Contacts of the helix formed by residues 78 - 89 (chain D) in PDB entry 2QXU
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 MET 78 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11D GLY* 3.9 1.3 - - - -
12D ILE* 3.5 48.9 - - + +
45D THR 4.5 3.6 - - - +
46D GLY* 3.1 30.3 - - - +
48D ASN* 5.5 0.9 - - - +
77D SER* 1.3 79.6 - - - +
79D GLY* 1.3 62.1 + - - +
80D GLY 3.0 0.4 - - - -
81D ALA* 3.0 24.8 + - - +
82D ASN* 3.0 15.2 + - - +
105D ALA* 4.4 8.6 - - + +
108D LEU* 3.4 35.7 - - + -
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Residues in contact with GLY 79 (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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9D VAL* 3.8 14.8 - - - +
10D HIS 3.3 23.1 + - - -
11D GLY* 3.6 0.2 - - - -
75D ALA* 3.5 6.9 - - - +
76D HIS 2.8 13.2 + - - -
78D MET* 1.3 78.4 - - - +
80D GLY* 1.3 55.8 + - - +
82D ASN* 3.7 6.1 - - - +
83D THR* 2.9 32.7 + - - -
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Residues in contact with GLY 80 (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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75D ALA* 3.7 15.8 - - - +
76D HIS 4.0 1.0 + - - -
77D SER 2.8 10.5 + - - -
79D GLY* 1.3 76.0 - - - +
81D ALA* 1.3 64.3 + - - +
83D THR* 3.3 3.6 + - - -
84D LEU* 3.0 28.2 + - - +
101D THR* 4.3 7.3 - - - +
104D GLY* 4.6 1.8 - - - -
106D ASN* 3.3 22.2 - - - -
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Residues in contact with ALA 81 (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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48D ASN* 3.3 9.4 - - - +
77D SER 4.0 1.6 + - - -
78D MET* 3.0 27.5 + - - +
80D GLY* 1.3 76.8 - - - +
82D ASN* 1.3 63.1 + - - +
84D LEU 3.3 0.7 + - - -
85D TYR 2.9 13.7 + - - -
105D ALA 3.3 24.1 + - - +
106D ASN* 4.0 4.5 + - - +
108D LEU* 4.1 6.3 - - + -
109D THR* 2.8 32.0 + - - +
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Residues in contact with ASN 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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9D VAL* 4.7 1.1 - - + -
10D HIS 4.5 1.2 + - - -
11D GLY* 5.7 0.6 - - - -
41D PHE* 3.6 18.3 - - + -
46D GLY* 3.1 18.2 + - - +
47D THR 3.7 4.7 - - - +
48D ASN* 2.9 20.7 - - - +
51D ASN* 2.9 43.8 - - + +
52D GLY* 4.8 3.3 - - - +
55D LEU* 4.1 5.3 - - + +
78D MET* 3.0 18.0 + - - +
79D GLY* 3.7 10.6 - - - +
80D GLY 3.3 0.2 - - - -
81D ALA* 1.3 76.7 - - - +
83D THR* 1.3 56.5 + - - +
85D TYR* 3.2 4.1 + - - +
86D TYR* 3.0 28.4 + - - +
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Residues in contact with THR 83 (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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9D VAL* 3.9 8.3 - - - +
55D LEU* 3.9 10.3 - - - +
73D ILE* 3.6 35.6 - - + +
75D ALA* 3.6 13.0 - - - +
79D GLY 2.9 21.7 + - - -
80D GLY* 3.5 8.3 - - - +
81D ALA 3.2 0.2 - - - -
82D ASN* 1.3 77.6 - - - +
84D LEU* 1.3 63.7 + - + +
86D TYR* 3.3 4.7 + - - +
87D ILE* 3.1 34.9 + - + +
99D VAL* 4.3 17.5 - - + -
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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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80D GLY 3.0 17.8 + - - +
81D ALA 3.8 3.6 - - - +
83D THR* 1.3 77.0 - - + +
85D TYR* 1.3 55.8 + - - +
87D ILE* 3.3 4.6 + - + +
88D LYS* 2.7 38.5 + - - +
99D VAL* 5.8 0.9 - - + -
106D ASN* 3.5 46.0 - - + +
109D THR* 3.8 11.7 - - + -
110D THR* 3.8 20.6 - - + -
112D LYS 4.5 4.9 - - - +
114D LEU* 4.1 4.7 - - + +
125D TYR* 3.6 37.0 - - + +
143D LEU* 4.0 12.8 - - + -
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Residues in contact with TYR 85 (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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48D ASN* 3.4 57.4 - - + +
49D TYR* 4.7 15.7 - - - -
52D GLY* 3.9 11.4 - - - -
53D PRO* 4.9 2.7 - - + -
81D ALA 2.9 16.8 + - - +
82D ASN 3.5 4.7 - - - +
84D LEU* 1.3 72.7 - - - +
86D TYR* 1.3 61.5 + - - +
88D LYS 4.4 0.2 - - - +
89D ASN* 2.8 65.7 + - + +
90D LEU* 3.3 26.8 + - + +
109D THR* 3.6 10.5 - - + +
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Residues in contact with TYR 86 (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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52D GLY* 4.8 2.2 - - - +
55D LEU* 3.9 20.6 - - + -
56D SER* 3.5 34.3 + - - -
59D VAL* 3.3 39.3 - - + +
73D ILE* 4.6 4.7 - - + -
82D ASN 3.0 13.0 + - - +
83D THR 3.3 10.8 - - - +
85D TYR* 1.3 77.2 - - - +
87D ILE* 1.3 62.3 + - + +
90D LEU* 3.2 36.3 + - + +
91D ASP* 3.6 10.5 + - - -
92D GLY* 3.1 43.8 + - - -
95D LYS* 3.4 20.3 - - - +
96D VAL* 3.8 17.7 - - + -
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Residues in contact with ILE 87 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83D THR* 3.1 22.2 + - + +
84D LEU* 3.7 8.5 - - - +
86D TYR* 1.3 88.5 - - + +
88D LYS* 1.3 61.2 + - - +
90D LEU 4.4 4.3 - - - +
92D GLY* 4.1 12.6 - - - +
93D GLY* 4.0 15.8 + - - -
96D VAL* 4.4 6.5 - - + -
99D VAL* 4.2 20.6 - - + -
114D LEU* 3.9 23.1 - - + +
116D GLY* 5.1 2.7 - - - -
123D ILE* 3.7 29.6 - - + -
125D TYR* 3.5 19.5 - - + +
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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
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84D LEU 2.7 21.6 + - - +
85D TYR* 4.5 0.2 - - - -
87D ILE* 1.3 77.3 - - - +
89D ASN* 1.3 79.8 + - - +
90D LEU 4.9 0.7 - - - +
109D THR* 4.3 26.0 - - + +
110D THR* 4.4 13.8 + - - -
114D LEU* 3.2 24.7 - - + +
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Residues in contact with ASN 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 TYR* 2.8 53.5 + - + +
88D LYS* 1.3 103.4 - - - +
90D LEU* 1.3 68.0 + - + +
109D THR* 5.0 0.2 - - - +
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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
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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