Contacts of the helix formed by residues 78 - 91 (chain C) in PDB entry 2PGW
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 78 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C LYS* 5.3 2.3 + - - -
74C HIS* 5.9 0.2 - - - +
75C SER* 3.0 29.0 + - - +
77C HIS* 1.3 85.0 - - - +
79C VAL* 1.3 64.8 + - - +
80C ALA 3.3 2.9 - - - -
81C PRO* 3.2 12.0 - - + +
82C LEU* 3.1 34.9 + - + +
127F GLN* 3.3 17.7 + - - +
130F GLY 3.4 5.4 - - - -
131F GLY* 3.6 12.4 - - - -
132F ALA 4.2 3.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 79 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76C PRO 3.6 5.1 + - - +
77C HIS 3.5 0.2 - - - -
78C ASP* 1.3 75.9 - - - +
80C ALA* 1.3 70.6 + - - +
82C LEU* 3.6 1.2 - - - +
83C ILE* 3.0 38.5 + - + +
110C ASP* 3.2 23.3 - - - +
113C MSE 3.7 41.0 - - + +
114C TRP* 3.8 22.7 - - + +
117C GLN* 3.7 20.2 - - - +
279C GLN* 4.1 3.1 - - - +
130F GLY* 3.8 7.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 80 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C VAL* 1.3 81.2 - - - +
81C PRO* 1.3 69.7 - - + +
83C ILE* 3.9 4.7 - - - +
84C ALA* 3.1 21.8 + - - +
110C ASP* 6.0 0.2 - - - -
279C GLN* 3.5 22.2 - - - +
129F LEU 5.2 0.4 - - - +
130F GLY* 3.0 15.1 + - - +
133F HIS* 3.7 21.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 81 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C ASP* 3.2 21.5 - - + +
80C ALA* 1.3 88.7 - - + +
82C LEU* 1.3 56.1 + - + +
84C ALA* 3.4 4.4 + - + +
85C ARG* 3.0 29.8 + - - +
130F GLY 3.1 18.4 - - - +
131F GLY 4.0 6.3 - - - -
132F ALA 3.2 27.8 - - - +
133F HIS* 3.7 25.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 82 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C ILE* 5.2 0.2 - - + -
70C HIS 5.2 0.2 - - - +
71C LEU* 4.0 20.0 - - + +
74C HIS* 3.8 43.3 - - + +
75C SER 3.6 21.5 - - - +
78C ASP* 3.1 33.0 + - + +
79C VAL* 3.6 3.6 - - - +
80C ALA 3.2 0.2 - - - -
81C PRO* 1.3 74.2 - - + +
83C ILE* 1.3 67.6 + - + +
85C ARG* 3.3 22.0 + - - +
86C ILE* 3.0 31.7 + - + +
113C MSE 3.8 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 83 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C LEU* 5.7 1.3 - - + -
79C VAL* 3.0 39.8 + - + +
80C ALA* 3.9 4.9 - - - +
82C LEU* 1.3 76.6 - - + +
84C ALA* 1.3 64.6 + - - +
86C ILE* 3.3 3.8 + - + -
87C PHE* 2.9 24.3 + - + +
106C PHE* 3.5 52.5 - - + +
109C ILE* 4.4 9.2 - - + -
110C ASP* 4.0 27.4 - - + +
276C GLY 5.1 2.0 - - - +
280C PRO* 6.5 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 84 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80C ALA 3.1 16.6 + - - +
81C PRO* 3.6 9.4 - - + +
82C LEU 3.3 0.2 - - - -
83C ILE* 1.3 79.6 - - - +
85C ARG* 1.3 59.4 + - - +
87C PHE* 3.5 9.4 + - - +
88C HIS* 3.1 23.4 + - - +
133F HIS* 4.9 8.5 - - + +
318F PRO* 6.4 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 85 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C HIS* 3.9 28.1 + - - +
74C HIS* 3.8 24.8 + - - -
81C PRO 3.0 17.4 + - - +
82C LEU* 3.6 20.1 - - - +
83C ILE 3.2 0.2 - - - -
84C ALA* 1.3 74.3 - - - +
86C ILE* 1.3 66.3 + - - +
88C HIS* 3.2 1.4 + - - -
89C GLN* 2.9 53.4 + - - +
26H TYR* 3.6 30.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 86 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C LEU* 3.5 48.9 - - + +
70C HIS* 3.6 32.8 - - + -
71C LEU* 3.8 23.1 - - + -
82C LEU* 3.0 19.5 + - + +
83C ILE* 3.8 7.4 - - + +
85C ARG* 1.3 86.0 - - - +
87C PHE* 1.3 57.8 + - - +
89C GLN* 4.5 4.7 - - - -
90C GLU* 3.0 30.4 + - + +
91C TYR* 4.5 0.2 - - - -
106C PHE* 3.7 16.2 - - + -
109C ILE* 5.7 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 87 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C ILE* 2.9 18.3 + - + +
84C ALA* 3.7 8.1 - - - +
86C ILE* 1.3 77.3 - - - +
88C HIS* 1.3 60.8 + - - +
91C TYR* 3.0 57.4 + + + +
92C LEU* 3.2 36.0 + - + -
96C ALA 4.9 0.2 - - - -
98C ILE 4.5 2.9 - - - -
99C MSE 4.0 27.8 - - + -
102C ALA* 3.4 27.6 - - + -
106C PHE* 3.7 15.4 - + + -
228H TRP* 3.8 22.7 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 88 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84C ALA 3.1 14.0 + - - +
85C ARG* 3.2 0.4 + - - -
87C PHE* 1.3 80.3 - - - +
89C GLN* 1.3 58.8 + - - +
92C LEU* 3.8 31.2 - - + -
93C GLY* 2.8 34.9 + - - -
25H SER* 3.1 30.1 + - - -
26H TYR* 3.1 24.4 + + - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 89 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C HIS* 3.6 25.0 - - - -
85C ARG* 2.9 41.2 + - - +
86C ILE* 3.9 4.5 - - - +
87C PHE 3.3 0.2 - - - -
88C HIS* 1.3 78.7 - - - +
90C GLU* 1.3 66.2 + - + +
94C HIS* 3.0 25.1 + - - -
24H TRP* 3.3 16.4 - - + -
26H TYR* 3.5 44.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 90 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C ARG* 2.8 50.6 + - - +
67C LEU* 3.8 22.4 - - + -
70C HIS* 2.8 35.2 + - + +
86C ILE 3.0 18.1 + - - +
89C GLN* 1.3 82.9 - - + +
91C TYR* 1.3 61.6 + - + +
94C HIS* 3.4 17.1 + - - -
54H ALA* 3.5 4.2 - - - +
55H PRO* 3.5 28.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 91 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63C ILE* 3.8 6.6 - - - +
67C LEU* 3.7 33.3 - - + +
87C PHE* 3.0 38.2 + + + +
89C GLN 3.5 0.4 - - - -
90C GLU* 1.3 84.1 - - + +
92C LEU* 1.3 66.3 + - - +
93C GLY 3.3 1.1 - - - -
94C HIS* 3.0 9.0 + - - +
96C ALA* 3.0 37.7 + - + +
98C ILE* 3.6 34.1 - - + -
101C ALA* 4.6 1.6 + - + -
102C ALA* 3.7 28.8 - - + -
105C ILE* 4.0 5.4 - - - +
106C PHE* 4.3 4.5 - + - -
55H PRO* 3.6 40.8 - - + +
----------------------------------------------------------
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