASN* 3.3 41.3 - - - -
56A VAL* 4.1 16.8 - - + -
59A ALA* 3.9 26.9 - - + -
60A ALA* 3.6 26.2 - - + -
63A ALA* 4.8 7.0 - - + -
65A GLU* 4.1 13.9 + - + -
66A ASP 2.8 12.1 + - - +
67A PRO 3.2 7.8 + - - +
69A ALA* 1.3 73.9 - - - +
71A VAL* 1.3 69.5 + - - +
72A ASP 3.1 1.6 - - - -
73A ARG* 3.1 35.2 + - - +
74A VAL* 3.1 35.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 71 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A VAL* 4.2 7.2 - - + -
51A GLU* 3.4 43.3 - - + +
56A VAL* 3.6 31.6 - - + -
67A PRO 3.1 11.0 + - - +
68A LYS* 3.4 18.4 - - + +
70A PHE* 1.3 79.3 - - + +
72A ASP* 1.3 57.4 + - - +
74A VAL* 3.3 8.1 - - + -
75A SER* 2.8 38.3 + - - -
94A ARG* 3.6 5.2 - - - +
96A THR* 4.3 10.3 - - + -
212A TRP* 4.3 2.9 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
68A LYS* 2.8 48.6 + - - +
69A ALA* 3.5 10.2 - - - +
70A PHE 3.1 0.2 - - - -
71A VAL* 1.3 78.2 - - - +
73A ARG* 1.3 59.0 + - - +
75A SER* 3.2 12.6 + - - -
76A GLY* 3.9 4.7 + - - -
79A LYS* 5.8 0.5 - - - -
94A ARG* 2.5 42.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 73 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A ALA* 5.5 3.4 - - - +
65A GLU* 2.6 42.1 + - - +
69A ALA 3.3 9.1 + - - +
70A PHE* 3.1 37.9 + - - +
72A ASP* 1.3 79.6 - - - +
74A VAL* 1.3 76.6 + - - +
76A GLY* 3.4 13.2 + - - -
77A ARG* 3.9 29.9 + - - +
80A ARG* 4.4 8.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 74 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A VAL* 4.2 27.0 - - + +
15A ASN* 3.9 18.4 - - - +
70A PHE* 3.1 28.0 + - + +
71A VAL* 3.3 14.6 - - + -
73A ARG* 1.3 93.7 - - - +
75A SER* 1.3 68.4 + - - +
76A GLY 3.0 2.5 - - - -
77A ARG* 3.1 51.4 + - - +
78A PHE* 4.1 3.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 75 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A VAL* 4.3 8.7 - - - -
49A THR* 3.9 11.0 - - - -
51A GLU* 3.5 22.2 - - - -
71A VAL 2.8 24.3 + - - -
72A ASP 3.2 9.4 + - - -
74A VAL* 1.3 74.1 - - - +
76A GLY* 1.3 59.0 + - - +
78A PHE* 3.1 27.5 + - - +
79A LYS* 3.4 14.5 + - - +
92A PHE* 4.0 3.8 - - - -
94A ARG* 3.5 18.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 76 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A ASP 3.9 3.3 + - - -
73A ARG 3.4 11.8 + - - -
74A VAL 3.0 1.4 - - - -
75A SER* 1.3 79.8 + - - +
77A ARG* 1.3 58.9 + - - +
78A PHE 3.1 2.5 - - - -
79A LYS* 3.7 15.8 - - - +
80A ARG* 2.9 40.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ASN* 5.0 4.9 - - - +
17A GLU* 4.6 17.6 + - - +
18A PRO* 3.8 18.8 - - + +
73A ARG* 3.9 25.9 + - - +
74A VAL* 3.1 42.0 + - - +
76A GLY* 1.3 76.5 - - - +
78A PHE* 1.3 58.4 + - + +
80A ARG* 3.7 32.7 + - - +
81A ALA* 3.1 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A TYR* 3.6 31.9 - + + -
13A TYR 3.6 14.8 - - - -
14A VAL* 3.8 11.2 - - - -
16A ALA 3.2 27.8 - - - -
18A PRO* 4.0 14.8 - - + -
22A HIS* 3.6 26.7 - + - -
48A GLY 5.5 0.2 - - - -
49A THR* 3.7 18.2 - - + -
74A VAL 4.4 5.2 - - - -
75A SER* 3.1 11.8 + - - +
77A ARG* 1.3 77.6 - - + +
79A LYS* 1.3 60.8 + - - +
80A ARG 3.2 0.2 - - - -
81A ALA* 3.2 3.0 + - - +
82A TRP* 2.9 61.5 + + - +
92A PHE* 4.0 14.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A ASP 5.8 0.4 - - - -
75A SER* 3.8 19.7 - - - +
76A GLY* 3.3 12.4 + - - +
78A PHE* 1.3 75.4 - - - +
80A ARG* 1.3 63.6 + - + +
82A TRP* 3.3 6.4 + - - +
83A ASP* 3.0 29.0 + - - +
89A TYR* 4.5 12.8 + - - +
92A PHE* 3.7 52.4 + - + +
94A ARG* 4.1 15.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A ARG* 4.4 9.3 + - - +
76A GLY* 2.9 18.5 + - - +
77A ARG* 3.7 45.2 + - - +
79A LYS* 1.3 78.2 - - + +
81A ALA* 1.3 60.1 - - - +
83A ASP* 3.2 12.5 + - - +
84A LEU* 3.1 31.6 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
18A PRO* 4.0 11.9 - - + -
77A ARG 3.1 21.0 + - - +
78A PHE 3.5 4.7 - - - +
79A LYS 3.2 0.4 - - - -
80A ARG* 1.3 77.0 - - - +
82A TRP* 1.3 71.0 + - + +
84A LEU* 3.3 11.1 + - - +
85A LEU* 3.1 24.9 + - - +
309A PHE* 3.7 30.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A TYR* 3.6 11.8 - + - -
18A PRO* 5.0 2.0 - - + -
22A HIS* 3.9 22.4 - - + -
23A ALA* 4.3 6.3 - - + -
26A THR* 3.5 37.0 - - + -
47A THR* 3.6 19.4 + - + -
48A GLY 5.7 0.4 + - - -
78A PHE* 2.9 45.6 + + - +
79A LYS* 3.8 3.8 - - - +
81A ALA* 1.3 84.5 - - + +
83A ASP* 1.3 66.5 + - - +
85A LEU* 3.3 22.3 + - + -
86A GLY 3.1 4.0 + - - -
87A ILE* 2.9 46.9 + - + +
89A TYR* 3.9 21.5 - + + -
92A PHE* 3.8 24.7 - + - -
309A PHE* 5.1 3.6 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A LYS* 3.0 17.8 + - - +
80A ARG* 3.3 15.9 - - - +
81A ALA 3.2 0.2 - - - -
82A TRP* 1.3 78.6 - - - +
84A LEU* 1.3 62.7 + - + +
86A GLY* 3.2 7.5 + - - -
87A ILE 5.1 3.7 - - - +
89A TYR* 5.2 6.9 + - - -
317A ARG* 3.0 19.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A ARG* 3.1 19.9 + - + +
81A ALA* 3.5 9.9 - - - +
82A TRP 3.2 0.2 - - - -
83A ASP* 1.3 80.2 - - + +
85A LEU* 1.3 57.1 + - - +
86A GLY 3.2 0.2 - - - -
309A PHE* 4.4 22.0 - - + -
312A LEU* 3.5 26.0 - - + +
317A ARG* 2.8 32.1 + - - +
----------------------------------------------------------
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