Contacts of the helix formed by residues 76 - 86 (chain A) in PDB entry 2NUG
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 76 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A ALA 3.7 11.7 - - - -
73A TYR* 2.6 33.8 + - - -
74A LEU 3.4 0.2 - - - -
75A ILE* 1.3 83.5 - - - +
77A GLU* 1.3 64.4 + - - +
78A GLU* 3.6 5.9 + - - +
79A PHE* 3.1 13.3 + - - -
80A PHE* 3.0 22.7 + - - -
11D C 3.8 5.4 - - - -
12D G 3.4 16.6 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
75A ILE 4.0 0.6 + - - -
76A SER* 1.3 73.2 - - - +
78A GLU* 1.3 65.4 + - - +
80A PHE* 3.3 10.6 + - - +
81A ASN* 2.9 31.8 + - - +
102A GLU* 3.7 38.1 - - + +
103A THR* 3.2 30.4 + - - +
106A GLY* 4.6 7.0 - - - -
503A MG 4.2 6.8 - - - -
12D G 3.2 12.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A TYR* 2.8 25.7 + - + +
76A SER* 3.1 9.2 + - - +
77A GLU* 1.3 80.2 + - - +
79A PHE* 1.3 63.7 + - - +
81A ASN* 3.2 17.0 + - + +
82A LEU* 3.3 18.4 + - + +
102A GLU* 5.3 9.9 - - - +
149A LYS* 2.8 45.1 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
51A ILE* 5.6 0.2 - - + -
73A TYR* 3.3 50.2 + + + +
74A LEU* 3.3 44.9 - - + +
76A SER* 3.1 6.6 + - - +
78A GLU* 1.3 79.4 - - - +
80A PHE* 1.3 62.5 + - - +
82A LEU* 3.0 27.0 + - + +
83A LEU* 3.0 50.4 + - + +
138A ASP 4.7 1.8 - - - -
139A ILE* 3.9 23.6 - - + -
142A ALA* 4.2 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A VAL* 3.5 32.1 - - + -
48A ASN* 4.4 2.7 - - - -
51A ILE* 4.9 2.2 - - + -
74A LEU 3.3 23.3 - - - -
75A ILE* 3.6 27.1 - - + -
76A SER 3.0 19.0 + - - +
77A GLU* 3.3 8.9 + - - +
79A PHE* 1.3 76.6 - - - +
81A ASN* 1.3 57.6 + - - +
83A LEU* 3.3 11.7 + - + +
84A ALA* 2.8 30.2 + - - +
106A GLY* 4.3 9.9 - - - -
109A PHE* 3.6 30.9 - + + -
110A GLU* 3.3 42.6 - - + -
501A MG 4.3 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A GLU* 2.9 29.9 + - - +
78A GLU* 3.4 11.4 - - + +
79A PHE 3.1 0.2 - - - -
80A PHE* 1.3 77.3 - - - +
82A LEU* 1.3 63.1 + - + +
84A ALA* 3.4 7.9 + - - +
85A GLN* 3.2 28.7 + - - +
102A GLU* 2.9 51.7 + - - +
105A ILE* 3.4 29.2 - - - +
106A GLY 3.7 9.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A TYR* 3.5 25.4 - - - +
78A GLU* 3.5 16.4 - - + +
79A PHE* 3.0 25.0 + - + +
81A ASN* 1.3 78.3 - - + +
83A LEU* 1.3 63.7 + - + +
85A GLN* 3.3 38.6 + - - +
86A LYS* 4.0 2.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A ILE* 5.5 0.7 - - + -
74A LEU 5.4 0.2 - - - +
79A PHE* 3.0 52.2 + - + +
80A PHE* 3.8 12.8 - - + +
82A LEU* 1.3 77.4 - - + +
84A ALA* 1.3 63.4 + - - +
86A LYS* 3.2 13.5 + - - +
87A LEU 4.1 0.7 + - - -
109A PHE* 3.8 30.7 - - + -
131A PHE* 4.2 16.8 - - + -
135A PHE* 3.3 48.7 - - + -
138A ASP* 4.4 13.7 - - + +
139A ILE* 4.7 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A PHE 2.8 18.4 + - - +
81A ASN 3.6 5.8 - - - +
82A LEU 3.2 0.2 - - - -
83A LEU* 1.3 75.8 - - - +
85A GLN* 1.3 59.4 + - - +
87A LEU* 2.8 23.7 + - - +
88A GLU 3.1 7.6 + - - -
89A LEU* 3.4 27.5 + - + -
105A ILE* 3.7 24.9 - - + -
109A PHE* 4.1 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A ASN* 3.2 13.4 + - - +
82A LEU* 3.3 43.0 + - - +
83A LEU 3.2 0.4 - - - -
84A ALA* 1.3 75.9 - - - +
86A LYS* 1.3 58.1 + - - +
88A GLU* 2.8 27.7 + - - +
90A HIS* 5.9 2.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A LYS* 4.6 10.0 + - - +
82A LEU 4.0 2.1 + - - +
83A LEU* 3.2 14.6 + - - +
84A ALA 3.1 0.6 - - - -
85A GLN* 1.3 78.7 - - - +
87A LEU* 1.3 64.1 + - + +
88A GLU* 4.9 1.5 - - - +
134A LEU* 2.9 32.5 + - + +
135A PHE* 3.9 12.8 - - + -
138A ASP* 2.5 35.5 + - - -
----------------------------------------------------------
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