Contacts of the helix formed by residues 77 - 88 (chain A) in PDB entry 1H4O
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 ASP 77 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A PRO* 5.7 2.7 - - + -
76A ASN* 1.3 76.5 + - - +
78A ALA* 1.3 60.8 + - - +
79A PHE* 3.0 21.1 + - + +
80A VAL* 2.9 45.0 + - - +
81A THR* 3.1 23.0 + - - +
98A ALA* 3.8 1.1 - - - -
100A PRO* 4.2 13.8 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
15A PHE* 4.1 9.6 - - + -
17A GLY 3.2 16.7 - - - +
18A GLU 3.5 33.0 - - - +
19A PRO* 3.7 11.9 - - + +
77A ASP* 1.3 72.2 - - - +
79A PHE* 1.3 66.3 + - - +
81A THR* 3.3 10.5 + - - +
82A GLY 3.0 17.2 + - - -
98A ALA* 3.6 14.3 - - + +
100A PRO* 5.4 1.6 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
17A GLY 4.3 3.4 - - - +
18A GLU* 4.4 17.0 - - + -
19A PRO* 3.6 36.1 - - + -
77A ASP* 3.0 14.0 + - + +
78A ALA* 1.3 78.8 - - - +
80A VAL* 1.3 65.7 + - + +
82A GLY* 3.4 0.7 + - - -
83A GLU* 3.1 31.5 + - + +
86A ARG* 4.9 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A ALA* 3.7 24.5 - - + +
43A PHE* 3.6 19.2 - - + -
76A ASN* 3.9 17.5 - - + +
77A ASP* 2.9 33.0 + - - +
79A PHE* 1.3 74.1 - - + +
81A THR* 1.3 65.7 + - - +
83A GLU* 3.3 3.9 + - - -
84A TRP* 2.9 21.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A GLY 4.7 2.1 + - - -
42A ALA* 4.7 3.6 - - + -
74A SER* 3.5 24.7 - - - +
76A ASN* 3.8 11.9 - - + -
77A ASP 3.1 12.4 + - - +
78A ALA* 3.3 17.2 + - - +
80A VAL* 1.3 76.6 - - - +
82A GLY* 1.3 59.1 + - - +
84A TRP* 3.2 9.2 + - + +
85A GLY 2.9 25.5 + - - -
96A LEU* 3.8 30.2 + - + +
97A LEU 4.2 4.3 - - - +
98A ALA* 3.5 20.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A GLY* 4.3 16.6 - - - -
78A ALA 3.0 17.5 + - - -
79A PHE 3.9 1.1 - - - -
81A THR* 1.3 79.2 + - - +
83A GLU* 1.3 60.0 + - - +
85A GLY* 3.4 1.8 + - - -
86A ARG* 3.1 44.1 + - - +
96A LEU* 5.3 2.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A PHE* 4.0 10.7 - - + -
79A PHE* 3.1 21.4 + - + +
80A VAL* 3.9 4.7 - - - +
82A GLY* 1.3 75.7 - - - +
84A TRP* 1.3 62.9 + - - +
86A ARG* 2.6 40.5 + - - +
87A ALA* 2.9 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A VAL* 3.9 21.8 - - + -
42A ALA* 3.6 23.3 - - + -
43A PHE* 3.1 44.1 - + + +
47A CYS* 3.6 30.5 - - + -
48A SER* 2.9 24.5 + - - -
52A LEU* 3.7 26.5 - - + -
72A CYS* 3.9 11.9 - - - -
74A SER* 5.0 3.8 - - - -
80A VAL 2.9 18.0 + - - +
81A THR* 3.5 5.6 - - - +
83A GLU* 1.3 76.2 - - - +
85A GLY* 1.3 63.1 + - - +
87A ALA* 3.1 9.4 + - - +
88A HIS* 3.3 38.4 + + - -
96A LEU* 3.7 30.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A LEU* 4.9 3.4 - - - -
81A THR 2.9 12.2 + - - -
82A GLY* 3.9 2.2 - - - -
84A TRP* 1.3 76.2 - - - +
86A ARG* 1.3 62.3 + - - +
88A HIS 3.0 8.0 + - - -
90A ALA* 3.0 29.2 + - - +
91A GLU 5.5 0.7 - - - -
96A LEU* 3.6 32.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A GLY* 4.7 12.3 + - - -
18A GLU* 5.1 8.9 + - - -
79A PHE 4.9 0.6 + - - -
82A GLY* 3.1 30.9 + - - +
83A GLU* 2.6 40.4 + - - +
84A TRP 3.2 0.2 - - - -
85A GLY* 1.3 77.1 - - - +
87A ALA* 1.3 62.1 + - - +
88A HIS 3.2 0.7 + - - -
89A LYS* 3.2 16.8 + - - +
90A ALA 5.0 0.2 - - - +
91A GLU* 6.1 1.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A PHE* 4.6 12.6 - - + -
83A GLU 2.9 13.8 + - - +
84A TRP* 3.1 12.5 + - - +
86A ARG* 1.3 77.1 - - - +
88A HIS* 1.3 72.3 + - + +
89A LYS* 3.5 3.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A PHE* 5.8 0.8 - - - -
48A SER* 2.8 34.5 + - - -
49A LYS* 3.5 21.7 + - + -
52A LEU* 3.9 26.0 - - + -
53A PRO* 4.5 10.0 - - + +
56A VAL* 3.9 16.5 - - + +
84A TRP* 3.3 48.6 + + - +
85A GLY 3.0 4.1 + - - +
87A ALA* 1.3 87.5 + - + +
89A LYS* 1.3 71.3 + - - +
90A ALA* 3.2 3.9 + - + +
----------------------------------------------------------
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