Contacts of the helix formed by residues 72 - 79 (chain B) in PDB entry 5HNK
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 72 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B LYS* 1.3 70.3 - - - +
73B VAL* 1.3 57.0 + - - +
74B PHE* 3.4 10.0 + - - +
75B ARG* 3.1 43.9 + - - +
76B LEU* 2.9 33.1 + - - +
82B TYR* 4.1 2.1 - - - -
126B GLY 3.6 9.1 + - - -
127B VAL* 5.4 0.7 - - - -
128B GLU* 3.5 37.1 + - - +
131B ASP* 4.3 2.9 + - - -
269B ALA* 4.9 1.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 73 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B LYS 3.1 3.6 + - - +
72B SER* 1.3 71.6 - - - +
74B PHE* 1.3 62.9 + - - +
76B LEU* 3.5 10.7 + - + +
77B GLU* 3.0 45.2 + - + +
126B GLY* 3.0 34.6 + - - +
272B ALA* 4.4 14.4 - - + +
273B VAL* 3.9 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 74 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B SER* 3.2 7.5 + - - +
73B VAL* 1.3 78.9 - - - +
75B ARG* 1.3 75.8 - - + +
77B GLU* 3.4 13.1 + - - +
78B HIS* 3.3 45.5 + + - -
126B GLY 4.7 0.6 + - - -
258B ILE* 3.6 38.1 - - + -
259B LEU* 6.1 0.2 - - + -
265B TYR* 3.8 32.1 - + + -
268B ASP* 3.7 29.2 - - + -
269B ALA* 3.6 30.0 + - + +
272B ALA* 4.0 11.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 75 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B SER* 3.1 19.8 + - - +
74B PHE* 1.3 88.0 - - + +
76B LEU* 1.3 52.3 + - - +
78B HIS* 3.3 1.6 + - - -
79B LEU* 2.7 40.1 + - - +
82B TYR* 3.6 39.5 - - + -
128B GLU* 3.5 16.0 + - - +
130B ASP* 4.9 6.5 + - - +
131B ASP* 2.8 41.6 + - - -
258B ILE 5.0 3.2 + - - -
259B LEU* 2.9 50.6 + - + +
261B ASP 5.7 0.6 - - - -
262B LEU* 4.0 21.0 - - - +
265B TYR* 6.0 3.2 - - - +
269B ALA* 4.8 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 76 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B LYS* 3.9 28.7 - - + +
72B SER 2.9 21.2 + - - +
73B VAL* 3.7 10.3 - - + +
75B ARG* 1.3 76.6 - - - +
77B GLU* 1.3 61.6 + - + +
79B LEU 3.5 3.4 - - - +
80B PRO* 3.1 53.9 - - - +
82B TYR* 3.9 21.9 - - + +
2Y A 3.6 44.0 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
73B VAL* 3.0 36.9 + - + +
74B PHE* 3.5 17.0 - - - +
75B ARG 3.3 0.2 - - - -
76B LEU* 1.3 76.1 - - + +
78B HIS* 1.3 65.6 + - + +
80B PRO* 4.9 3.5 - - - +
272B ALA* 4.1 15.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 78 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B PHE* 3.3 54.0 + + - +
75B ARG 3.3 6.5 + - - +
77B GLU* 1.3 82.3 + - + +
79B LEU* 1.3 59.2 + - - +
80B PRO* 4.1 4.4 - - - +
255B ARG* 3.4 29.3 + - + +
258B ILE* 4.0 33.4 - - + +
259B LEU* 4.2 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 79 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B ARG 2.7 15.6 + - - +
76B LEU* 3.2 4.6 + - - +
78B HIS* 1.3 74.8 - - - +
80B PRO* 1.3 62.6 - - + +
81B GLU* 3.9 19.7 - - + +
82B TYR* 2.9 44.7 + - + +
205B ASN 3.8 21.3 - - - +
206B ILE* 3.9 15.9 - - + -
207B ARG 5.9 1.6 - - - +
255B ARG* 3.5 35.4 - - - +
256B ASN* 5.5 1.1 - - - +
259B LEU* 3.8 27.4 - - + -
----------------------------------------------------------
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