Contacts of the helix formed by residues 81 - 94 (chain C) in PDB entry 1QDV
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 ASN 81 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B TYR* 3.9 22.8 - - + +
93B GLN* 4.4 5.6 + - - -
39C ILE* 3.6 8.6 - - - +
80C ARG* 1.3 75.4 - - - +
82C ARG* 1.3 65.0 + - - +
83C PRO* 3.6 16.2 - - - +
84C SER* 2.6 39.7 + - - -
85C PHE* 3.8 8.0 + - - +
104C VAL* 4.2 1.6 - - - +
108C ILE* 3.6 24.2 - - + +
112C GLU* 3.7 27.9 + - + +
116C TYR* 5.3 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 82 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B LEU* 3.6 37.6 - - - +
43B ARG 3.3 15.9 + - - -
44B PHE* 3.3 31.4 - - - -
86B ASP* 3.1 19.8 + - - +
89B LEU* 4.4 5.8 - - + -
39C ILE* 3.6 25.1 - - - +
40C SER* 3.5 17.3 + - - -
41C GLY 3.3 0.8 + - - -
42C LEU* 2.8 75.2 - - + +
44C PHE* 4.6 0.3 - - - -
80C ARG 3.3 1.1 + - - +
81C ASN* 1.3 69.8 - - - +
83C PRO* 1.3 75.2 - - + +
84C SER 3.1 1.6 + - - -
85C PHE* 3.1 15.1 + - - +
86C ASP* 4.4 2.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 83 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B ASP* 3.8 24.9 - - + +
42C LEU* 5.8 0.2 - - + -
81C ASN* 3.6 18.8 - - - +
82C ARG* 1.3 96.2 - - + +
84C SER* 1.3 57.5 + - - -
86C ASP* 3.5 15.5 - - - +
101C PRO* 3.5 14.0 - - + +
103C ASN* 5.5 8.3 - - + +
104C VAL* 3.8 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 84 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C ASN* 2.6 29.5 + - - -
82C ARG 3.1 1.0 - - - -
83C PRO* 1.3 77.4 - - - +
85C PHE* 1.4 66.2 + - - +
86C ASP 3.4 0.2 - - - -
87C ALA* 3.4 16.4 + - - +
88C ILE* 3.4 12.6 + - - +
101C PRO* 4.4 1.3 - - - -
104C VAL* 3.4 22.6 - - - +
109C PHE* 3.8 15.4 - - - -
112C GLU* 3.7 27.6 - - - +
116C TYR* 6.1 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 85 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C ILE* 3.8 28.7 - - + -
39C ILE* 3.6 21.1 - - + -
44C PHE* 3.5 44.0 - + + -
59C LEU* 3.8 21.3 - - + -
81C ASN 3.8 6.8 + - - +
82C ARG 3.1 8.4 + - - +
84C SER* 1.4 77.9 - - - +
86C ASP* 1.3 67.2 + - - +
88C ILE* 3.0 17.3 + - + +
89C LEU* 2.9 36.7 + - + -
116C TYR* 3.6 40.8 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 86 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C PHE* 3.7 26.6 - - + -
82C ARG 4.4 1.2 + - - -
83C PRO* 3.5 16.8 - - - +
85C PHE* 1.3 74.2 - - - +
87C ALA* 1.3 65.7 + - - +
89C LEU* 3.4 3.5 + - - +
90C TYR* 2.8 30.4 + - - +
93C GLN* 5.2 0.2 - - - +
101C PRO* 4.2 4.9 - - - +
82D ARG* 4.0 20.8 + - + +
83D PRO* 3.7 27.2 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
84C SER 3.6 9.4 - - - +
85C PHE 3.1 0.6 - - - -
86C ASP* 1.3 78.8 + - - +
88C ILE* 1.3 65.3 + - - +
90C TYR* 3.9 7.4 - - - +
91C TYR* 3.0 22.2 + - - +
97C ARG 4.6 2.6 - - - +
98C LEU* 4.2 6.0 - - - +
99C ARG 3.2 27.8 + - - +
101C PRO* 3.8 19.1 - - + -
109C PHE* 3.9 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 88 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C LEU* 4.8 0.7 - - + -
84C SER* 3.5 17.9 - - - +
85C PHE* 3.0 29.7 + - + +
87C ALA* 1.3 78.4 - - - +
89C LEU* 1.3 62.6 + - - +
91C TYR* 3.2 20.8 - - - +
92C TYR* 3.3 24.6 - - + -
98C LEU* 4.9 0.4 - - - -
109C PHE* 4.3 21.1 - - + -
112C GLU* 4.5 2.0 - - + -
113C ILE* 4.4 13.0 - - + +
116C TYR* 4.0 37.0 - - + -
118C LEU* 3.8 23.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 89 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C ILE* 5.1 2.5 - - + -
44C PHE* 4.1 23.3 - - + -
45C GLU 4.2 9.2 - - - +
46C THR* 3.8 31.4 - - + +
50C THR* 4.9 2.0 - - + -
51C LEU* 4.5 12.6 - - + -
59C LEU* 6.1 0.4 - - + -
85C PHE* 2.9 27.9 + - + +
86C ASP* 3.8 8.1 - - - +
88C ILE* 1.3 75.7 - - - +
90C TYR* 1.3 63.1 + - - +
92C TYR* 2.9 20.7 + - + +
93C GLN* 3.1 34.8 + - + +
40D SER* 4.1 17.0 - - - -
82D ARG* 5.4 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 90 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C ASP 2.8 17.9 + - - +
87C ALA* 3.9 8.7 - - - +
89C LEU* 1.3 73.3 - - - +
91C TYR* 1.3 66.2 + - - +
93C GLN* 3.4 22.8 + - + +
94C SER* 2.8 55.6 + - - -
97C ARG* 3.9 19.7 - - + -
99C ARG* 5.9 2.5 - - + -
81D ASN* 3.5 44.9 - - + +
108D ILE* 3.6 41.5 - - + +
111D GLU* 3.8 16.6 + - - -
112D GLU* 4.8 7.4 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
54C PHE* 3.4 46.9 - + + -
87C ALA 3.0 13.7 + - - +
88C ILE* 3.2 11.7 - - - +
90C TYR* 1.3 78.0 - - - +
92C TYR* 1.3 68.8 + + - +
94C SER* 3.3 0.3 + - - -
96C GLY* 2.8 63.5 + - - -
97C ARG 3.4 11.8 + - - +
98C LEU* 3.7 25.1 - - + -
118C LEU* 3.7 31.8 + - + -
121C GLU* 5.9 0.9 - - - +
122C ALA* 3.6 29.7 + - + +
125C MET* 4.6 2.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 92 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C THR* 3.5 32.4 - - + +
51C LEU* 3.5 31.4 - - + -
53C GLN* 2.8 29.1 - - - +
54C PHE* 3.8 25.1 - + + -
57C THR* 2.6 37.4 + - + -
59C LEU* 3.7 31.9 + - + +
60C GLY 4.7 1.6 - - - -
88C ILE* 3.3 20.6 - - + -
89C LEU* 2.9 15.4 + - + +
91C TYR* 1.3 84.7 - + - +
93C GLN* 1.3 63.1 + - - +
95C GLY* 3.2 4.7 + - - -
116C TYR* 4.6 1.0 + - - +
118C LEU* 3.8 14.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 93 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C THR* 3.7 20.9 - - + -
53C GLN* 4.0 6.0 - - - +
86C ASP 5.2 0.2 - - - +
89C LEU* 3.1 26.7 + - + +
90C TYR* 3.4 30.7 + - + +
92C TYR* 1.3 77.5 - - - +
94C SER* 1.3 60.5 + - - +
95C GLY 3.5 0.3 + - - -
40D SER* 2.9 23.0 + - - -
79D ASP* 2.8 42.1 + - - +
80D ARG* 3.7 14.4 - - - +
81D ASN* 4.5 0.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 94 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C GLN* 4.7 0.2 - - - -
90C TYR* 2.8 50.8 + - - -
91C TYR 3.3 1.0 + - - -
93C GLN* 1.3 76.7 - - - +
95C GLY* 1.3 61.1 + - - +
97C ARG* 2.8 44.9 + - - +
111D GLU* 5.7 1.6 - - - -
----------------------------------------------------------
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