Contacts of the helix formed by residues 77 - 83 (chain B) in PDB entry 2P1N
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 PRO 77 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B GLY 3.6 1.0 - - - +
76B LYS* 1.4 95.8 - - + +
78B HIS* 1.3 67.4 + - - +
79B PHE 3.0 5.6 + - - +
80B ALA* 3.1 17.2 + - - +
85B VAL* 4.5 9.6 - - + -
89B TRP* 4.0 15.5 - - + -
114B ARG* 3.9 1.6 - - - -
487B GLU* 5.8 0.9 - - - +
510B SER* 5.7 1.8 - - - +
512B TRP* 3.8 29.4 - - + -
557B PHE* 3.2 44.4 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
77B PRO* 1.3 73.7 - - - +
79B PHE* 1.4 57.9 + + - +
81B ASP* 3.0 32.4 + - + +
82B PHE* 4.0 28.4 - + - -
114B ARG* 3.4 29.7 + - - +
403B ARG* 4.8 3.8 + - - -
436B ARG* 3.6 18.8 - - - -
460B MET* 3.7 8.0 - - + +
462B SER* 4.6 3.4 - - - -
485B LYS* 6.3 0.9 - - + -
487B GLU* 2.5 38.2 + - - +
601B IHP 3.4 29.6 + - - +
602B CFA 4.8 8.0 + + - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 79 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B PRO* 3.0 2.5 + - + +
78B HIS* 1.4 74.3 - - - +
80B ALA* 1.3 55.8 - - - +
81B ASP 3.0 1.3 - - - -
82B PHE* 2.8 52.6 + + - +
84B LEU* 3.3 36.5 + - + +
85B VAL* 4.3 3.8 - - + -
463B VAL 4.8 0.2 - - - -
487B GLU* 3.3 43.0 + - + -
488B ILE 4.1 7.6 - - - -
489B ARG* 4.1 20.0 - - + -
512B TRP* 3.5 46.7 - + + -
602B CFA 3.6 30.5 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 80 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B LYS* 3.9 26.2 - - + +
77B PRO 3.1 15.6 + - - +
78B HIS 3.1 0.6 - - - +
79B PHE* 1.3 77.5 - - - +
81B ASP* 1.3 65.6 + - - +
82B PHE 3.1 1.0 + - - -
83B ASN* 3.3 16.3 + - - +
85B VAL* 3.5 29.2 - - + +
114B ARG* 4.7 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 81 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B HIS* 3.0 20.6 + - - +
80B ALA* 1.3 78.1 - - - +
82B PHE* 1.3 78.4 + - + +
83B ASN* 3.5 6.1 + - - -
114B ARG* 2.8 40.1 + - - +
139B SER* 4.7 0.7 + - - -
601B IHP 4.5 0.5 + - - -
8C VAL 4.4 2.4 - - - +
9C ARG* 3.7 54.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 82 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B HIS* 4.0 23.3 - + - -
79B PHE* 2.8 48.1 + + - +
81B ASP* 1.3 93.1 - - + +
83B ASN* 1.3 67.3 - - - +
84B LEU* 3.0 23.8 + - + +
602B CFA 4.1 16.6 - + - -
4C GLY* 3.6 25.3 - - - +
7C PRO* 3.4 40.6 - - + -
8C VAL* 3.6 22.0 - - - -
9C ARG* 4.9 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 83 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B ALA 3.3 17.3 + - - +
81B ASP 3.5 4.6 + - - -
82B PHE* 1.3 68.6 - - - +
84B LEU* 1.3 64.1 + - - +
85B VAL 3.4 11.0 - - - +
3C VAL* 4.7 10.4 - - - +
4C GLY* 5.7 1.4 + - - -
----------------------------------------------------------
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