Contacts of the helix formed by residues 78 - 92 (chain N) in PDB entry 5G04
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 VAL 78 (chain N).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1849A LYS* 4.4 13.2 - - - +
1915A LEU 4.7 1.8 - - - +
1918A LYS* 3.4 33.9 - - + +
1919A PHE* 3.6 36.1 - - + +
74N TRP* 6.1 0.7 - - - +
75N PHE* 2.6 12.8 + - + +
76N VAL 2.6 4.6 + - - -
77N GLU* 1.3 81.9 - - - +
79N LEU* 1.3 58.2 + - + +
80N GLN 2.8 3.2 + - - -
81N ASN* 2.4 38.9 + - - +
82N ASP* 3.0 16.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 79 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1915A LEU* 6.0 6.1 - - + -
1919A PHE* 6.3 0.2 - - + -
27N VAL* 5.4 7.4 - - + +
75N PHE* 3.6 54.8 + - + -
76N VAL 3.4 1.4 + - - -
78N VAL* 1.3 79.1 - - + +
80N GLN* 1.3 57.7 + - - +
82N ASP* 4.1 20.1 - - + +
83N LEU* 3.6 27.4 + - + +
129N LEU* 5.8 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 80 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76N VAL* 2.7 34.9 + - + +
77N GLU* 3.0 28.0 + - - +
79N LEU* 1.3 72.6 - - - +
81N ASN* 1.3 59.0 + - - +
82N ASP 3.4 0.4 - - - -
83N LEU* 3.4 6.8 + - - +
84N GLN* 2.8 71.3 + - - +
129N LEU* 3.8 39.6 - - + +
153N VAL* 3.5 23.0 + - - +
156N MET* 4.4 2.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 81 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1849A LYS* 5.6 3.0 - - - +
1850A CYS* 3.4 30.0 - - - +
1853A ASP* 4.0 23.2 + - - +
76N VAL 3.8 0.6 + - - -
78N VAL* 2.4 33.2 + - - +
80N GLN* 1.3 72.4 + - - +
82N ASP* 1.3 61.4 + - - +
84N GLN* 3.1 6.6 + - - +
85N ALA* 2.9 31.3 + - - +
156N MET* 3.3 32.7 - - + +
160N VAL* 4.0 11.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 82 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1853A ASP* 5.9 3.1 - - - +
1857A ASP* 4.2 16.5 - - - +
1915A LEU* 5.4 8.1 - - - +
1918A LYS* 5.2 6.8 - - - +
78N VAL* 3.0 18.4 + - - +
79N LEU* 4.1 24.8 - - + +
81N ASN* 1.3 77.6 + - - +
83N LEU* 1.3 58.1 + - - +
85N ALA* 3.3 14.5 + - - +
86N ASN* 2.7 32.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 83 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79N LEU* 3.6 19.5 + - + +
80N GLN* 3.4 9.6 + - - +
82N ASP* 1.3 76.8 - - - +
84N GLN* 1.3 52.5 + - - +
86N ASN* 3.1 13.9 + - + +
87N ILE* 2.6 54.9 + - + +
125N TYR 5.9 2.2 - - - +
129N LEU* 4.0 30.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 84 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80N GLN* 2.8 58.4 + - + +
81N ASN* 3.1 9.0 + - - +
83N LEU* 1.3 69.2 - - - +
85N ALA* 1.3 56.9 + - - +
86N ASN 3.0 4.5 - - - -
87N ILE* 3.8 19.1 - - + +
88N SER* 3.0 32.7 + - - -
126N LEU* 5.9 1.2 + - - +
129N LEU* 5.4 2.2 - - + +
156N MET* 3.4 20.1 - - - +
157N LEU* 3.3 41.5 - - + +
160N VAL* 3.8 16.4 - - + +
161N LEU* 5.0 5.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 85 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1854A ASN* 4.5 16.8 - - + +
81N ASN* 2.9 15.0 + - - +
82N ASP* 3.3 10.5 + - - +
84N GLN* 1.3 74.3 - - - +
86N ASN* 1.3 61.8 + - - +
88N SER* 4.1 2.0 - - - -
89N PRO* 3.7 14.5 - - - +
160N VAL* 4.0 16.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 86 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82N ASP* 2.7 26.7 + - - +
83N LEU* 3.3 15.7 - - + +
84N GLN 3.0 0.8 - - - -
85N ALA* 1.3 85.9 - - - +
87N ILE* 1.3 60.9 - - - +
89N PRO* 3.5 11.7 - - - +
90N GLU* 3.0 37.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 87 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83N LEU* 2.6 42.2 + - + +
84N GLN* 3.3 17.7 + - + +
86N ASN* 1.3 73.5 - - - +
88N SER* 1.3 60.3 + - - +
90N GLU* 3.5 5.0 + - - +
91N PHE* 2.9 32.9 + - + +
122N LEU* 4.8 5.2 - - + +
125N TYR* 4.0 37.6 - - + -
126N LEU* 4.0 31.0 - - + +
129N LEU* 4.2 15.9 - - + -
161N LEU* 4.8 11.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 88 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84N GLN 3.0 17.0 + - - -
85N ALA* 4.1 1.2 - - - -
87N ILE* 1.3 76.2 - - - +
89N PRO* 1.4 65.6 - - - +
91N PHE* 3.7 6.7 - - - -
92N TRP* 3.0 45.8 + - - -
160N VAL* 3.6 24.1 + - - +
161N LEU* 3.7 23.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 89 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85N ALA 3.7 16.2 - - - +
86N ASN* 3.5 24.9 - - - +
88N SER* 1.4 97.9 - - - +
90N GLU* 1.3 64.0 + - + +
91N PHE 3.5 5.0 + - - -
92N TRP* 3.9 11.8 - - + -
93N ASN 5.2 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 90 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86N ASN* 3.0 29.3 - - - +
87N ILE* 3.5 4.4 + - - +
89N PRO* 1.3 78.8 - - + +
91N PHE* 1.3 66.8 + - - +
93N ASN* 3.7 13.7 + - - +
125N TYR* 4.9 20.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 91 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87N ILE* 2.9 22.8 + - + +
88N SER* 3.2 10.8 - - - +
90N GLU* 1.3 76.2 - - - +
92N TRP* 1.3 94.7 + + - +
93N ASN* 2.6 39.9 + - + +
94N ALA* 3.8 23.3 - - + -
118N LEU* 5.0 6.3 - - + -
119N GLU* 5.0 14.8 - - + -
122N LEU* 4.3 29.8 - - + -
161N LEU* 4.0 27.1 - - + -
162N PHE* 4.7 4.3 - + - -
169N PHE* 5.9 1.8 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 92 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88N SER* 3.0 38.6 + - - +
89N PRO* 3.9 13.0 - - + +
91N PHE* 1.3 102.3 - + - +
93N ASN 3.0 17.2 + - - -
94N ALA* 3.6 33.4 + - + +
95N ILE* 3.7 19.2 + - + +
96N SER* 4.4 1.2 + - - -
160N VAL 4.8 1.0 + - - -
161N LEU* 3.3 28.9 + - - +
162N PHE* 3.8 19.7 - + - -
164N SER* 3.9 14.4 - - - -
165N THR 3.2 26.9 - - - -
166N PRO* 4.7 9.0 - - + -
169N PHE* 3.7 34.8 - + + -
----------------------------------------------------------
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