Contacts of the helix formed by residues 78 - 91 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A GLN* 3.5 18.9 + - - +
130A GLY 3.4 4.9 - - - -
131A GLY* 3.6 12.9 - - - -
132A ALA* 4.0 4.9 + - - -
352A ARG* 5.0 6.6 + - - -
74B HIS* 5.8 0.6 - - + +
75B SER* 3.1 25.3 + - - +
77B HIS* 1.3 86.5 - - - +
79B VAL* 1.3 65.5 + - - +
80B ALA 3.2 2.9 - - - -
81B PRO* 3.1 12.2 - - + +
82B LEU* 2.9 36.9 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
130A GLY* 3.8 8.7 - - - +
76B PRO 3.8 2.3 + - - +
78B ASP* 1.3 77.0 - - - +
80B ALA* 1.3 69.5 + - - +
82B LEU* 3.7 2.5 - - - +
83B ILE* 3.0 39.0 + - + +
110B ASP* 3.2 24.0 - - - +
113B MSE 3.6 44.8 - - + +
114B TRP* 3.8 21.1 - - + +
117B GLN* 3.5 22.0 - - - +
279B GLN* 4.3 2.7 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
129A LEU 5.2 0.4 - - - +
130A GLY* 3.0 16.3 + - - +
133A HIS* 3.6 22.3 + - + +
79B VAL* 1.3 81.4 - - - +
81B PRO* 1.3 69.8 - - + +
83B ILE* 3.9 4.0 - - - +
84B ALA* 3.1 22.3 + - - +
279B GLN* 3.6 22.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 81 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A GLY 3.1 15.3 - - - +
131A GLY* 3.9 7.9 - - - -
132A ALA 3.2 29.2 - - - +
133A HIS* 3.6 24.7 - - + -
78B ASP* 3.1 31.9 - - + +
80B ALA* 1.3 86.5 - - + +
82B LEU* 1.3 58.6 + - + +
84B ALA* 3.5 3.2 + - + +
85B ARG* 3.1 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 82 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B ILE* 5.4 0.2 - - + -
70B HIS 5.0 0.4 - - - +
71B LEU* 4.0 21.8 - - + -
74B HIS* 3.9 40.4 - - + +
75B SER 3.6 22.2 - - - +
78B ASP* 2.9 35.2 + - + +
79B VAL 3.7 3.4 - - - +
80B ALA 3.1 0.2 - - - -
81B PRO* 1.3 75.6 - - + +
83B ILE* 1.3 66.3 + - - +
85B ARG* 3.2 23.3 + - - +
86B ILE* 3.0 29.7 + - - +
113B MSE 4.0 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 83 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B LEU* 5.6 1.6 - - + -
79B VAL* 3.0 41.4 + - + +
80B ALA* 3.9 4.3 - - - +
82B LEU* 1.3 75.8 - - + +
84B ALA* 1.3 58.8 + - - +
86B ILE* 3.3 4.6 + - + -
87B PHE* 2.9 29.7 + - + +
106B PHE* 3.4 49.8 - - + +
109B ILE* 4.3 12.3 - - + -
110B ASP* 4.0 26.9 - - + +
276B GLY 5.2 2.0 - - - +
280B PRO* 6.4 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 84 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A HIS* 4.9 9.6 - - + +
318A PRO* 6.4 0.2 - - + -
80B ALA 3.1 16.6 + - - +
81B PRO* 3.7 8.5 - - + +
82B LEU 3.2 0.2 - - - -
83B ILE* 1.3 79.2 - - - +
85B ARG* 1.3 56.7 + - - +
87B PHE* 3.4 9.3 + - - +
88B HIS* 3.0 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 85 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B HIS* 3.8 39.8 + - - +
74B HIS* 4.3 12.7 + - - -
81B PRO 3.1 16.8 + - - +
82B LEU* 3.2 18.3 + - - +
84B ALA* 1.3 73.8 - - - +
86B ILE* 1.3 68.5 + - - +
88B HIS* 3.1 1.3 + - - -
89B GLN* 2.8 60.4 + - - +
26F TYR* 3.5 31.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 86 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B LEU* 3.5 46.9 - - + +
70B HIS* 3.6 30.1 - - + -
71B LEU* 4.0 22.9 - - + -
82B LEU* 3.0 22.2 + - + +
83B ILE* 3.7 8.1 - - + +
85B ARG* 1.3 85.4 - - - +
87B PHE* 1.3 59.6 + - - +
89B GLN* 4.4 5.2 - - - -
90B GLU* 2.9 30.8 + - + +
106B PHE* 3.9 19.7 - - + -
109B ILE* 5.5 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 87 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B ILE* 2.9 18.2 + - + +
84B ALA* 3.5 9.2 - - - +
86B ILE* 1.3 77.9 - - - +
88B HIS* 1.3 62.3 + - - +
91B TYR* 3.0 57.3 + + + +
92B LEU* 3.2 27.9 + - + -
96B ALA 5.0 0.2 - - - -
98B ILE 4.6 1.8 - - - -
99B MSE 3.9 35.9 - - + -
102B ALA* 3.4 27.6 - - + -
106B PHE* 3.7 14.8 - + + -
228F TRP* 3.9 21.5 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 88 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B ALA 3.0 15.8 + - - +
87B PHE* 1.3 76.6 - - - +
89B GLN* 1.3 58.4 + - - +
92B LEU* 3.8 31.2 - - + -
93B GLY* 2.8 34.0 + - - -
25F SER* 3.2 33.5 + - - -
26F TYR* 3.1 26.3 + + - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 89 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B HIS* 3.3 27.7 + - - -
85B ARG* 2.8 49.4 + - - +
86B ILE* 3.9 3.8 - - - +
88B HIS* 1.3 75.6 - - - +
90B GLU* 1.3 66.2 + - + +
94B HIS* 3.3 11.6 + - - -
24F TRP* 3.2 30.7 - - + -
26F TYR* 3.6 39.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 90 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B ARG* 3.0 48.3 + - - +
67B LEU* 3.9 23.8 - - + -
70B HIS* 2.8 35.4 + - + +
86B ILE* 2.9 22.1 + - + +
89B GLN* 1.3 82.6 - - + +
91B TYR* 1.3 64.2 + - + +
94B HIS* 3.3 18.7 + - - -
54F ALA* 3.6 2.4 - - - +
55F PRO* 3.5 25.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 91 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B ILE* 3.8 7.1 - - - +
67B LEU* 3.7 33.6 - - + +
87B PHE* 3.0 40.3 + + + +
89B GLN 3.5 0.2 - - - -
90B GLU* 1.3 83.9 - - + +
92B LEU* 1.3 67.7 + - - +
93B GLY 3.3 1.1 - - - -
94B HIS* 3.0 13.7 + - - +
96B ALA* 3.1 32.0 + - + +
98B ILE* 3.7 33.4 - - + -
101B ALA* 4.5 1.6 + - + -
102B ALA* 3.8 28.7 - - + -
105B ILE* 4.0 4.7 - - - +
106B PHE* 4.4 3.4 - + - -
55F PRO* 3.6 39.3 - - + +
----------------------------------------------------------
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