Contacts of the helix formed by residues 155 - 174 (chain B) in PDB entry 1QZG
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 GLY 155 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154B THR* 1.3 79.9 + - - +
156B ASP* 1.3 62.3 + - - -
157B LYS 3.4 2.9 - - - -
158B GLU* 3.7 7.5 + - - -
159B GLU* 3.3 24.1 + - - +
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Residues in contact with ASP 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155B GLY* 1.3 70.5 - - - -
157B LYS* 1.3 60.7 + - - +
159B GLU* 3.5 12.9 - - - +
160B GLN* 2.6 61.7 + - - +
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Residues in contact with LYS 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B ASP* 4.6 3.4 - - - +
22B ILE* 3.9 14.6 - - + +
23B GLY* 5.1 6.3 - - - +
155B GLY* 3.4 1.4 - - - -
156B ASP* 1.3 76.7 - - - +
158B GLU* 1.3 77.0 + - - +
160B GLN* 3.6 6.6 + - - +
161B PHE* 3.5 14.4 + - - +
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Residues in contact with GLU 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B ILE* 3.6 25.6 - - + +
23B GLY* 3.9 17.9 + - - -
24B GLU 5.0 0.5 + - - -
25B LEU* 6.1 0.9 - - - +
46B PHE* 3.7 7.9 - - + -
106B LEU* 3.9 22.7 - - + -
132B TRP* 3.8 21.5 - - + -
152B MET* 5.4 3.3 - - + +
154B THR* 3.9 24.3 - - + +
155B GLY 3.7 4.7 + - - +
156B ASP 3.3 0.4 - - - -
157B LYS* 1.3 90.9 + - - +
159B GLU* 1.3 64.1 + - - +
161B PHE 3.4 0.7 + - - -
162B ALA* 3.0 25.3 + - - +
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Residues in contact with GLU 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B TRP* 2.8 37.6 + - - +
133B PRO* 5.6 0.5 - - - +
135B PHE* 3.9 15.1 - - - -
154B THR* 5.1 1.9 + - - -
155B GLY 3.3 16.1 + - - +
156B ASP* 3.2 25.3 + - - +
158B GLU* 1.3 80.5 - - - +
160B GLN* 1.3 65.1 + - - +
162B ALA* 3.4 3.3 + - - +
163B LEU* 3.1 29.7 + - + +
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Residues in contact with GLN 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B ASP* 2.8 32.7 - - - +
156B ASP* 2.6 54.8 + - - +
157B LYS* 3.9 4.3 - - - +
158B GLU 3.3 0.2 - - - -
159B GLU* 1.3 79.2 - - - +
161B PHE* 1.3 58.0 + - - +
163B LEU* 3.2 22.5 + - - +
164B LEU* 3.0 23.7 + - - +
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Residues in contact with PHE 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B ASP* 3.1 12.3 + - - +
10B GLN* 3.9 22.9 - - + -
11B LEU* 4.4 12.3 - - + -
14B LEU* 4.2 17.9 - - + -
20B TYR* 3.3 38.1 - + - -
22B ILE* 3.9 17.9 - - + -
46B PHE* 3.7 20.4 - + + -
157B LYS 3.5 9.8 + - - +
158B GLU 3.4 7.3 + - - +
159B GLU 3.3 0.2 - - - -
160B GLN* 1.3 76.1 - - - +
162B ALA* 1.3 61.0 + - - +
164B LEU* 3.1 16.2 + - + +
165B LEU* 2.8 68.9 + - + +
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Residues in contact with ALA 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B PHE* 4.0 9.1 - - + -
104B PRO* 3.5 20.0 - - + +
132B TRP* 3.6 35.7 - - + -
135B PHE* 4.0 4.0 - - + -
158B GLU 3.0 18.1 + - - +
159B GLU 3.7 5.2 - - - +
161B PHE* 1.3 76.8 - - - +
163B LEU* 1.3 62.9 + - - +
165B LEU* 3.3 3.6 + - - +
166B ASN* 3.0 25.5 + - - +
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Residues in contact with LEU 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135B PHE* 3.8 41.7 - - + -
159B GLU* 3.1 24.3 + - + +
160B GLN* 3.2 32.3 - - - +
161B PHE 3.1 0.2 - - - -
162B ALA* 1.3 77.1 - - - +
164B LEU* 1.3 57.0 + - - +
166B ASN* 3.3 3.6 + - - +
167B LYS* 2.8 30.8 + - + +
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Residues in contact with LEU 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B ASP* 3.8 37.0 - - + +
8B SER* 4.7 2.0 - - - +
11B LEU* 4.1 25.1 - - + -
160B GLN 3.0 13.6 + - - +
161B PHE* 3.5 16.6 - - + +
163B LEU* 1.3 73.0 - - - +
165B LEU* 1.3 70.4 + - + +
167B LYS* 3.0 8.9 + - + +
168B ILE* 2.8 44.3 + - + +
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Residues in contact with LEU 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B LEU* 5.9 0.4 - - + -
14B LEU* 4.9 0.2 - - + -
46B PHE* 3.7 35.7 - - + +
47B GLY* 4.0 7.6 - - - +
48B ILE* 3.6 23.0 - - + +
72B TRP* 4.2 2.9 - - + +
73B ASP* 4.7 4.0 - - + -
74B PRO* 3.7 33.9 - - + -
161B PHE* 2.8 59.0 + - + +
162B ALA* 3.5 5.6 - - - +
164B LEU* 1.3 75.3 - - + +
166B ASN* 1.3 58.0 + - - +
168B ILE* 3.4 5.5 + - + +
169B TRP* 2.9 28.6 + - - +
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Residues in contact with ASN 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B ILE* 3.7 6.4 - - - +
102B GLY 2.7 27.1 + - - -
104B PRO* 4.0 8.9 - - + +
134B ASP* 3.0 22.3 + - - +
135B PHE* 3.6 15.4 - - + +
136B SER* 2.6 36.7 + - - -
162B ALA 3.0 17.9 + - - +
163B LEU 3.6 4.4 - - - +
165B LEU* 1.3 74.3 - - - +
167B LYS* 1.3 59.8 + - - +
169B TRP* 3.2 10.6 + - - +
170B ASP* 2.8 28.9 + - - +
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Residues in contact with LYS 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136B SER* 4.6 2.5 - - - -
163B LEU* 2.8 20.2 + - + +
164B LEU* 3.5 13.0 - - + +
166B ASN* 1.3 74.4 + - - +
168B ILE* 1.3 58.3 + - + +
170B ASP* 3.4 5.1 + - - +
171B GLU* 2.9 30.4 + - - +
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Residues in contact with ILE 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B LEU* 3.8 37.9 - - + -
15B LEU* 6.3 0.2 - - + -
72B TRP* 3.8 12.1 - - + -
74B PRO* 4.0 16.6 - - + -
164B LEU* 2.8 34.0 + - + +
165B LEU* 3.7 5.2 - - + +
167B LYS* 1.3 73.2 - - + +
169B TRP* 1.3 67.1 + - - +
171B GLU* 3.8 5.3 - - - +
172B GLN* 3.0 46.8 + - + +
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Residues in contact with TRP 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B ILE* 3.9 19.1 - - + +
50B LYS* 4.4 27.0 - - + +
72B TRP* 3.8 30.5 - + + -
101B VAL* 3.8 24.3 - - + +
102B GLY* 3.5 33.2 - - - -
134B ASP* 3.7 19.1 - - - -
136B SER* 4.8 1.3 - - - -
165B LEU 2.9 17.9 + - - +
166B ASN* 3.5 13.7 - - - +
168B ILE* 1.3 79.1 - - - +
170B ASP* 1.3 81.8 + - + +
172B GLN* 3.3 2.5 + - + +
173B THR* 2.8 57.0 + - + -
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Residues in contact with ASP 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136B SER* 3.1 38.5 + - - +
166B ASN 2.8 14.7 + - - +
167B LYS* 3.7 3.8 - - - +
169B TRP* 1.3 87.2 - - + +
171B GLU* 1.3 56.9 + - - +
173B THR* 3.1 5.5 + - - +
174B ASN* 2.6 56.1 + - - +
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Residues in contact with GLU 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167B LYS 2.9 17.9 + - - +
168B ILE* 3.8 6.1 - - - +
169B TRP 3.3 0.2 - - - -
170B ASP* 1.3 78.1 + - - +
172B GLN* 1.3 63.0 + - + +
173B THR 3.3 1.0 + - - -
174B ASN* 3.7 20.4 - - - -
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Residues in contact with GLN 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B TRP* 3.8 18.3 - - + -
74B PRO* 5.1 7.3 + - - +
76B CYS 4.5 4.2 + - - +
77B ASP* 4.8 0.9 - - - -
78B THR* 3.7 43.0 + - - -
168B ILE* 3.0 36.5 + - + +
169B TRP* 3.6 5.4 - - + +
171B GLU* 1.3 77.8 - - + +
173B THR* 1.3 60.7 + - - +
174B ASN 5.0 0.2 - - - -
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Residues in contact with THR 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B LYS* 5.4 2.1 + - - -
78B THR* 6.0 0.2 - - - -
169B TRP* 2.8 55.1 + - + -
170B ASP* 3.1 9.8 + - - +
172B GLN* 1.3 82.0 - - - +
174B ASN* 1.3 66.6 + - + +
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Residues in contact with ASN 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170B ASP* 2.6 50.1 + - - +
171B GLU* 3.7 16.1 - - - +
172B GLN 5.0 0.2 - - - -
173B THR* 1.3 84.2 - - + +
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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
------------------------------------------------------------
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