Contacts of the helix formed by residues 110 - 123 (chain A) in PDB entry 1QZW
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 THR 110 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108A GLY 2.7 2.6 + - - -
109A LYS* 1.3 80.0 - - + +
111A THR* 1.3 104.5 + - + +
112A THR* 2.3 14.0 + - - -
113A ALA* 2.9 10.4 + - - +
136A ARG* 5.0 12.6 - - - +
138A ALA 5.6 0.4 - - - +
139A ALA* 5.5 2.7 - - - -
142A GLN* 3.2 29.9 + - - +
143A LEU* 3.9 20.3 - - - +
146A LEU* 5.6 1.0 - - - +
185A ASP* 3.4 14.4 - - - -
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Residues in contact with THR 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A GLY* 2.4 33.2 + - - +
110A THR* 1.3 101.5 + - + +
112A THR* 1.3 81.8 + - - +
113A ALA* 2.4 3.1 + - - +
114A GLY* 2.6 14.7 + - - -
115A LYS* 6.3 0.4 - - - -
142A GLN* 3.7 23.8 - - - +
146A LEU* 5.4 6.7 - - - +
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Residues in contact with THR 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A LEU* 5.3 6.1 - - - +
108A GLY* 2.5 35.7 + - - +
109A LYS 2.9 7.3 + - - -
110A THR 2.3 26.2 + - - -
111A THR* 1.3 87.4 + - - +
113A ALA* 1.3 56.5 + - - +
114A GLY* 2.4 20.8 + - - -
115A LYS* 3.2 17.4 + - - +
116A LEU* 3.4 8.6 + - - -
217A VAL* 4.9 11.9 - - + -
245A THR* 4.1 18.4 - - + -
279A LEU* 5.6 0.8 - - - +
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Residues in contact with ALA 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A LEU* 6.1 2.9 - - + +
110A THR* 3.3 10.8 - - - +
111A THR 2.4 5.7 + - - +
112A THR* 1.3 79.9 + - - +
114A GLY* 1.3 72.1 + - - +
116A LEU* 2.7 19.3 - - - +
117A ALA* 2.5 21.9 + - - +
129A LEU* 4.8 8.5 - - + -
183A ILE* 4.1 15.9 - - + -
185A ASP* 5.2 10.3 - - + +
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Residues in contact with GLY 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A THR 2.6 11.8 + - - -
112A THR 2.4 6.8 + - - -
113A ALA* 1.3 82.6 - - - +
115A LYS* 1.3 54.7 + - - -
116A LEU 2.7 0.2 - - - -
117A ALA* 2.5 3.5 + - - -
118A TYR* 2.4 34.5 + - - -
129A LEU* 5.2 2.9 - - - +
146A LEU* 4.7 18.0 - - - +
150A ILE* 6.1 2.2 - - - -
276A ILE* 3.8 6.1 - - - -
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Residues in contact with LYS 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A THR 6.3 0.4 - - - -
112A THR* 3.2 11.0 + - - +
114A GLY* 1.3 69.4 - - - -
116A LEU* 1.3 48.9 + - - +
118A TYR* 2.8 16.9 - - + -
119A PHE* 2.3 45.1 + - - +
271A GLY* 4.0 4.0 + - - -
273A GLY* 2.3 33.5 + - - +
274A GLU 3.1 0.4 - - - -
275A LYS 2.8 20.9 - - - +
276A ILE* 3.0 27.0 - - + +
277A ASP* 4.2 0.7 - - - -
278A GLU* 2.8 25.4 - - - +
279A LEU* 3.0 40.1 - - + +
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Residues in contact with LEU 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A ILE* 4.6 12.6 - - + -
101A LEU* 5.4 7.9 - - + -
112A THR* 3.4 6.2 + - - +
113A ALA* 2.7 20.0 - - - +
114A GLY 2.5 3.8 + - - -
115A LYS* 1.3 76.5 - - - +
117A ALA* 1.3 75.9 + - - +
119A PHE* 2.9 16.3 - - + +
120A TYR* 3.1 31.5 + - + -
183A ILE* 3.2 35.4 - - + -
269A PHE* 5.0 11.9 - - + -
279A LEU* 3.7 17.6 - - + +
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Residues in contact with ALA 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A ALA 2.5 6.3 + - - +
114A GLY* 2.5 9.1 + - - +
116A LEU* 1.3 82.0 - - - +
118A TYR* 1.3 69.8 + - - +
120A TYR* 2.5 18.9 + - - +
121A LYS 3.4 3.7 + - - -
127A VAL* 4.5 14.6 - - + -
129A LEU* 3.4 35.0 - - + -
150A ILE* 5.3 5.4 - - + -
183A ILE* 4.1 16.4 - - + -
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Residues in contact with TYR 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A GLY* 2.4 16.4 + - - +
115A LYS* 2.8 15.3 - - + -
117A ALA* 1.3 76.7 - - - +
119A PHE* 1.3 83.3 + + + +
121A LYS* 3.2 15.3 + - - +
122A LYS* 3.5 43.6 + - + +
150A ILE* 4.3 23.5 - - + +
276A ILE* 2.8 46.4 - - + -
277A ASP* 2.9 38.0 - - + +
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Residues in contact with PHE 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A VAL* 5.2 4.0 - - + -
115A LYS 2.3 35.3 + - - +
116A LEU* 2.9 7.2 - - + +
117A ALA 2.5 1.6 + - - -
118A TYR* 1.3 84.8 - - + +
120A TYR* 1.3 107.1 + + - -
122A LYS* 3.2 13.2 + - - +
123A ARG* 2.7 65.1 - - - +
269A PHE* 4.7 12.6 - + - -
279A LEU* 4.7 11.9 - - + -
281A THR* 5.9 3.6 - - - -
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Residues in contact with TYR 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A VAL* 2.4 48.5 + - - +
91A ASN* 4.4 8.7 - - - -
92A PRO* 5.3 4.5 - - + -
116A LEU* 3.1 29.6 + - + -
117A ALA* 2.5 14.4 + - - +
119A PHE* 1.3 112.5 - + - +
121A LYS* 1.3 58.8 + - - +
123A ARG* 2.6 48.7 - - + +
125A TYR* 3.3 21.6 + + + +
127A VAL* 4.8 8.5 - - + -
181A ILE* 5.4 20.6 - - + -
183A ILE* 6.3 0.2 - - + -
269A PHE* 4.1 5.3 - + - -
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Residues in contact with LYS 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A ALA 3.4 2.4 + - - -
118A TYR* 3.2 12.7 + - - +
120A TYR* 1.3 72.4 - - - +
122A LYS* 1.3 55.6 + - + +
123A ARG 2.7 5.8 + - - -
124A GLY* 2.5 27.7 + - - -
125A TYR 4.0 16.6 - - - +
127A VAL* 4.1 16.7 - - + +
150A ILE* 2.7 27.3 + - + +
151A GLY* 3.6 16.2 + - - -
152A VAL* 3.6 22.0 - - + -
148G ASN 5.3 0.4 + - - -
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Residues in contact with LYS 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A TYR* 3.5 37.8 + - + +
119A PHE* 3.2 10.1 + - - +
121A LYS* 1.3 76.9 - - + +
123A ARG* 1.3 69.2 - - - +
124A GLY 3.5 0.2 - - - -
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Residues in contact with ARG 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A VAL* 5.2 1.2 - - - +
91A ASN* 3.6 30.6 + - - +
119A PHE* 2.7 62.5 - - - +
120A TYR* 2.6 36.2 - - - +
122A LYS* 1.3 80.8 - - - +
124A GLY* 1.3 60.4 + - - +
125A TYR* 2.9 33.1 + - + -
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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
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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