Contacts of the helix formed by residues 55 - 63 (chain B) in PDB entry 1NSH
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 VAL 55 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B PHE* 4.8 11.0 - - + +
52B ASP* 3.7 29.3 + - + +
53B PRO 3.7 0.2 - - - -
54B GLY* 1.3 80.9 - - - +
56B LEU* 1.3 65.5 + - + +
58B ARG* 4.3 1.3 + - - +
59B MET* 3.3 22.7 + - - +
83B LEU* 3.4 28.3 - - + +
86B ALA* 3.3 48.6 - - + +
87B CYS* 4.2 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 56 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B LEU* 5.4 14.8 - - + -
39B MET* 3.2 48.5 - - + -
40B ASN* 5.6 2.9 - - - +
46B PHE* 5.5 3.1 - - + +
47B THR* 4.5 12.1 - - + +
50B GLN* 4.3 21.5 - - - +
52B ASP 4.6 2.2 + - - +
55B VAL* 1.3 77.4 - - + +
57B ASP* 1.3 90.9 + - + +
59B MET* 3.0 14.9 + - + +
60B MET* 2.9 40.0 + - + +
83B LEU* 4.0 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 57 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B GLN* 5.1 3.2 - - - +
53B PRO* 3.0 32.4 + - + +
56B LEU* 1.3 93.4 - - + +
58B ARG* 1.3 57.1 + - + +
60B MET* 4.6 2.5 - - - +
61B LYS* 3.0 35.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 58 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B PRO 4.7 1.6 - - - +
54B GLY* 2.6 60.1 + - - +
55B VAL* 4.3 2.9 + - - +
56B LEU 3.2 0.8 - - - -
57B ASP* 1.3 77.6 - - + +
59B MET* 1.3 54.3 + - - +
61B LYS* 3.0 33.5 + - + +
62B LYS* 2.7 31.1 - - - +
86B ALA* 5.7 5.5 - - - +
101B PHE* 5.6 8.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 59 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B PHE* 5.3 2.9 - - + -
39B MET* 4.5 4.9 - - + -
55B VAL 3.3 13.8 + - - +
56B LEU* 3.0 14.9 + - + +
58B ARG* 1.3 76.4 - - - +
60B MET* 1.3 78.9 + - + +
61B LYS 3.1 1.8 - - - -
62B LYS* 3.3 16.2 + - - +
63B LEU* 2.8 33.3 + - - +
78B ASN 4.0 4.9 - - - +
79B LEU* 3.0 63.5 - - + +
82B GLY* 5.3 3.1 - - - -
83B LEU* 2.9 42.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 60 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B LYS* 3.3 50.2 - - + +
35B PHE* 4.1 10.8 - - + -
36B LEU* 4.0 14.6 - - + -
56B LEU* 2.9 26.5 + - + +
57B ASP* 4.6 3.1 - - - +
59B MET* 1.3 85.0 - - + +
61B LYS* 1.3 57.9 + - - +
63B LEU* 2.7 42.3 - - + +
79B LEU* 3.3 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 61 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B ASP* 3.0 30.1 + - - +
58B ARG* 3.0 35.7 + - + +
60B MET* 1.3 80.9 - - - +
62B LYS* 1.3 77.7 + - - +
63B LEU 3.2 2.0 + - - -
64B ASP* 3.9 7.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 62 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A PHE* 6.4 0.2 - - - -
58B ARG 2.7 25.1 + - - +
59B MET* 3.5 23.8 - - - +
61B LYS* 1.3 86.6 - - + +
63B LEU* 1.3 61.0 + - - +
64B ASP* 2.9 18.3 + - - +
78B ASN* 5.0 18.0 + - - -
79B LEU* 5.9 1.1 - - - -
82B GLY* 5.8 4.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 63 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B LYS* 5.0 1.1 - - + -
59B MET 2.8 7.7 + - - +
60B MET* 2.7 41.5 - - + +
61B LYS 3.2 0.2 - - - -
62B LYS* 1.3 82.7 - - - +
64B ASP* 1.3 71.3 + - - +
65B LEU* 3.1 50.0 - - + +
71B LEU* 5.1 2.0 - - + -
75B GLU* 4.2 12.3 - - + +
78B ASN* 6.3 0.7 - - - -
79B LEU* 3.1 53.2 - - + -
----------------------------------------------------------
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