Contacts of the helix formed by residues 72 - 81 (chain B) in PDB entry 6NUF
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 PHE 72 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B ILE* 4.6 13.9 - - + -
23B LEU* 4.0 4.9 - - + -
24B GLY* 3.7 33.4 - - - -
27B PHE* 3.6 39.7 - + + -
36B GLY 4.4 2.3 + - - +
71B ASP* 1.3 76.5 - - - +
73B LYS* 1.3 61.3 + - - +
75B PHE* 3.1 3.2 + + - +
76B ILE* 3.0 65.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 73 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B ASP* 3.0 9.5 + - - +
72B PHE* 1.3 81.8 - - - +
74B GLU* 1.3 66.1 + - + +
76B ILE* 3.4 6.7 + - - +
77B GLU* 2.4 72.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 74 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B PHE* 3.3 28.5 - - - +
63B ASP* 3.2 2.9 - - - +
64B THR* 3.6 12.3 - - - +
65B ASP* 3.0 28.3 + - - +
69B GLU 2.9 4.7 - - - +
70B VAL* 3.2 8.1 - - + -
71B ASP* 2.8 46.0 + - - +
73B LYS* 1.3 73.9 - - + +
75B PHE* 1.3 57.6 + - - +
77B GLU* 3.8 8.8 - - - +
78B GLY* 2.8 27.5 + - - -
201B CA 2.2 30.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 75 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368A VAL* 3.9 28.9 - - + -
369A LEU* 4.3 8.5 - - + -
23B LEU* 3.9 34.8 - - + -
26B ARG* 4.9 3.1 - - + -
27B PHE* 3.7 24.0 - + + -
30B LEU* 4.2 16.6 - - + -
38B LEU* 4.1 16.4 - - + -
43B PHE* 5.0 4.0 - + - -
62B PHE* 4.1 10.2 - + - -
70B VAL* 3.8 11.4 - - + -
71B ASP 2.9 17.7 + - - +
72B PHE* 3.1 6.2 + + - +
74B GLU* 1.3 76.6 - - - +
76B ILE* 1.3 70.1 + - + +
78B GLY* 3.5 1.0 + - - -
79B VAL* 2.9 49.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 76 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B MET* 4.3 19.0 - - + +
20B ILE* 5.4 8.3 - - + +
23B LEU* 3.3 35.0 - - + -
72B PHE* 3.0 53.9 + - + +
73B LYS* 4.0 7.2 - - - +
75B PHE* 1.3 77.8 - - + +
77B GLU* 1.3 68.4 + - + +
79B VAL* 3.4 3.8 + - - +
80B SER* 3.0 25.3 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
64B THR* 4.5 13.1 + - + +
73B LYS* 2.4 67.3 + - - +
74B GLU* 3.9 8.3 - - - +
76B ILE* 1.3 75.8 - - + +
78B GLY* 1.3 65.3 + - - +
80B SER* 2.8 23.8 + - - -
81B GLN* 3.4 16.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 78 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B PHE* 3.4 36.8 - - - -
74B GLU 2.8 17.7 + - - -
77B GLU* 1.3 76.3 - - - +
79B VAL* 1.3 62.3 + - - +
81B GLN* 3.2 25.6 + - - +
82B PHE* 3.8 4.7 - - - -
94B PHE* 5.6 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 79 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A LEU* 3.8 26.2 - - + -
368A VAL* 5.8 0.2 - - + -
369A LEU* 4.3 14.6 - - + -
15B MET* 3.8 9.3 - - + +
23B LEU* 4.3 9.6 - - + -
62B PHE* 4.3 6.3 - - + -
75B PHE* 2.9 44.7 + - + +
76B ILE* 4.0 4.9 - - - +
78B GLY* 1.3 75.7 - - - +
80B SER* 1.3 61.5 + - - +
82B PHE* 3.1 19.3 + - - +
83B SER 3.8 2.9 + - - -
168B VAL* 4.7 2.3 - - + +
170B VAL* 3.8 28.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 80 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B MET* 3.5 21.9 - - - +
76B ILE* 3.0 16.4 + - - -
77B GLU* 2.8 22.1 + - - -
78B GLY 3.2 0.2 - - - -
79B VAL* 1.3 74.2 - - - +
81B GLN* 1.3 71.4 + - - +
83B SER* 3.2 21.2 + - - +
86B GLY* 5.4 0.2 - - - -
90B GLN* 4.1 10.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 81 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B GLU* 3.4 19.0 + - - +
78B GLY* 3.2 19.4 + - - +
80B SER* 1.3 82.3 + - - +
82B PHE* 1.3 59.0 + - + +
83B SER 3.4 0.4 - - - -
90B GLN* 2.7 55.9 + - + +
91B LYS* 2.8 32.6 + - - +
94B PHE* 4.2 27.5 - - + +
97B ARG* 6.1 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