Contacts of the helix formed by residues 69 - 81 (chain A) in PDB entry 5A36
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 GLY 69 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A PHE 3.0 13.5 + - - -
67A ARG 3.4 0.4 - - - -
68A ASN* 1.3 77.2 + - - +
70A LEU* 1.3 57.2 + - - +
71A LYS 3.7 1.3 - - - -
72A LEU* 3.6 10.1 - - - +
73A MET* 3.1 34.8 + - - +
99A ASN* 3.9 10.8 - - - -
100A VAL* 3.6 21.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 70 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A ASN* 3.0 32.8 + - + +
69A GLY* 1.3 75.1 - - - +
71A LYS* 1.3 69.3 + - + +
73A MET* 3.4 7.3 + - - +
74A LEU* 3.2 20.8 + - - +
87A PRO* 3.6 34.6 - - + +
88A ASP 4.3 4.5 - - - +
99A ASN* 3.7 15.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 71 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A LEU* 3.7 8.8 - - + +
57A THR* 2.8 37.2 + - + +
58A GLN 2.9 15.7 + - - +
59A ILE* 3.7 20.8 - - + +
65A ASP* 4.2 15.0 + - + +
66A PHE* 3.7 15.6 - - + -
68A ASN* 4.3 2.8 + - - +
70A LEU* 1.3 81.3 - - + +
72A LEU* 1.3 56.8 + - - +
74A LEU* 3.6 9.9 - - + +
75A LEU* 2.9 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 72 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A PHE* 3.5 24.8 - - + +
69A GLY* 3.6 12.3 - - - +
71A LYS* 1.3 75.9 - - - +
73A MET* 1.3 63.7 + - - +
75A LEU* 3.5 7.0 + - + +
76A LEU* 3.1 28.2 + - + +
100A VAL* 4.5 21.1 - - + -
103A ALA* 3.5 26.2 - - + -
104A LEU* 5.7 0.4 - - + -
107A ILE* 5.6 0.4 - - + -
133A MET* 3.7 39.7 - - + -
134A ILE* 4.1 10.1 - - + -
137A ILE* 4.0 25.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 73 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A GLY 3.1 21.4 + - - +
70A LEU* 3.4 5.6 + - - +
72A LEU* 1.3 73.7 - - - +
74A LEU* 1.3 57.8 + - - +
76A LEU* 3.3 5.0 + - - +
77A GLU* 3.1 35.6 + - - +
84A LEU* 3.9 28.6 - - + +
85A PRO 3.1 28.3 - - - +
87A PRO* 4.0 28.0 - - + -
99A ASN* 3.6 43.5 - - - +
102A LYS* 4.2 15.0 - - + -
103A ALA* 4.2 5.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 74 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A LEU* 4.4 3.4 - - + -
55A ALA* 3.8 27.4 - - + +
57A THR* 3.7 30.7 - - + -
70A LEU 3.2 10.5 + - - +
71A LYS* 3.6 13.7 - - + +
73A MET* 1.3 76.3 - - - +
75A LEU* 1.3 65.4 + - - +
77A GLU* 3.3 21.7 + - + +
78A VAL* 2.9 30.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 75 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A TRP* 4.3 10.1 - - + -
48A CYS* 3.8 50.3 - - - +
51A HIS* 3.9 8.1 - - + -
52A LEU* 3.7 14.2 - - + +
66A PHE* 4.2 12.6 - - + -
71A LYS 2.9 18.4 + - - +
72A LEU* 3.5 10.1 - - + +
74A LEU* 1.3 73.7 - - - +
76A LEU* 1.3 63.5 + - + +
78A VAL* 3.2 3.9 + - - +
79A ILE* 3.1 51.5 + - + +
134A ILE* 4.6 9.0 - - + -
137A ILE* 4.7 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 76 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A LEU* 3.1 17.5 + - + +
73A MET 3.6 6.7 - - - +
74A LEU 3.2 0.2 - - - -
75A LEU* 1.3 79.6 - - + +
77A GLU* 1.3 52.4 + - - +
79A ILE* 3.7 4.3 - - + +
80A SER* 2.7 39.7 + - - -
84A LEU* 4.1 16.4 - - + -
103A ALA* 3.5 42.4 - - + +
106A TYR* 4.3 11.0 - - + -
107A ILE* 3.9 23.8 - - + -
137A ILE* 3.9 25.8 - - + -
141A PHE* 4.2 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A MET* 3.1 16.1 + - - +
74A LEU* 3.5 30.5 - - + +
76A LEU* 1.3 73.2 - - - +
78A VAL* 1.3 59.8 + - + +
81A GLY* 2.9 31.2 + - - -
82A GLU 3.5 22.4 + - - +
83A ARG* 3.6 15.9 - - - +
84A LEU* 3.2 33.2 + - + +
85A PRO 5.5 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A HIS* 3.2 39.0 - - + +
52A LEU* 4.9 1.1 - - - -
54A LYS* 4.3 13.2 - - + -
55A ALA* 3.7 31.0 - - + +
74A LEU* 2.9 28.2 + - + +
75A LEU* 3.2 6.9 + - - +
77A GLU* 1.3 74.2 - - + +
79A ILE* 1.3 62.3 + - + +
81A GLY* 4.1 4.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A TRP* 4.1 5.8 - - + -
51A HIS* 3.5 47.3 - - + +
75A LEU* 3.1 25.7 + - + +
76A LEU* 3.7 12.3 - - + +
78A VAL* 1.3 76.6 - - - +
80A SER* 1.3 62.0 + - - +
137A ILE* 3.7 31.0 - - + -
141A PHE* 3.7 40.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A LEU 2.7 22.9 + - - -
77A GLU 3.5 0.2 + - - -
79A ILE* 1.3 77.5 - - - +
81A GLY* 1.3 62.3 + - - +
82A GLU* 2.9 31.1 + - - +
106A TYR* 3.0 30.2 + - - -
110A LYS* 5.9 0.4 - - - -
141A PHE* 4.0 15.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A GLU 2.9 14.8 + - - -
78A VAL 4.1 3.9 + - - -
79A ILE 3.6 1.8 - - - -
80A SER* 1.3 76.8 - - - +
82A GLU* 1.3 58.6 + - - +
----------------------------------------------------------
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