Contacts of the helix formed by residues 77 - 88 (chain D) 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 D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19D PRO* 5.6 3.4 - - + -
76D ASN* 1.3 78.9 + - - +
78D ALA* 1.3 62.7 + - - +
79D PHE* 3.0 20.3 + - + +
80D VAL* 3.0 44.3 + - - +
81D THR* 3.1 20.1 + - - +
98D ALA* 3.7 1.1 - - - -
100D PRO* 4.2 13.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 78 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15D PHE* 4.1 9.6 - - + -
17D GLY 3.2 17.1 - - - +
18D GLU* 3.5 34.5 - - - +
19D PRO* 3.6 10.4 - - + +
77D ASP* 1.3 71.8 - - - +
79D PHE* 1.3 65.0 + - - +
80D VAL 3.3 0.2 - - - -
81D THR* 3.3 11.0 + - - +
82D GLY 3.0 17.5 + - - -
98D ALA* 3.6 14.7 - - + +
100D PRO* 5.5 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 79 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17D GLY 4.2 8.4 - - - +
18D GLU* 4.2 13.0 - - + -
19D PRO* 3.5 37.7 - - + -
77D ASP* 3.0 13.3 + - + +
78D ALA* 1.3 76.9 - - - +
80D VAL* 1.3 63.6 + - + +
82D GLY* 3.9 0.7 - - - -
83D GLU* 3.1 30.8 + - + +
86D ARG* 5.0 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 80 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42D ALA* 3.6 24.2 - - + +
43D PHE* 3.5 18.8 - - + -
76D ASN* 3.9 17.9 - - + +
77D ASP* 3.0 34.2 + - - +
79D PHE* 1.3 78.1 - - + +
81D THR* 1.3 62.8 + - - +
83D GLU* 3.3 3.3 + - - -
84D TRP* 3.0 21.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 81 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17D GLY 4.7 2.1 + - - -
42D ALA* 4.7 2.9 - - + -
74D SER* 3.5 25.1 - - - +
76D ASN* 3.7 11.7 - - + -
77D ASP 3.1 13.1 + - - +
78D ALA* 3.3 17.5 + - - +
79D PHE 3.4 0.2 - - - -
80D VAL* 1.3 74.9 - - - +
82D GLY* 1.3 65.3 + - - +
84D TRP* 3.2 9.0 + - + +
85D GLY 3.0 19.4 + - - -
96D LEU* 3.7 28.4 + - + +
97D LEU 4.2 4.3 - - - +
98D ALA* 3.5 20.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 82 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17D GLY* 4.3 9.2 - - - -
78D ALA 3.0 17.6 + - - -
79D PHE 3.9 1.1 - - - -
81D THR* 1.3 77.8 + - - +
83D GLU* 1.3 62.2 + - - +
85D GLY* 3.3 1.2 + - - -
86D ARG* 3.1 50.2 + - - +
96D LEU* 5.1 4.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 83 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43D PHE* 4.0 10.8 - - + -
79D PHE* 3.1 19.6 + - + +
80D VAL* 3.9 4.5 - - - +
82D GLY* 1.3 76.7 - - - +
84D TRP* 1.3 61.5 + - - +
86D ARG* 2.8 35.7 + - - +
87D ALA* 3.0 22.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 84 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39D VAL* 3.9 24.5 - - + -
42D ALA* 3.6 17.9 - - + -
43D PHE* 3.1 45.1 - + + +
47D CYS* 3.7 26.9 - - + -
48D SER* 2.9 26.9 + - - -
52D LEU* 3.8 24.7 - - + -
72D CYS* 3.9 13.9 - - - -
74D SER* 5.0 3.6 - - - -
80D VAL 3.0 17.8 + - - +
81D THR* 3.5 5.4 - - - +
83D GLU* 1.3 74.8 - - - +
85D GLY* 1.3 65.4 + - - +
87D ALA 3.0 10.4 + - - -
88D HIS* 3.3 35.5 + + - -
96D LEU* 3.7 29.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 85 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52D LEU* 4.8 3.4 - - - -
81D THR 3.0 11.5 + - - -
82D GLY 3.8 2.7 - - - -
84D TRP* 1.3 76.2 - - - +
86D ARG* 1.3 63.1 + - - +
88D HIS* 3.1 7.1 + - - -
89D LYS 3.2 0.2 + - - -
90D ALA* 3.1 29.3 + - - +
91D GLU 5.5 0.7 - - - -
96D LEU* 3.6 31.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 86 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17D GLY* 3.8 32.1 + - - -
79D PHE 5.0 0.6 + - - -
82D GLY* 3.1 28.5 + - - +
83D GLU* 2.8 46.8 + - - +
84D TRP 3.2 0.2 - - - -
85D GLY* 1.3 78.1 - - - +
87D ALA* 1.3 60.9 + - - +
88D HIS 3.2 0.7 + - - -
89D LYS* 3.3 17.9 + - - +
90D ALA 5.1 0.4 - - - +
91D GLU* 6.1 2.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 87 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43D PHE* 4.6 11.9 - - + -
83D GLU 3.0 12.8 + - - +
84D TRP* 3.0 13.4 + - - +
86D ARG* 1.3 74.9 - - - +
88D HIS* 1.3 76.5 + - + +
89D LYS* 3.5 3.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 88 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43D PHE* 5.7 1.4 - - - -
48D SER* 3.1 34.7 + - - -
52D LEU* 3.9 26.9 - - + -
53D PRO* 4.4 10.3 - - + +
56D VAL* 3.9 17.5 - - + +
84D TRP* 3.3 48.8 + + - +
85D GLY 3.1 3.4 + - - +
86D ARG 3.1 0.6 - - - -
87D ALA* 1.3 89.6 + - + +
89D LYS* 1.3 70.5 + - - +
90D ALA 3.2 3.1 + - - -
----------------------------------------------------------
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