Contacts of the helix formed by residues 68 - 77 (chain B) in PDB entry 1NBI
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 68 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B CYS* 2.5 36.8 + - - -
66B GLY 2.9 0.6 + - - -
67B THR* 1.3 74.2 - - - +
69B VAL* 1.3 64.7 + - - +
70B ASP 3.3 2.7 - - - -
71B SER* 3.8 8.7 - - - -
72B ILE* 2.9 33.5 + - - +
94B ALA* 4.2 3.4 - - - -
110B TRP* 4.4 2.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 69 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B ILE* 4.3 14.4 - - + -
37B THR* 3.7 30.7 - - + -
40B ARG* 3.7 20.6 - - + +
41B THR* 5.0 7.6 + - - +
65B CYS 4.0 1.4 + - - +
67B THR* 3.6 5.9 + - - +
68B GLY* 1.3 77.5 - - - +
70B ASP* 1.3 90.5 + - - +
72B ILE* 4.1 7.0 - - - +
73B MET* 3.6 15.4 + - - +
1293B SAM 3.7 25.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 70 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B ARG* 3.0 20.2 + - - -
41B THR* 4.6 5.4 + - - -
44B TYR* 2.7 30.1 + - - -
48B LEU* 5.6 2.9 - - + -
62B ASP* 4.8 3.1 + - - +
65B CYS 5.4 0.4 + - - -
69B VAL* 1.3 90.2 - - - +
71B SER* 1.3 67.8 + - - +
72B ILE 3.2 0.4 - - - -
73B MET* 3.1 12.7 + - - +
74B LEU* 3.0 26.4 + - + +
134B ILE* 4.6 17.0 - - + -
136B LEU* 4.1 22.2 - - + +
1293B SAM 4.0 6.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 71 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B ASP* 2.7 30.5 + - - +
68B GLY* 3.3 7.5 + - - -
70B ASP* 1.3 77.8 - - - +
72B ILE* 1.3 52.6 + - - +
74B LEU* 2.8 11.6 + - - +
75B VAL* 2.7 38.3 + - - +
81B VAL* 3.3 8.8 - - - +
83B SER* 2.7 30.2 + - - -
110B TRP* 3.7 17.3 - - - -
134B ILE* 5.4 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 72 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B THR 4.3 5.6 - - - +
68B GLY 2.9 26.6 + - - +
69B VAL* 4.1 6.3 - - - +
71B SER* 1.3 76.0 - - - +
73B MET* 1.3 54.9 + - - +
75B VAL* 3.1 9.2 + - - +
76B GLU* 2.8 48.7 + - - +
97B GLU* 3.7 25.8 - - + +
101B ARG* 4.1 6.5 - - - +
107B PHE* 3.7 20.6 - - + -
110B TRP* 3.4 30.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 73 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B THR* 3.4 25.1 - - - +
44B TYR* 5.1 3.6 - - + -
45B LYS* 3.3 42.8 - - + +
48B LEU* 4.5 15.3 - - + -
49B LEU* 3.1 33.7 - - + -
69B VAL 3.6 11.3 + - - +
70B ASP* 3.1 20.9 + - + +
71B SER 3.1 0.2 - - - -
72B ILE* 1.3 78.7 - - - +
74B LEU* 1.3 62.0 + - + +
76B GLU* 3.4 12.4 + - - +
77B GLU* 2.8 38.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 74 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B LEU* 5.0 5.2 - - + -
49B LEU* 3.7 28.9 - - + -
52B LEU* 3.8 21.1 - - + -
60B VAL* 3.9 23.6 - - + -
70B ASP* 3.0 11.4 + - + +
71B SER* 2.8 12.1 + - - +
73B MET* 1.3 74.6 - - + +
75B VAL* 1.3 67.0 + - - +
77B GLU* 3.2 0.9 + - - -
78B GLY 3.0 6.1 + - - -
79B PHE* 3.0 40.4 + - + -
81B VAL* 4.1 14.1 - - + -
134B ILE* 3.7 30.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 75 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B SER 2.7 17.1 + - - +
72B ILE* 3.3 10.8 - - - +
74B LEU* 1.3 71.6 - - - +
76B GLU* 1.3 54.5 + - - +
78B GLY* 2.6 28.2 + - - -
79B PHE 4.6 3.1 - - - +
81B VAL* 3.2 26.7 - - + +
106B ALA* 3.7 15.8 - - + +
107B PHE* 3.4 49.4 - - + +
110B TRP* 3.5 32.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 76 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B ILE* 2.8 30.2 + - - +
73B MET* 3.5 10.1 - - - +
75B VAL* 1.3 69.4 - - - +
77B GLU* 1.3 59.8 + - + +
78B GLY* 2.8 10.2 + - - -
101B ARG* 2.9 42.4 + - - +
104B GLU* 5.3 0.2 - - - +
106B ALA* 5.2 3.3 - - - +
107B PHE* 3.7 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 77 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B LYS* 2.8 29.1 + - - +
49B LEU* 3.2 28.8 - - + +
53B ARG* 2.9 25.7 + - - -
73B MET* 2.8 22.1 + - + +
74B LEU* 3.2 2.2 + - - -
76B GLU* 1.3 76.3 - - + +
78B GLY* 1.3 62.9 + - - +
79B PHE* 3.2 27.7 - - + -
----------------------------------------------------------
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