Contacts of the helix formed by residues 89 - 100 (chain X) in PDB entry 2QW0
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 LYS 89 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87X ARG 4.6 8.9 + - - -
88X LEU* 1.3 74.6 - - - +
90X SER* 1.3 67.1 + - - +
91X ALA* 4.1 7.6 - - + +
92X GLU* 2.9 48.5 + - + +
93X LEU* 3.0 14.0 + - - +
488X ASN* 3.0 36.3 + - - +
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Residues in contact with SER 90 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88X LEU 3.8 1.8 + - - -
89X LYS* 1.3 71.7 - - - +
91X ALA* 1.3 64.2 + - - +
93X LEU* 3.3 9.7 + - - +
94X ALA* 2.9 26.0 + - - +
112X GLN* 4.0 5.2 + - - +
113X VAL* 3.7 21.9 + - - +
116X ALA* 3.8 24.1 - - - +
117X ILE* 5.9 0.2 - - - +
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Residues in contact with ALA 91 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89X LYS* 3.2 7.5 - - + +
90X SER* 1.3 79.1 - - - +
92X GLU* 1.3 58.8 + - + +
94X ALA* 3.4 5.4 + - - +
95X GLU* 3.0 30.2 + - - +
116X ALA* 4.9 1.5 - - - +
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Residues in contact with GLU 92 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88X LEU* 3.4 25.5 - - + +
89X LYS* 2.9 49.9 + - + +
91X ALA* 1.3 77.5 - - + +
93X LEU* 1.3 58.1 + - - +
95X GLU* 3.3 6.1 + - - +
96X LEU* 2.9 35.9 + - + +
167X LEU* 3.9 29.0 - - + +
168X PRO* 5.6 0.3 - - - +
488X ASN 4.9 11.6 - - - +
490X LEU* 5.6 0.2 - - - +
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Residues in contact with LEU 93 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60X VAL* 4.0 25.6 - - + -
84X LEU* 3.8 22.2 - - + -
85X ASN 3.7 20.2 - - - +
86X PRO 4.8 3.4 - - - +
88X LEU* 3.7 32.5 - - + +
89X LYS 3.0 21.3 + - - +
90X SER* 3.9 6.5 - - - +
92X GLU* 1.3 73.2 - - - +
94X ALA* 1.3 66.2 + - - +
96X LEU* 3.2 5.9 + - - +
97X ILE* 2.9 38.6 + - + +
113X VAL* 4.9 14.8 - - + -
117X ILE* 5.7 4.7 - - + -
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Residues in contact with ALA 94 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90X SER 2.9 18.7 + - - +
91X ALA* 3.7 6.1 - - - +
93X LEU* 1.3 76.9 - - - +
95X GLU* 1.3 57.4 + - - +
97X ILE* 3.8 2.5 - - - +
98X LYS* 2.9 29.5 + - - +
116X ALA* 4.0 18.2 - - + +
117X ILE* 4.4 13.6 - - + +
120X SER* 3.8 30.5 + - - +
122X SER* 4.7 0.2 - - - -
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Residues in contact with GLU 95 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91X ALA 3.0 17.2 + - - +
92X GLU* 3.6 6.5 - - - +
94X ALA* 1.3 78.2 - - - +
96X LEU* 1.3 56.4 + - - +
98X LYS* 3.3 23.5 + - - +
99X ARG* 2.8 72.4 + - - +
120X SER* 5.5 2.6 - - - -
167X LEU* 4.1 11.7 - - + -
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Residues in contact with LEU 96 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84X LEU* 3.9 31.2 - - + -
88X LEU* 4.1 17.0 - - + -
92X GLU* 2.9 24.8 + - + +
93X LEU* 3.2 4.2 + - - +
95X GLU* 1.3 73.9 - - - +
97X ILE* 1.3 60.2 + - - +
99X ARG* 3.6 12.2 + - + +
100X GLY* 2.8 27.0 + - - -
102X MET* 4.7 0.2 - - - +
160X TYR* 4.1 21.6 + - + -
167X LEU* 4.4 15.9 - - + -
168X PRO* 3.3 41.1 - - + +
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Residues in contact with ILE 97 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58X ALA* 3.7 27.1 - - + -
60X VAL* 4.7 6.1 - - + -
84X LEU* 4.1 13.9 - - + -
93X LEU* 2.9 30.7 + - + +
94X ALA* 3.9 3.8 - - - +
96X LEU* 1.3 74.5 - - - +
98X LYS* 1.3 66.8 + - - +
100X GLY 3.4 6.2 + - - -
102X MET* 3.6 31.1 + - + +
105X ALA* 4.3 9.0 - - + -
117X ILE* 4.1 27.1 - - + -
122X SER* 3.9 7.5 + - - +
124X ALA* 3.8 28.9 - - + -
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Residues in contact with LYS 98 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94X ALA 2.9 19.9 + - - +
95X GLU* 3.5 26.2 - - - +
97X ILE* 1.3 75.2 - - - +
99X ARG* 1.3 63.5 + - + +
101X GLU* 3.2 18.0 + - - +
120X SER* 3.7 23.6 - - - +
121X GLY 5.5 0.2 - - - -
122X SER* 3.7 25.3 - - - +
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Residues in contact with ARG 99 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95X GLU* 2.8 56.6 + - - +
96X LEU* 3.9 12.4 - - + +
98X LYS* 1.3 74.7 - - + +
100X GLY* 1.3 57.7 + - - +
101X GLU* 3.1 7.8 + - - +
167X LEU* 3.2 31.6 - - - +
366X LEU* 4.9 0.2 - - - +
367X ASN* 3.3 22.4 - - + +
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Residues in contact with GLY 100 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56X ARG* 2.8 22.4 + - - -
96X LEU 2.8 21.5 + - - -
97X ILE 3.4 1.1 + - - -
98X LYS 3.2 1.4 - - - -
99X ARG* 1.3 71.2 - - - +
101X GLU* 1.3 67.3 + - - +
102X MET* 2.9 25.5 + - - +
160X TYR* 5.4 0.9 - - - -
366X LEU* 3.7 14.9 - - - +
367X ASN* 5.0 0.7 - - - -
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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