Contacts of the helix formed by residues 162 - 174 (chain B) 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 SER 162 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154B VAL* 4.1 17.1 - - - +
158B GLY 3.5 11.9 - - - -
159B LEU 4.2 1.2 + - - -
160B LEU 3.8 1.2 - - - -
161B TYR* 1.3 77.3 - - - +
163B SER* 1.3 60.4 + - - +
164B GLN* 3.4 8.1 + - - +
165B VAL* 3.1 37.6 + - - +
166B ASN* 2.8 36.5 + - - +
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Residues in contact with SER 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B TYR* 5.6 0.2 - - - -
161B TYR 4.3 1.0 + - - -
162B SER* 1.3 71.4 + - - +
164B GLN* 1.3 65.7 + - - +
166B ASN* 3.3 13.7 + - - +
167B SER* 3.2 25.9 + - - -
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Residues in contact with GLN 164 (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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149B VAL* 6.1 0.4 - - - +
150B GLN 5.6 0.4 + - - -
151B ILE* 3.5 43.4 - - + +
152B HIS 4.6 7.6 + - - +
154B VAL* 4.9 2.8 - - + +
162B SER* 3.3 6.8 + - - +
163B SER* 1.3 82.0 + - - +
165B VAL* 1.3 63.6 + - + +
167B SER* 3.3 8.3 + - - -
168B LEU* 3.3 26.8 + - + +
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Residues in contact with VAL 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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22B ILE* 5.6 0.2 - - + -
102B LEU* 3.7 17.0 - - + -
128B ILE* 4.4 6.5 - - + -
151B ILE* 3.7 25.4 - - + -
159B LEU* 3.3 32.8 - - + +
162B SER* 3.1 29.5 + - - +
164B GLN* 1.3 75.9 - - - +
166B ASN* 1.3 67.5 + - - +
168B LEU* 2.9 12.4 + - - +
169B ILE* 2.9 38.4 + - + +
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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
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21B GLY 5.1 1.8 + - - -
22B ILE* 4.0 23.6 + - - +
25B TYR* 3.1 54.7 - - + +
159B LEU 5.6 0.2 - - - +
160B LEU 5.0 1.9 - - - +
161B TYR* 5.0 1.6 - - - +
162B SER 2.8 36.3 + - - +
163B SER* 3.3 11.0 + - - +
165B VAL* 1.3 74.2 - - - +
167B SER* 1.3 56.3 + - - +
169B ILE* 3.1 9.9 + - - +
170B LYS 2.9 24.3 + - - -
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Residues in contact with SER 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B TYR* 3.7 14.5 + - - -
163B SER 3.2 11.2 + - - -
164B GLN* 3.6 10.5 - - - -
165B VAL 3.2 0.2 - - - -
166B ASN* 1.3 78.9 - - - +
168B LEU* 1.3 61.4 + - - +
170B LYS* 3.5 4.5 + - - +
171B GLU* 3.1 30.0 + - - +
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Residues in contact with LEU 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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126B THR* 4.5 8.5 - - + +
128B ILE* 3.4 44.9 - - + -
147B ARG* 3.7 28.7 + - - +
149B VAL* 3.7 25.6 - - + -
151B ILE* 4.0 11.4 - - + -
164B GLN* 3.5 19.3 - - + +
165B VAL* 2.9 5.2 + - - +
167B SER* 1.3 76.6 - - - +
169B ILE* 1.3 66.5 + - - +
171B GLU* 3.2 11.5 + - - +
172B GLY* 2.9 20.4 + - - -
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Residues in contact with ILE 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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22B ILE* 3.8 39.0 - - + -
25B TYR* 5.3 0.7 - - + -
26B LEU* 4.3 10.1 - - + -
74B VAL* 4.1 15.5 - - + -
100B VAL* 4.1 13.7 - - + +
102B LEU* 4.1 16.4 - - + -
128B ILE* 4.4 0.4 - - + -
165B VAL* 2.9 38.2 + - + +
166B ASN* 3.4 12.6 - - - +
168B LEU* 1.3 77.0 - - - +
170B LYS* 1.3 57.0 + - - +
172B GLY* 3.3 0.5 + - - -
173B LEU* 2.9 53.0 + - + +
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Residues in contact with LYS 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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25B TYR* 3.6 32.3 - - + +
26B LEU* 4.9 1.3 - - - -
29B GLN* 3.0 34.9 + - + +
31B TRP* 4.0 18.6 - - + -
166B ASN 2.9 6.2 + - - +
167B SER* 3.6 7.0 - - - +
169B ILE* 1.3 79.0 - - - +
171B GLU* 1.3 63.7 + - + +
173B LEU* 3.4 1.3 + - - +
174B ASN* 3.1 43.2 + - - +
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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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180A THR* 3.9 33.6 + - + +
147B ARG* 2.9 39.4 + - - +
167B SER* 3.1 17.7 - - - +
168B LEU* 3.2 14.7 + - - +
170B LYS* 1.3 78.5 - - + +
172B GLY* 1.3 55.0 + - - +
174B ASN* 3.3 11.6 + - - +
175B GLY 3.6 0.3 + - - -
176B GLY* 2.7 31.9 + - - -
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Residues in contact with GLY 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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98B ASN* 3.5 15.8 - - - +
99B VAL 5.7 0.2 - - - -
100B VAL* 3.8 13.5 - - - -
126B THR* 3.7 23.7 + - - -
147B ARG* 5.1 0.4 - - - +
168B LEU 2.9 13.2 + - - -
169B ILE 3.7 2.5 - - - -
171B GLU* 1.3 77.6 - - - +
173B LEU* 1.3 56.3 + - - +
175B GLY* 3.0 16.1 + - - -
176B GLY 3.5 6.4 + - - -
177B GLY 4.3 2.9 + - - -
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Residues in contact with LEU 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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3B HIS* 4.7 4.5 - - - -
6B VAL* 4.1 15.0 - - + -
26B LEU* 3.8 29.8 - - + -
31B TRP* 3.5 21.7 + - + +
72B ASP* 3.5 34.7 - - + +
73B ILE 4.6 4.0 - - - +
74B VAL* 4.0 18.6 - - + -
98B ASN* 3.3 19.1 + - + -
100B VAL* 4.5 9.0 - - + -
169B ILE* 2.9 40.4 + - + +
170B LYS 4.0 0.2 - - - +
172B GLY* 1.3 72.4 - - - +
174B ASN* 1.3 60.2 + - - +
175B GLY 3.1 1.1 - - - -
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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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122A LYS* 3.0 27.1 + - - +
180A THR 5.7 2.0 - - - +
181A ASN 4.9 3.8 - - - +
3B HIS* 2.8 32.2 + - - -
31B TRP* 3.6 14.1 - - - -
98B ASN* 4.5 0.4 - - - -
170B LYS* 3.1 39.2 + - - +
171B GLU* 3.9 5.6 - - - +
172B GLY 3.1 1.0 - - - -
173B LEU* 1.3 75.6 - - - +
175B GLY* 1.3 58.1 + - - +
176B GLY 3.4 1.3 - - - -
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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