Contacts of the helix formed by residues 152 - 162 (chain A) in PDB entry 1QZZ
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 ASP 152 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143A ARG* 5.3 3.8 - - - +
148A ASP* 3.0 14.8 + - - +
149A LEU 3.1 7.8 - - - +
150A SER 3.3 0.8 - - - -
151A ALA* 1.3 79.8 - - + +
153A VAL* 1.3 63.8 + - - +
154A ALA* 2.9 24.5 + - - +
155A LEU* 3.0 32.0 + - + +
156A ALA 3.0 18.5 + - - -
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Residues in contact with VAL 153 (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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150A SER 5.0 3.8 + - - +
151A ALA 4.8 5.8 - - - +
152A ASP* 1.3 73.0 + - - +
154A ALA* 1.3 57.8 + - - +
156A ALA* 4.1 7.9 - - + -
157A ASP* 2.8 55.0 + - - +
219A GLU* 5.4 8.5 - - - +
220A ARG* 5.6 7.4 - - + +
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Residues in contact with ALA 154 (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 ASN 4.9 7.2 - - - +
152A ASP* 2.9 11.6 + - - +
153A VAL* 1.3 77.5 - - - +
155A LEU* 1.3 59.4 + - + +
157A ASP* 4.4 2.5 - - - +
158A SER* 3.0 30.5 + - - -
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Residues in contact with LEU 155 (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 ASN 3.7 21.3 - - - +
114A GLY 4.1 0.9 - - - -
115A ALA* 3.3 24.9 - - + +
118A HIS* 4.1 22.2 - - + +
137A TYR* 4.1 7.4 - - - +
148A ASP* 3.4 28.3 - - - +
149A LEU* 3.8 18.4 - - + -
152A ASP* 3.0 35.8 + - + +
154A ALA* 1.3 75.9 - - + +
156A ALA* 1.3 56.2 + - - +
158A SER* 2.8 5.1 + - - -
159A PHE* 2.8 31.5 + - - +
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Residues in contact with ALA 156 (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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149A LEU* 3.2 36.9 + - + +
152A ASP 3.0 7.3 + - - +
153A VAL* 3.8 9.0 - - + +
155A LEU* 1.3 78.3 - - - +
157A ASP* 1.3 63.3 + - - +
159A PHE* 3.7 1.4 - - - +
160A ASP* 3.0 28.8 + - - +
220A ARG* 3.5 29.4 - - - +
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Residues in contact with ASP 157 (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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153A VAL* 2.8 39.6 + - - +
154A ALA* 4.4 2.2 - - - +
156A ALA* 1.3 72.5 - - - +
158A SER* 1.3 58.0 + - - +
160A ASP* 3.3 5.8 + - - +
161A ALA* 2.8 32.3 + - - +
220A ARG* 3.4 26.0 + - - -
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Residues in contact with SER 158 (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 ASN 5.0 0.2 - - - -
114A GLY* 3.5 18.0 - - - -
115A ALA* 2.8 22.7 + - - -
116A VAL* 5.9 0.4 - - - -
154A ALA 3.0 17.5 + - - -
155A LEU* 2.8 18.7 + - - -
157A ASP* 1.3 75.7 - - - +
159A PHE* 1.3 64.6 + - - +
161A ALA* 3.5 12.1 + - - +
162A LEU* 3.8 19.4 + - - +
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Residues in contact with PHE 159 (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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115A ALA* 3.6 9.2 - - + -
116A VAL* 4.1 19.7 - - + -
145A PHE* 3.6 26.7 - + - -
146A TRP* 3.5 29.6 - + - -
149A LEU* 3.3 31.6 - - + -
155A LEU 2.8 11.7 + - - +
156A ALA 3.7 0.7 - - - +
158A SER* 1.3 76.9 + - - +
160A ASP* 1.3 74.6 + - - +
162A LEU* 3.4 7.4 + - - +
163A MET* 3.5 50.0 - - + +
311A PHE* 5.3 7.0 - + - -
312A MET* 4.8 7.2 - - + -
635A SAM 5.7 2.5 - - + -
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Residues in contact with ASP 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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146A TRP* 5.9 1.4 - - - -
149A LEU* 6.3 0.2 - - - -
156A ALA 3.0 14.3 + - - +
157A ASP* 3.7 6.3 - - - +
159A PHE* 1.3 89.3 - - - +
161A ALA* 1.3 62.4 + - - +
162A LEU 3.0 2.0 + - - -
163A MET* 3.1 16.2 + - - +
166A ASP* 3.2 34.4 - - + +
193A ASN* 4.0 14.5 - - - +
220A ARG* 2.7 32.4 + - - -
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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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105A GLN* 3.9 18.9 + - - +
157A ASP 2.8 21.2 + - - +
158A SER* 4.0 7.9 - - - +
159A PHE 3.3 1.2 - - - -
160A ASP* 1.3 71.3 - - - +
162A LEU* 1.3 62.4 + - + +
163A MET 3.4 2.3 + - - +
166A ASP* 4.1 10.3 - - - +
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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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105A GLN* 3.8 22.8 - - + +
108A ALA* 3.8 29.6 - - + +
109A TRP* 3.5 77.4 + - + +
116A VAL* 3.9 16.6 - - + -
158A SER 3.8 12.6 - - - +
159A PHE 3.4 6.9 + - - +
160A ASP 3.0 1.4 + - - -
161A ALA* 1.3 81.8 - - + +
163A MET* 1.3 67.3 + - + +
164A SER 4.0 1.0 + - - -
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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