Contacts of the helix formed by residues 159 - 169 (chain A) in PDB entry 1QAP
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 ARG 159 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152A ARG* 3.8 27.0 + - - +
154A THR* 3.1 35.7 + - - +
155A LEU 3.8 3.4 + - - -
157A GLY 3.1 3.0 + - - -
158A LEU* 1.3 77.9 - - - +
160A THR* 1.3 68.3 + - + +
162A LEU* 3.3 2.9 + - - +
163A LYS* 3.1 35.8 + - - +
176A LEU* 2.7 41.5 + - + +
177A GLY* 4.1 0.4 - - - -
29B ALA 5.3 0.4 + - - -
32B GLU* 3.2 49.8 + - + +
33B ASP* 3.0 36.6 + - - +
118B ARG* 5.2 1.0 - - - +
119B THR* 5.3 2.4 + - - -
122B ASN* 4.8 6.3 - - - +
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Residues in contact with THR 160 (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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14A LEU* 5.2 5.3 - - - +
17A ARG* 3.9 26.7 - - + +
18A ILE* 3.2 27.4 - - - +
21A ASP* 3.0 35.4 + - - +
157A GLY 4.7 1.9 + - - +
158A LEU 3.4 0.4 - - - -
159A ARG* 1.3 84.0 - - + +
161A ALA* 1.3 65.2 + - - +
163A LYS* 3.2 13.3 + - - +
164A TYR* 3.1 20.1 + - - +
176A LEU* 4.9 7.4 - - + -
32B GLU* 5.2 4.7 - - + +
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Residues in contact with ALA 161 (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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18A ILE* 4.1 1.8 - - - -
72A TRP* 3.6 36.1 - - + +
123A PHE* 6.3 0.7 - - + -
127A LEU* 3.8 26.1 - - + +
158A LEU* 3.1 20.5 + - + +
160A THR* 1.3 81.9 + - - +
162A LEU* 1.3 57.5 + - - +
164A TYR* 3.2 5.5 + - - +
165A ALA 3.0 21.7 + - - -
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Residues in contact with LEU 162 (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* 5.4 3.6 - - + -
127A LEU* 4.7 8.7 - - + -
130A VAL* 3.6 35.2 - - + +
154A THR* 3.5 31.0 - - + -
155A LEU* 3.5 30.1 - - + +
158A LEU* 2.8 31.3 + - + +
159A ARG 3.6 4.0 - - - +
161A ALA* 1.3 68.0 - - - +
163A LYS* 1.3 61.0 + - - +
164A TYR 3.1 1.8 - - - -
165A ALA* 3.3 4.9 + - - +
166A VAL* 2.9 35.5 + - - +
283A THR* 3.8 23.3 - - + +
286A VAL* 5.6 0.2 - - + -
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Residues in contact with LYS 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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14A LEU* 3.7 23.3 - - + -
150A ASP* 3.0 34.4 + - - +
151A THR 3.7 13.1 + - - -
152A ARG* 6.0 0.4 - - - +
154A THR* 5.6 2.9 - - + +
159A ARG* 3.1 27.8 + - - +
160A THR* 3.4 8.1 - - - +
162A LEU* 1.3 77.4 - - + +
164A TYR* 1.3 57.3 + - - +
166A VAL* 3.5 5.5 - - - +
167A LEU* 3.1 21.6 + - - +
173A ASN* 2.8 40.7 + - - +
174A HIS 3.8 9.2 - - - -
175A ARG 3.8 14.3 + - - -
176A LEU* 3.9 21.0 + - + +
283A THR* 5.7 0.4 - - + -
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Residues in contact with TYR 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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14A LEU* 5.7 0.4 - - - +
15A LEU* 4.6 13.5 - - + -
18A ILE* 3.6 28.5 - - + +
68A CYS* 3.5 23.8 - - - -
71A ARG* 5.9 1.2 - - + +
72A TRP* 3.2 28.5 - + + -
93A ASP* 3.0 37.9 + - - +
160A THR 3.1 10.4 + - - +
161A ALA* 3.2 12.6 - - - +
163A LYS* 1.3 75.3 - - - +
165A ALA* 1.3 59.3 + - - +
167A LEU* 2.9 21.2 - - + +
168A CYS* 2.9 37.4 + - - -
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Residues in contact with ALA 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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68A CYS* 3.7 17.5 - - - -
127A LEU* 3.3 33.9 - - + +
130A VAL* 4.2 8.3 - - + -
131A ALA* 3.5 14.6 - - + +
134A VAL* 4.7 0.2 - - - -
161A ALA 3.0 12.4 + - - +
162A LEU* 3.3 8.9 + - - +
164A TYR* 1.3 72.9 - - - +
166A VAL* 1.3 57.3 + - - +
168A CYS* 3.2 0.6 + - - +
169A GLY* 2.7 32.6 + - - -
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Residues in contact with VAL 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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130A VAL* 4.7 2.0 - - + -
134A VAL* 3.6 24.3 - - + +
149A LEU 5.4 0.4 - - - -
150A ASP* 4.0 24.2 - - + +
162A LEU 2.9 27.6 + - - +
163A LYS* 3.5 9.9 - - - +
164A TYR 3.2 0.2 - - - -
165A ALA* 1.3 77.1 - - - +
167A LEU* 1.3 60.6 + - - +
169A GLY 3.3 0.7 + - - -
170A GLY 3.1 5.2 + - - -
171A GLY* 2.8 44.1 + - - -
172A ALA 4.2 4.7 - - - +
173A ASN* 4.1 4.5 - - - +
282A LEU* 5.3 8.1 - - + -
283A THR* 3.5 25.6 - - + -
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Residues in contact with LEU 167 (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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11A ARG* 4.9 19.7 - - + +
14A LEU* 4.1 15.7 - - + -
15A LEU* 5.8 6.3 - - + -
163A LYS 3.1 6.7 + - - +
164A TYR* 2.9 28.2 + - + +
166A VAL* 1.3 79.6 - - - +
168A CYS* 1.3 56.6 + - - +
170A GLY* 3.0 20.1 + - - -
171A GLY 3.2 18.2 + - - +
172A ALA* 4.5 3.6 - - - -
173A ASN* 3.1 30.7 - - - +
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Residues in contact with CYS 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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66A VAL* 3.9 14.1 - - + +
67A PHE 4.3 0.7 - - - +
68A CYS* 3.4 31.0 - - + -
93A ASP 2.9 29.4 - - - +
94A GLY* 4.1 13.2 - - - +
131A ALA* 4.4 2.0 - - + -
135A ARG* 5.6 1.7 - - - -
164A TYR* 2.9 40.8 + - - -
165A ALA 3.7 4.7 - - - +
167A LEU* 1.3 73.2 - - - +
169A GLY* 1.3 59.7 + - - +
170A GLY* 3.2 0.7 + - - -
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Residues in contact with GLY 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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66A VAL* 4.9 0.2 - - - -
131A ALA* 3.3 25.5 - - - +
134A VAL* 3.7 9.2 - - - -
135A ARG* 3.2 35.5 + - - +
138A VAL* 3.8 2.6 - - - +
165A ALA 2.7 14.9 + - - -
166A VAL 3.3 3.8 + - - -
167A LEU 3.1 0.4 - - - -
168A CYS* 1.3 79.0 - - - +
170A GLY* 1.3 58.1 + - - +
171A GLY 3.7 1.1 - - - -
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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