Contacts of the helix formed by residues 71 - 87 (chain D) in PDB entry 1O94
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 71 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67D SER* 3.6 23.7 - - - +
69D ASP 3.3 1.2 + - - -
70D PHE* 1.3 81.3 - - - +
72D PRO* 1.3 73.6 - - - +
73D ASP 2.8 18.7 + - - -
74D VAL* 2.9 16.1 + - + -
75D PHE* 3.0 26.5 + - - +
181D SER* 2.5 32.7 + - - -
183D SER* 3.4 13.7 + - - +
184D GLN* 5.3 0.5 - - - -
185D ASN* 4.4 8.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 72 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142C HIS* 3.6 35.4 - - + +
143C ALA* 5.2 3.4 - - + -
172C VAL* 6.2 1.3 - - + -
70D PHE* 3.6 24.4 - - + -
71D ASP* 1.3 93.3 - - - +
73D ASP* 1.3 57.7 + - - +
76D GLU* 3.0 32.9 + - - +
101D GLY* 3.5 24.7 - - - +
102D TYR* 4.1 4.6 - - + +
183D SER* 4.0 13.7 - - - +
185D ASN* 5.7 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 73 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141C PRO* 5.4 1.3 - - - +
142C HIS* 4.0 11.4 + - - -
71D ASP* 2.8 12.9 + - - +
72D PRO* 1.3 77.4 - - - +
74D VAL* 1.3 62.5 + - + +
76D GLU* 3.9 5.6 - - - +
77D ALA* 3.1 25.6 + - - +
180D GLN 4.8 0.3 - - - +
181D SER* 3.6 15.2 - - - +
182D ARG* 2.8 68.5 + - - +
183D SER* 5.5 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 74 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41D ILE* 4.2 16.2 - - + -
42D GLY* 6.4 0.2 - - - -
65D GLY* 4.5 15.3 - - - -
66D SER* 4.1 22.9 - - - +
67D SER* 3.9 22.4 - - - +
71D ASP* 2.9 22.9 + - + +
73D ASP* 1.3 78.0 - - + +
75D PHE* 1.3 60.5 + - + +
77D ALA* 3.3 4.8 + - - +
78D SER* 2.8 43.8 + - - +
176D ALA* 4.7 5.2 - - + -
177D PRO* 5.5 0.6 - - - +
179D VAL 5.3 6.1 - - - +
181D SER* 4.6 7.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 75 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6D ILE* 4.6 10.1 - - + -
7D ALA 4.8 7.4 - - - -
8D GLU* 6.1 3.6 - - + -
9D HIS* 5.2 4.0 - + - -
41D ILE* 3.7 59.7 - - + -
42D GLY* 5.7 0.7 - - - -
67D SER* 5.3 1.1 - - - -
69D ASP 4.4 3.6 - - - -
70D PHE* 3.5 52.0 - + + -
71D ASP 3.0 24.3 + - - +
72D PRO 4.1 0.7 - - - +
74D VAL* 1.3 77.2 - - + +
76D GLU* 1.3 68.2 + - - +
78D SER* 3.2 4.1 + - - -
79D VAL* 2.9 28.9 + - - +
98D ASP* 5.6 2.7 - - + -
102D TYR* 4.0 25.6 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 76 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142C HIS* 4.2 17.3 + - - -
72D PRO 3.0 18.6 + - - +
73D ASP* 3.9 6.1 - - - +
75D PHE* 1.3 76.3 - - - +
77D ALA* 1.3 63.2 + - - +
80D SER* 3.0 37.5 + - - +
102D TYR* 3.9 16.3 - - + +
105D SER* 2.5 28.6 + - - +
106D LEU* 4.0 9.9 - - + +
109D LYS* 2.5 36.9 + - + +
182D ARG* 5.7 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 77 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73D ASP 3.1 19.0 + - - +
74D VAL* 3.7 4.7 - - - +
76D GLU* 1.3 76.9 - - - +
78D SER* 1.3 63.5 + - - +
80D SER* 4.0 4.5 - - - -
81D ALA* 3.2 23.7 + - - +
177D PRO* 3.9 29.4 - - + +
179D VAL* 6.4 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 78 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41D ILE* 3.9 27.5 - - - +
63D VAL* 3.6 26.4 - - - +
74D VAL* 2.8 22.8 + - - +
75D PHE 3.2 3.3 + - - -
77D ALA* 1.3 74.4 - - - +
79D VAL* 1.3 57.8 + - - +
81D ALA* 3.2 8.1 + - - +
82D LEU* 2.9 30.8 + - - +
176D ALA* 3.8 15.4 - - - +
177D PRO* 4.6 4.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 79 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4D LEU* 4.9 0.2 - - + -
6D ILE* 3.9 26.7 - - + -
41D ILE* 3.8 20.6 - - + -
75D PHE 2.9 23.1 + - - +
78D SER* 1.3 67.2 - - - +
80D SER* 1.3 60.5 + - - +
81D ALA 3.1 1.6 - - - -
82D LEU* 3.1 7.6 + - - +
83D ILE* 2.8 42.4 + - + +
91D VAL* 4.8 3.4 - - + -
93D LEU* 5.1 0.4 - - + -
102D TYR* 3.7 22.4 - - + +
106D LEU* 3.6 31.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 80 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76D GLU* 3.0 24.3 + - - +
77D ALA* 4.0 4.9 - - - -
79D VAL* 1.3 77.1 - - - +
81D ALA* 1.3 57.6 + - - +
83D ILE* 3.5 8.1 + - - +
84D ALA* 3.0 29.9 + - - +
106D LEU* 3.4 17.7 - - - +
109D LYS* 6.1 1.2 - - - +
110D THR* 6.0 2.1 - - - +
112D TYR* 5.7 0.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 81 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77D ALA 3.2 14.2 + - - +
78D SER* 3.4 11.4 - - - +
79D VAL 3.1 0.6 - - - -
80D SER* 1.3 75.4 - - - +
82D LEU* 1.3 64.2 + - + +
84D ALA* 3.5 5.9 + - - +
85D ALA* 3.2 25.8 + - - +
177D PRO* 5.1 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 82 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4D LEU* 3.9 17.0 - - + +
6D ILE* 4.0 13.9 - - + -
39D ALA* 3.5 27.1 - - + -
41D ILE* 4.6 4.5 - - + -
61D VAL* 4.0 27.8 - - + -
63D VAL* 4.1 14.6 - - + -
78D SER 2.9 21.1 + - - +
79D VAL* 3.1 9.8 + - - +
81D ALA* 1.3 71.7 - - - +
83D ILE* 1.3 66.6 + - - +
85D ALA* 3.5 1.1 + - + -
86D HIS* 3.0 55.6 + - + +
174D VAL* 5.5 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 83 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4D LEU* 3.8 17.3 - - + -
79D VAL* 2.8 39.2 + - + +
80D SER* 3.8 7.0 - - - +
82D LEU* 1.3 72.3 - - - +
84D ALA* 1.3 56.5 + - - +
87D ASN* 2.8 36.7 + - - -
88D PRO* 3.2 12.0 - - + +
91D VAL* 4.0 20.4 - - + -
106D LEU* 4.3 15.0 - - + -
112D TYR* 3.7 36.8 - - + +
150D THR* 4.1 20.9 - - + +
152D VAL* 4.7 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 84 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80D SER 3.0 17.9 + - - +
81D ALA* 4.0 6.3 - - - +
82D LEU 3.3 0.2 - - - -
83D ILE* 1.3 78.9 - - - +
85D ALA* 1.3 58.2 + - - +
86D HIS 3.6 0.2 - - - -
87D ASN* 4.4 6.5 + - - +
112D TYR* 5.9 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 85 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2D LYS* 5.4 1.4 + - - -
81D ALA 3.2 17.3 + - - +
82D LEU* 4.0 3.1 - - - +
83D ILE 3.2 0.4 - - - -
84D ALA* 1.3 79.5 - - + +
86D HIS* 1.3 69.5 + - + +
87D ASN* 5.5 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 86 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2D LYS* 3.5 44.8 + - + +
4D LEU* 5.6 2.2 - - + -
37D VAL* 4.0 23.6 - - + +
59D GLU* 4.0 14.4 - - - -
61D VAL* 3.8 30.4 - - + +
82D LEU* 3.0 42.9 + - + +
85D ALA* 1.3 85.1 + - + +
87D ASN* 1.3 70.0 + - - +
88D PRO* 3.0 10.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 87 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1D SER* 5.9 0.5 - - - -
2D LYS 5.1 3.1 + - - -
83D ILE* 2.8 14.2 + - - +
84D ALA* 4.3 6.2 - - - +
85D ALA 3.6 1.8 - - - +
86D HIS* 1.3 77.2 - - - +
88D PRO* 1.3 67.3 - - - +
89D SER 3.9 0.7 + - - -
150D THR* 5.1 2.0 - - - -
----------------------------------------------------------
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