Contacts of the helix formed by residues 80 - 91 (chain A) in PDB entry 2O38
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 SER 80 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A LYS* 4.4 1.1 - - - +
78A GLY 4.2 1.2 + - - -
79A PHE* 1.3 75.9 - - - +
81A VAL* 1.3 64.2 + - - +
82A GLU* 3.6 9.9 + - - +
83A ARG* 2.9 27.0 + - - +
84A LEU* 3.0 24.7 + - - +
32B GLU* 5.2 4.1 + - - -
82B GLU* 3.4 14.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A GLU* 4.3 3.4 - - + +
35A THR* 4.2 20.4 - - + -
36A LYS* 3.9 17.7 - - + +
39A LEU* 3.7 22.2 - - + +
80A SER* 1.3 71.1 - - - +
82A GLU* 1.3 65.0 + - - +
84A LEU* 3.3 7.6 + - - +
85A MSE 3.0 35.7 + - + +
81B VAL* 4.7 2.5 - - + -
82B GLU* 2.9 46.9 + - + +
85B MSE 4.4 15.9 - - - -
97B ILE* 5.0 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A SER* 3.2 8.8 + - - +
81A VAL* 1.3 78.6 - - - +
83A ARG* 1.3 59.2 + - - +
85A MSE 3.0 23.6 + - - +
86A THR* 2.9 48.2 + - + +
28B PRO 4.9 0.7 - - - +
31B GLU* 3.8 2.4 - - - +
32B GLU* 3.3 56.6 + - + +
35B THR* 3.5 20.0 + - - +
81B VAL* 3.8 18.9 - - + +
82B GLU* 5.6 0.2 - - - +
111B ILE* 3.8 7.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A LEU 3.5 8.7 + - - -
62A GLY* 3.9 7.1 + - - -
63A ILE* 3.4 28.1 - - - +
67A LYS* 5.1 8.8 - - - +
78A GLY 5.8 0.2 - - - +
79A PHE* 4.4 11.4 - - + -
80A SER* 2.9 29.8 + - - +
82A GLU* 1.3 76.6 - - - +
84A LEU* 1.3 58.6 + - - +
86A THR* 2.8 39.7 + - - -
87A LEU* 2.8 63.7 + - + +
90A ALA* 5.9 0.8 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
36A LYS* 3.6 47.6 - - + +
39A LEU* 3.9 17.0 - - + -
40A ALA* 4.6 6.1 - - + -
43A LEU* 3.7 24.8 - - + +
71A LEU* 4.2 10.1 - - + -
76A LEU* 4.7 3.6 - - + -
79A PHE* 3.9 33.2 - - + -
80A SER 3.0 18.9 + - - +
81A VAL* 3.6 7.6 - - - +
83A ARG* 1.3 74.6 - - - +
85A MSE 1.3 61.9 + - - +
87A LEU* 3.3 5.9 + - + +
88A LEU* 3.0 28.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A LEU* 4.1 17.9 - - + -
81A VAL* 3.0 21.2 + - + +
82A GLU* 3.0 38.5 + - - +
84A LEU* 1.3 76.3 - - - +
86A THR* 1.3 63.8 + - - +
88A LEU* 3.2 6.7 + - - +
89A ASN* 3.1 24.8 + - - +
95A VAL* 3.7 32.9 - - + +
97A ILE* 3.9 22.0 - - + -
35B THR* 4.5 2.0 - - + -
81B VAL* 3.9 20.2 - - + -
85B MSE 5.0 0.9 - - + -
97B ILE* 4.5 9.6 - - - -
111B ILE* 3.8 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A GLU* 2.9 39.3 + - + +
83A ARG* 2.8 45.3 + - - -
85A MSE 1.3 77.2 - - - +
87A LEU* 1.3 56.5 + - - +
89A ASN* 3.2 10.5 + - - +
90A ALA* 3.0 24.6 + - - +
28B PRO 5.7 2.0 - - - +
31B GLU* 3.5 24.2 - - + +
111B ILE* 3.6 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A LEU* 3.6 28.5 - - + -
61A LEU* 3.5 37.5 - - + +
63A ILE* 3.7 15.9 - - + -
71A LEU* 5.1 1.8 - - + -
79A PHE* 3.9 34.3 - - + -
83A ARG* 2.8 57.5 + - + +
84A LEU* 3.6 0.9 - - - +
86A THR* 1.3 73.9 - - - +
88A LEU* 1.3 64.9 + - - +
90A ALA* 3.1 15.2 + - + +
91A LEU* 3.2 10.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A LEU* 3.9 26.0 - - + +
42A ALA* 4.3 5.6 - - + +
43A LEU* 3.9 35.9 - - + +
46A VAL* 4.6 2.5 - - + -
84A LEU 3.0 18.9 + - - +
85A MSE 3.2 8.7 + - - +
87A LEU* 1.3 75.6 - - - +
89A ASN* 1.3 62.3 + - - +
91A LEU* 3.0 14.4 + - + -
92A ASP 3.3 0.2 + - - -
93A GLN* 3.1 42.9 + - + +
95A VAL* 4.0 19.3 - - + -
99B ILE* 3.9 30.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 89 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A MSE 3.1 15.6 + - - +
86A THR* 3.2 10.8 + - - +
88A LEU* 1.3 75.8 - - - +
90A ALA* 1.3 58.1 + - - +
92A ASP* 2.8 24.3 + - - +
93A GLN 2.8 25.6 - - - +
95A VAL* 3.9 6.2 - - - +
31B GLU* 3.4 30.8 + - - +
109B ALA* 3.5 18.2 + - - +
110B ARG* 3.2 33.3 + - - +
111B ILE* 3.5 10.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 90 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A ARG* 4.0 29.4 - - - +
61A LEU* 4.0 19.5 - - + +
83A ARG* 5.9 0.7 - - - +
86A THR 3.0 12.3 + - - +
87A LEU* 3.1 15.9 + - + +
89A ASN* 1.3 75.3 - - - +
91A LEU* 1.3 61.9 + - - +
92A ASP* 3.3 7.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 91 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A LEU* 3.7 25.4 - - + -
46A VAL* 3.7 26.5 - - + +
47A ILE* 3.7 26.2 - - + +
52A LEU* 4.6 10.5 - - + -
60A ARG* 3.8 35.2 - - + +
61A LEU* 3.6 23.3 - - + -
87A LEU 3.2 1.3 + - - +
88A LEU* 3.0 8.4 + - - +
90A ALA* 1.3 76.5 - - - +
92A ASP* 1.3 63.7 + - - +
93A GLN* 2.9 22.8 + - + -
101B LYS* 4.2 2.9 + - - -
----------------------------------------------------------
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