Contacts of the helix formed by residues 80 - 96 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70D ARG* 3.8 10.3 - - - +
75D SER* 4.3 15.9 - - - +
76D PRO* 4.5 2.5 - - - -
79D GLY* 1.3 72.6 - - - +
81D PRO* 1.3 77.4 - - + +
82D GLU* 4.0 15.5 - - + +
83D LEU* 3.1 14.8 + - + +
84D LEU* 3.0 19.6 + - - +
297D THR* 4.4 12.1 - - - +
300D GLN* 2.9 50.1 + - + +
301D LEU* 3.2 31.6 - - + -
304D SER* 4.0 4.9 - - - -
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Residues in contact with PRO 81 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70D ARG* 3.6 9.4 - - - +
76D PRO* 4.7 12.6 - - + -
79D GLY 3.7 3.5 - - - +
80D ILE* 1.3 85.3 - - + +
82D GLU* 1.3 69.9 + - - +
84D LEU* 3.2 11.4 + - + +
85D SER* 2.9 32.7 + - - -
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Residues in contact with GLU 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67D MET* 5.3 2.1 - - - +
70D ARG* 2.7 46.3 + - - -
80D ILE* 3.9 10.0 - - + +
81D PRO* 1.3 87.4 - - - +
83D LEU* 1.3 60.8 + - - +
85D SER* 3.2 7.2 + - - -
86D TRP 3.2 16.1 + - - -
301D LEU* 4.5 4.1 - - + +
304D SER* 3.4 20.4 - - - +
308D HIS* 3.3 22.6 + - + +
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Residues in contact with LEU 83 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80D ILE* 3.1 21.7 + - + +
82D GLU* 1.3 77.5 - - - +
84D LEU* 1.3 68.5 + - - +
86D TRP* 4.5 5.6 - - + +
87D LEU* 3.0 52.9 + - + +
113D VAL* 4.1 17.9 - - + -
261D PHE* 5.0 0.9 - - + -
271D ILE* 4.4 9.2 - - + -
300D GLN* 3.8 38.8 - - + +
303D ILE* 4.6 5.8 - - + -
304D SER* 3.9 18.4 + - - -
307D LEU* 4.1 24.9 - - + -
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Residues in contact with LEU 84 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76D PRO* 5.8 0.7 - - + -
78D ALA* 3.0 39.0 - - + +
79D GLY* 3.5 21.5 - - - +
80D ILE 3.0 7.0 + - - +
81D PRO* 3.5 13.5 - - + +
83D LEU* 1.3 80.0 - - - +
85D SER* 1.3 57.1 + - - +
87D LEU* 3.9 1.6 - - - +
88D LYS* 3.1 45.0 + - - +
111D LEU* 3.9 28.2 - - + +
113D VAL* 3.5 17.7 - - + -
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Residues in contact with SER 85 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81D PRO 2.9 17.8 + - - -
82D GLU* 3.2 10.0 + - - -
84D LEU* 1.3 75.4 - - - +
86D TRP* 1.3 65.4 + - - +
88D LYS* 4.1 6.8 - - - +
89D GLN* 3.1 25.1 + - - +
308D HIS* 5.3 2.4 - - - -
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Residues in contact with TRP 86 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82D GLU 3.2 15.2 + - - +
83D LEU* 3.4 8.7 + - + +
85D SER* 1.3 80.4 + - - +
87D LEU* 1.3 82.3 + - + +
89D GLN* 4.7 1.3 - - - -
90D LEU* 3.0 54.0 + - + -
261D PHE* 4.9 2.0 - + - -
307D LEU* 3.2 54.2 + - + -
308D HIS* 3.6 38.1 - + + +
311D GLY* 5.1 1.0 - - - -
312D GLU* 3.5 39.8 + - + +
315D PHE* 3.9 17.9 - + + -
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Residues in contact with LEU 87 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83D LEU* 3.0 49.4 + - + +
84D LEU 3.9 2.9 - - - +
86D TRP* 1.3 99.6 - - + +
88D LYS* 1.3 65.1 + - - +
90D LEU* 3.4 7.0 + - + +
91D GLN* 3.1 28.8 + - - +
111D LEU* 4.0 15.5 - - + -
113D VAL* 4.5 12.1 - - + -
261D PHE* 3.8 27.1 - - + -
271D ILE* 6.0 0.7 - - + -
273D PHE* 4.1 35.4 - - + -
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Residues in contact with LYS 88 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84D LEU* 3.1 33.8 + - + +
85D SER* 4.1 6.1 - - - +
86D TRP 3.4 0.2 - - - -
87D LEU* 1.3 74.3 - - - +
89D GLN* 1.3 65.6 + - - +
91D GLN* 3.2 6.2 + - - +
92D ILE* 3.1 31.6 + - + +
109D MET* 3.9 21.4 - - + +
110D ASP* 3.0 27.1 + - - +
111D LEU* 3.5 35.9 + - + +
278D LYS* 4.8 5.7 - - - +
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Residues in contact with GLN 89 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85D SER 3.1 19.6 + - - +
86D TRP* 4.4 1.1 - - - -
88D LYS* 1.3 76.2 - - - +
90D LEU* 1.3 63.5 + - - +
92D ILE* 3.0 31.6 + - - +
93D LYS* 2.9 34.7 + - - +
312D GLU* 3.7 20.2 - - - +
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Residues in contact with LEU 90 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86D TRP* 3.0 42.9 + - + +
87D LEU* 3.6 15.5 - - + +
88D LYS 3.2 0.2 - - - -
89D GLN* 1.3 75.9 - - - +
91D GLN* 1.3 61.0 + - - +
93D LYS* 3.1 4.2 + - + +
94D LEU* 2.8 69.2 + - + +
235D PHE* 4.1 14.4 - - + -
261D PHE* 5.5 0.9 - - + -
273D PHE* 4.6 6.5 - - + -
312D GLU* 3.6 31.5 + - + +
315D PHE* 3.8 21.8 - - + -
316D MET* 4.9 1.3 - - - -
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Residues in contact with GLN 91 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87D LEU 3.1 20.8 + - - +
88D LYS* 3.7 6.1 - - - +
90D LEU* 1.3 82.8 - - - +
92D ILE* 1.3 56.6 + - - +
94D LEU* 4.5 1.4 - - - +
95D HIS* 2.6 54.8 + - + +
96D ASN 3.2 4.5 + - - -
97D PRO* 3.6 2.4 - - - +
109D MET* 4.5 16.8 - - + -
111D LEU* 3.8 16.4 - - + -
235D PHE* 5.7 0.2 - - - -
247D LEU* 4.1 5.1 - - + +
257D ARG* 3.5 12.1 - - - +
259D ASP* 3.3 21.2 + - - +
273D PHE* 3.8 15.7 - - - -
275D THR* 2.8 26.2 + - + +
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Residues in contact with ILE 92 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88D LYS* 3.1 21.9 + - + +
89D GLN* 3.0 31.9 + - - +
91D GLN* 1.3 75.1 - - - +
93D LYS* 1.3 58.8 + - - +
96D ASN* 2.7 32.1 + - - +
97D PRO* 3.8 7.4 - - + -
100D ILE* 3.7 46.9 - - + -
109D MET* 5.1 4.9 - - + -
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Residues in contact with LYS 93 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89D GLN* 2.9 21.9 + - - +
90D LEU* 3.1 7.2 + - + +
92D ILE* 1.3 77.5 - - - +
94D LEU* 1.3 69.2 + - + +
96D ASN* 3.1 12.3 - - - +
312D GLU* 3.8 25.3 + - + +
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Residues in contact with LEU 94 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90D LEU* 2.8 47.5 + - + +
91D GLN* 4.5 1.6 - - - +
93D LYS* 1.3 80.0 - - + +
95D HIS* 1.3 88.0 + - + +
96D ASN* 4.0 6.7 + - - +
234D TYR* 4.1 13.7 + - + +
235D PHE* 3.6 37.2 - - + -
242D ARG* 4.8 13.0 + - - +
248D SER* 5.4 0.5 - - - -
316D MET* 4.5 14.8 - - + -
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Residues in contact with HIS 95 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91D GLN* 2.6 51.0 + - - +
94D LEU* 1.3 91.7 + - + +
96D ASN* 1.3 85.0 + - - +
97D PRO* 3.0 1.7 - - + -
234D TYR* 3.6 26.1 + + - -
245D THR* 3.0 43.5 + - + +
247D LEU* 3.8 25.1 - - + -
248D SER* 3.2 17.4 - - - +
257D ARG* 4.1 14.3 + - - -
259D ASP* 5.1 0.6 + - - -
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Residues in contact with ASN 96 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92D ILE* 2.7 27.3 + - - +
93D LYS 3.1 23.0 - - - +
94D LEU 4.0 4.3 + - - +
95D HIS* 1.3 88.7 + - - +
97D PRO* 1.4 70.0 - - - +
98D PRO* 3.3 8.7 - - - +
100D ILE* 5.8 0.9 - - - -
248D SER* 4.2 13.0 + - - +
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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