Contacts of the helix formed by residues 81 - 91 (chain C) in PDB entry 2P5V
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 ASP 81 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C ALA 3.5 0.8 + - - -
80C LYS* 1.3 99.6 + - - +
82C ALA* 1.3 57.6 + - - +
83C ARG 3.3 3.5 + - - +
84C GLU* 3.3 12.7 + - + +
85C ASP* 2.8 53.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 82 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76C ILE* 3.8 3.4 - - + +
77C ARG* 3.5 25.1 - - + +
79C ALA* 3.3 20.1 + - + +
80C LYS 3.2 4.8 + - - -
81C ASP* 1.3 76.1 - - - +
83C ARG* 1.3 58.7 + - + +
85C ASP* 3.8 5.1 - - - +
86C PHE* 2.9 32.7 + - - +
132C HIS* 5.1 3.1 - - + +
133C GLY* 4.0 26.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 83 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A LEU* 4.0 11.9 - - - +
129A LEU* 3.8 31.7 - - - +
136A ASP* 5.3 2.6 + - - -
76C ILE* 4.1 32.1 - - + +
77C ARG 5.5 0.4 - - - +
78C LYS* 5.4 2.8 - - - +
79C ALA 4.8 0.6 + - - -
81C ASP 3.3 1.0 - - - +
82C ALA* 1.3 81.1 - - + +
84C GLU* 1.3 58.5 + - - +
86C PHE* 3.7 2.1 + - - +
87C ALA* 3.0 28.4 + - - +
101C ALA* 4.3 6.5 - - - +
107C ASP* 4.3 18.8 + - - +
108C TYR* 2.9 46.6 + - - +
1016C CL 3.2 21.4 - - + +
143D LEU* 6.2 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 84 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C ASP* 3.3 16.2 + - - +
83C ARG* 1.3 77.8 - - - +
85C ASP* 1.3 61.4 + - - +
87C ALA* 3.2 5.1 + - - +
88C ALA* 2.8 38.4 + - + +
91C ARG* 4.3 14.4 + - - -
144D LYS* 5.5 4.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 85 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C ASP* 2.8 43.0 + - - +
82C ALA 3.8 2.9 - - - +
84C GLU* 1.3 75.4 - - - +
86C PHE* 1.3 57.4 + - - +
88C ALA* 3.5 7.4 + - - +
89C SER* 3.0 33.3 + - - -
131C HIS* 3.7 2.5 - - + -
132C HIS* 2.5 44.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 86 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74C VAL* 4.1 10.8 - - + -
76C ILE* 3.5 22.2 - - + -
82C ALA 2.9 19.1 + - - +
83C ARG 3.8 1.8 - - - +
85C ASP* 1.3 75.1 - - - +
87C ALA* 1.3 61.7 + - - +
89C SER* 3.2 2.9 + - - -
90C VAL* 2.9 60.2 + - + +
93C TRP* 3.9 16.2 - + - -
99C CYS* 4.0 8.1 - - - -
108C TYR* 3.9 35.4 - + + -
110C LEU* 4.1 19.1 - - + -
128C LEU* 3.9 2.9 - - + -
131C HIS* 3.5 14.3 - - + +
133C GLY* 5.1 0.2 - - - -
134C VAL* 3.7 28.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 87 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C ARG 3.0 18.9 + - - +
84C GLU* 3.5 8.1 - - - +
86C PHE* 1.3 80.0 - - + +
88C ALA* 1.3 62.3 + - - +
90C VAL* 3.3 3.4 + - - +
91C ARG* 3.1 44.2 + - - +
108C TYR* 5.6 0.4 - - + +
146D ILE* 3.5 35.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 88 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84C GLU* 2.8 23.3 + - + +
85C ASP* 3.6 8.5 - - - +
87C ALA* 1.3 73.4 - - - +
89C SER* 1.3 58.6 + - - +
91C ARG* 3.7 22.8 + - - +
92C LYS* 3.2 26.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 89 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C ASP 3.0 9.4 + - - -
86C PHE 3.2 2.2 + - - -
88C ALA* 1.3 72.6 - - - +
90C VAL* 1.3 61.0 + - - +
91C ARG 3.1 2.0 - - - -
92C LYS* 2.8 33.5 + - - +
93C TRP* 3.3 28.1 + - - +
131C HIS* 2.7 40.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 90 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C PHE* 2.9 64.1 + - + +
87C ALA* 3.3 6.9 + - - +
89C SER* 1.3 71.7 - - - +
91C ARG* 1.3 59.1 + - - +
93C TRP* 3.1 24.1 + - + +
96C VAL* 3.7 26.7 - - + -
99C CYS* 3.7 22.9 - - + -
110C LEU* 4.6 1.8 - - + -
146D ILE* 4.9 0.7 - - + -
147D LYS* 2.9 28.6 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 91 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84C GLU* 4.3 11.9 + - - -
87C ALA* 3.1 38.9 + - - +
88C ALA* 3.7 18.6 - - - +
89C SER 3.1 0.2 - - - -
90C VAL* 1.3 76.0 - - - +
92C LYS* 1.3 61.1 + - + +
144D LYS* 6.3 1.0 - - - +
145D GLU 5.2 0.6 + - - -
146D ILE* 2.9 42.5 + - - +
147D LYS* 3.6 29.5 + - + -
----------------------------------------------------------
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