Contacts of the helix formed by residues 80 - 96 (chain C) in PDB entry 2QLR
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 ILE 80 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70C ARG* 3.9 9.6 - - - +
75C SER* 4.3 16.8 - - - -
76C PRO* 4.5 2.9 - - + +
79C GLY* 1.3 71.8 - - - -
81C PRO* 1.3 77.6 - - + +
82C GLU* 3.1 13.0 + - - +
83C LEU* 3.3 21.4 + - + +
84C LEU* 2.9 21.5 + - - +
297C THR* 4.5 9.2 - - - +
300C GLN* 3.2 46.0 + - + +
301C LEU* 3.4 35.4 - - + +
304C SER* 4.1 6.5 - - - -
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Residues in contact with PRO 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70C ARG* 3.8 8.3 - - - +
76C PRO* 4.6 15.0 - - + -
79C GLY 3.7 4.2 - - - +
80C ILE* 1.3 83.1 - - + +
82C GLU* 1.3 63.8 + - - +
84C LEU* 3.3 9.5 + - + +
85C SER* 2.5 37.8 + - - -
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Residues in contact with GLU 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C ARG* 2.7 45.9 + - - -
80C ILE* 3.9 11.7 - - + +
81C PRO* 1.3 85.1 - - - +
83C LEU* 1.3 57.7 + - - +
85C SER* 3.2 7.7 + - - -
86C TRP 2.9 20.1 + - - -
301C LEU* 4.3 3.4 - - + +
304C SER* 3.4 17.7 - - - +
308C HIS* 3.1 29.6 + - + +
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Residues in contact with LEU 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80C ILE* 3.3 18.4 + - + +
82C GLU* 1.3 76.9 - - - +
84C LEU* 1.3 68.7 + - - +
86C TRP* 4.2 5.6 - - + -
87C LEU* 2.9 58.6 + - + +
113C VAL* 4.1 16.6 - - + -
261C PHE* 5.2 0.4 - - + -
271C ILE* 4.2 11.0 - - + -
300C GLN* 3.9 34.3 - - + +
303C ILE* 4.2 11.4 - - + -
304C SER* 3.8 15.7 + - - -
307C LEU* 4.0 25.4 - - + -
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Residues in contact with LEU 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76C PRO* 6.1 0.4 - - + -
78C ALA* 3.4 35.2 - - + +
79C GLY* 3.7 21.1 - - - +
80C ILE 2.9 18.0 + - - +
81C PRO* 3.5 7.9 - - + +
83C LEU* 1.3 78.4 - - - +
85C SER* 1.3 56.6 + - - +
87C LEU* 3.8 1.0 - - - +
88C LYS* 2.9 49.4 + - + +
111C LEU* 3.5 42.4 - - + +
113C VAL* 3.7 5.5 - - + +
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Residues in contact with SER 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C PRO 2.5 28.0 + - - -
82C GLU* 3.2 14.4 + - - -
84C LEU* 1.3 70.5 - - - +
86C TRP* 1.3 57.6 + - - +
88C LYS* 3.9 8.3 - - - +
89C GLN* 2.9 30.3 + - - +
308C HIS* 5.6 0.4 + - - -
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Residues in contact with TRP 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82C GLU 2.9 21.0 + - - +
83C LEU* 3.2 8.3 + - + +
85C SER* 1.3 76.9 - - - +
87C LEU* 1.3 74.0 + - + +
89C GLN* 3.5 5.0 + - + +
90C LEU* 2.8 47.2 + - + -
261C PHE* 5.1 0.9 - + - -
304C SER* 6.3 0.2 - - - -
307C LEU* 3.4 57.0 + - + -
308C HIS* 3.5 37.3 - + + +
311C GLY* 4.1 22.2 - - - -
312C GLU* 4.2 12.2 - - + +
315C PHE* 3.9 26.2 - + + -
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Residues in contact with LEU 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C LEU* 2.9 50.7 + - + +
84C LEU 3.9 1.8 - - - +
86C TRP* 1.3 92.0 - - + +
88C LYS* 1.3 61.6 + - - +
89C GLN 3.2 0.9 - - - -
90C LEU* 3.5 7.6 - - + +
91C GLN* 2.9 34.3 + - - +
111C LEU* 3.7 16.4 - - + -
113C VAL* 4.4 12.3 - - + -
261C PHE* 3.5 29.4 - - + -
271C ILE* 6.1 0.2 - - + -
273C PHE* 3.8 35.7 - - + -
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Residues in contact with LYS 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84C LEU* 2.9 38.4 + - + +
85C SER* 4.0 7.4 - - - +
87C LEU* 1.3 77.2 - - - +
89C GLN* 1.3 61.7 + - - +
91C GLN* 3.1 6.3 + - - +
92C ILE* 3.0 32.4 + - + +
109C MET* 4.4 16.9 - - + +
110C ASP* 3.4 28.2 + - - +
111C LEU* 3.7 28.9 + - + +
278C LYS* 5.9 2.3 - - - +
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Residues in contact with GLN 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C SER 2.9 20.4 + - - +
86C TRP* 3.7 5.6 - - + +
88C LYS* 1.3 74.4 - - - +
90C LEU* 1.3 69.5 + - - +
92C ILE* 3.9 27.3 - - - +
93C LYS* 2.9 35.9 + - + +
312C GLU* 3.8 14.1 - - - +
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Residues in contact with LEU 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C TRP* 2.8 50.0 + - + +
87C LEU* 3.5 18.6 - - + +
89C GLN* 1.3 76.3 - - - +
91C GLN* 1.3 67.2 + - - +
93C LYS* 3.3 3.1 + - + +
94C LEU* 2.8 63.7 + - + +
235C PHE* 4.1 15.0 - - + -
261C PHE* 5.6 0.2 - - + -
273C PHE* 4.6 5.4 - - + -
312C GLU* 3.8 21.0 + - + +
315C PHE* 4.1 15.7 - - + -
316C MET* 5.3 2.0 - - - -
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Residues in contact with GLN 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C LEU 2.9 27.3 + - - +
88C LYS* 3.1 5.4 + - - +
90C LEU* 1.3 88.4 - - - +
92C ILE* 1.3 58.8 + - - +
94C LEU* 4.8 1.6 - - - +
95C HIS* 2.7 58.7 + - - +
96C ASN 3.3 1.2 + - - -
97C PRO* 3.6 4.1 - - + +
109C MET* 4.3 16.2 - - - -
111C LEU* 3.7 17.0 - - + -
235C PHE* 5.8 1.2 - - - -
247C LEU* 4.2 1.5 - - + +
257C ARG* 3.7 9.9 - - - -
259C ASP* 3.3 14.7 + - - +
273C PHE* 4.1 11.8 - - - -
275C THR* 3.0 25.7 + - + +
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Residues in contact with ILE 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88C LYS* 3.0 23.3 + - + +
89C GLN* 3.8 29.2 - - - +
91C GLN* 1.3 73.8 - - - +
93C LYS* 1.3 67.9 + - + +
96C ASN* 3.0 36.3 + - - +
97C PRO* 4.0 7.2 - - - -
100C ILE* 3.5 40.8 - - + -
101C HIS* 6.0 0.7 - - - +
109C MET* 4.8 6.1 - - + -
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Residues in contact with LYS 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89C GLN* 2.9 28.4 + - + +
90C LEU* 3.4 5.6 - - + +
92C ILE* 1.3 80.8 - - + +
94C LEU* 1.3 66.4 + - + +
96C ASN* 5.7 0.3 - - - +
312C GLU* 3.2 42.2 + - - +
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Residues in contact with LEU 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90C LEU* 2.8 52.9 + - + +
91C GLN* 4.8 2.9 - - - +
93C LYS* 1.3 82.8 - - + +
95C HIS* 1.3 80.5 + - + +
234C TYR* 4.3 18.7 + - + +
235C PHE* 4.0 22.2 - - + -
242C ARG* 3.9 22.3 + - - +
248C SER* 5.4 0.3 - - - -
316C MET* 4.9 10.3 - - + -
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Residues in contact with HIS 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91C GLN* 2.7 45.6 + - - +
94C LEU* 1.3 90.3 - - + +
96C ASN* 1.3 70.6 + - - +
97C PRO* 4.0 1.8 - - + -
234C TYR* 3.7 17.8 + + - -
235C PHE* 6.4 0.4 - + - -
244C PRO* 6.2 0.2 - - + -
245C THR* 3.0 42.1 - - + +
247C LEU* 3.7 26.0 - - + +
248C SER* 3.1 29.2 - - - +
257C ARG* 3.9 22.4 - - - -
259C ASP* 5.1 0.9 - - - -
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Residues in contact with ASN 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92C ILE* 3.0 23.0 + - - +
93C LYS 5.7 0.4 - - - +
95C HIS* 1.3 79.7 - - - +
97C PRO* 1.3 75.9 + - - +
98C PRO* 3.1 8.7 - - - +
100C ILE* 4.1 22.2 - - - +
248C SER 4.0 3.1 - - - +
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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
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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) + - + + + + + -
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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