Contacts of the helix formed by residues 162 - 174 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154A VAL* 4.0 17.0 - - - +
158A GLY 3.6 10.8 - - - -
159A LEU 4.4 1.2 + - - -
160A LEU 3.8 1.2 - - - -
161A TYR* 1.3 77.1 - - - +
163A SER* 1.3 59.3 + - - +
164A GLN* 3.4 8.8 + - - +
165A VAL* 3.2 36.4 + - - +
166A ASN* 2.9 37.5 + - - +
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Residues in contact with SER 163 (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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25A TYR* 5.6 0.3 - - - -
162A SER* 1.3 71.7 + - - +
164A GLN* 1.3 62.2 + - - +
166A ASN* 3.2 10.5 + - - +
167A SER* 3.0 27.0 + - - -
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Residues in contact with GLN 164 (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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151A ILE* 3.7 38.9 - - + +
152A HIS 4.6 8.1 + - - +
154A VAL* 5.5 1.7 - - + +
162A SER* 3.3 6.8 + - - +
163A SER* 1.3 80.5 - - - +
165A VAL* 1.3 64.1 + - + +
167A SER* 3.4 6.9 + - - -
168A LEU* 3.3 27.7 + - + +
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Residues in contact with VAL 165 (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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102A LEU* 3.9 27.6 - - + -
128A ILE* 4.3 6.7 - - + -
151A ILE* 3.5 25.8 - - + -
159A LEU* 3.4 32.8 - - + +
162A SER* 3.2 28.5 + - - +
164A GLN* 1.3 75.8 - - - +
166A ASN* 1.3 60.6 + - - +
168A LEU* 3.0 11.6 + - - +
169A ILE* 2.8 34.4 + - + +
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Residues in contact with ASN 166 (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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21A GLY 4.6 5.5 + - - -
22A ILE* 3.8 22.7 - - - +
25A TYR* 3.1 59.3 - - + +
159A LEU 5.4 0.2 - - - +
160A LEU 5.0 1.4 + - - +
161A TYR* 5.5 1.8 - - - +
162A SER 2.9 30.0 + - - +
163A SER* 3.2 10.0 + - - +
165A VAL* 1.3 77.8 - - - +
167A SER* 1.3 62.8 + - - +
169A ILE* 3.1 9.2 + - - +
170A LYS 2.9 18.7 + - - -
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Residues in contact with SER 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A TYR* 3.6 13.8 + - - -
163A SER 3.0 14.4 + - - -
164A GLN* 3.7 10.7 - - - -
166A ASN* 1.3 75.4 - - - +
168A LEU* 1.3 63.8 + - - +
170A LYS* 3.4 6.8 - - - +
171A GLU* 3.2 27.4 + - - +
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Residues in contact with LEU 168 (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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126A THR* 4.6 8.7 - - + +
128A ILE* 3.5 27.4 - - + -
147A ARG* 3.6 30.1 - - - +
149A VAL* 3.8 28.5 - - + -
151A ILE* 3.9 20.0 - - + -
164A GLN* 3.3 19.0 + - + +
165A VAL 3.0 7.9 + - - +
167A SER* 1.3 77.2 - - - +
169A ILE* 1.3 66.3 + - - +
171A GLU* 3.2 13.0 + - - +
172A GLY* 2.9 19.8 + - - -
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Residues in contact with ILE 169 (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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22A ILE* 3.7 39.5 - - + -
25A TYR* 5.3 0.7 - - + -
26A LEU* 4.2 13.9 - - + -
74A VAL* 4.2 13.7 - - + -
100A VAL* 4.0 24.7 - - + +
102A LEU* 4.0 13.5 - - + -
128A ILE* 4.2 0.4 - - + -
165A VAL* 2.8 28.8 + - + +
166A ASN* 3.1 12.5 + - - +
168A LEU* 1.3 75.1 - - - +
170A LYS* 1.3 58.7 + - - +
172A GLY* 3.2 1.7 + - - -
173A LEU* 2.9 51.5 + - + +
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Residues in contact with LYS 170 (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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25A TYR* 3.6 28.7 - - + +
26A LEU* 4.8 1.6 - - - -
29A GLN* 2.9 35.8 + - + +
31A TRP* 3.9 19.7 - - + -
166A ASN 2.9 6.0 + - - +
167A SER* 3.4 10.8 - - - +
168A LEU 3.2 0.2 - - - -
169A ILE* 1.3 79.1 - - - +
171A GLU* 1.3 64.6 + - + +
173A LEU* 3.3 1.9 + - - +
174A ASN* 3.0 47.4 + - - +
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Residues in contact with GLU 171 (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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147A ARG* 2.8 40.4 + - - +
167A SER* 3.2 15.1 + - - +
168A LEU* 3.2 16.2 + - - +
170A LYS* 1.3 78.3 - - + +
172A GLY* 1.3 56.0 + - - +
174A ASN* 3.3 12.1 + - - +
175A GLY 3.5 0.2 + - - -
176A GLY* 2.7 31.3 + - - -
122B LYS* 5.3 0.3 + - - -
180B THR* 3.8 31.5 + - - +
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Residues in contact with GLY 172 (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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98A ASN* 3.5 15.3 - - - +
100A VAL* 3.9 13.9 - - - -
124A LEU* 5.9 0.2 - - - +
126A THR* 3.7 23.8 + - - -
147A ARG* 5.0 0.4 - - - +
168A LEU 2.9 11.3 + - - -
169A ILE 3.7 2.9 - - - -
171A GLU* 1.3 77.0 - - - +
173A LEU* 1.3 56.2 + - - +
175A GLY* 3.0 18.4 + - - -
176A GLY 3.5 4.3 + - - -
177A GLY 4.3 2.7 + - - -
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Residues in contact with LEU 173 (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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3A HIS* 4.6 5.7 - - - -
6A VAL* 4.1 12.3 - - + -
26A LEU* 3.7 35.7 - - + -
31A TRP* 3.6 21.4 - - + +
72A ASP* 3.6 36.6 - - + +
73A ILE 4.5 4.0 - - - +
74A VAL* 4.0 19.7 - - + -
98A ASN* 3.4 19.1 + - + +
100A VAL* 4.2 9.8 - - + +
169A ILE* 2.9 33.9 + - + +
170A LYS 4.0 0.2 - - - +
172A GLY* 1.3 72.1 - - - +
174A ASN* 1.3 59.6 + - - +
175A GLY 3.1 1.1 - - - -
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Residues in contact with ASN 174 (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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3A HIS* 3.0 28.3 + - - -
31A TRP* 3.7 14.8 - - - -
98A ASN* 4.8 0.2 - - - -
170A LYS* 3.0 38.4 + - - +
171A GLU* 3.8 6.2 - - - +
172A GLY 3.1 0.6 - - - -
173A LEU* 1.3 74.5 - - - +
175A GLY* 1.3 57.8 + - - +
176A GLY 3.5 1.3 - - - -
122B LYS* 2.8 30.6 + - - +
180B THR 5.7 2.2 - - - +
181B ASN 5.1 3.8 - - - +
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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