Contacts of the helix formed by residues 142 - 155 (chain A) in PDB entry 1QWN
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 142 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140A ASP 3.8 1.6 + - - -
141A LEU* 1.3 79.2 - - - +
143A GLU* 1.3 60.7 + - - -
144A ASN 3.3 3.1 - - - -
145A LYS* 3.2 9.5 + - - +
146A LYS* 2.9 24.6 + - - +
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Residues in contact with GLU 143 (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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141A LEU 3.9 0.4 + - - -
142A GLY* 1.3 71.4 - - - -
144A ASN* 1.3 62.3 + - - +
146A LYS* 3.2 24.7 + - - +
147A LEU* 3.0 45.3 + - + +
150A LYS* 4.8 7.8 + - - -
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Residues in contact with ASN 144 (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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142A GLY 3.3 0.8 - - - -
143A GLU* 1.3 78.5 - - - +
145A LYS* 1.3 74.7 + - + +
147A LEU* 3.3 10.8 + - - +
148A GLN* 3.0 46.4 + - - +
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Residues in contact with LYS 145 (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 LEU* 3.8 15.2 - - + +
141A LEU* 3.9 25.6 - - + -
142A GLY* 3.2 12.3 + - - +
144A ASN* 1.3 90.4 + - + +
146A LYS* 1.3 59.1 + - - +
148A GLN* 3.2 30.3 + - - +
149A MET* 2.9 30.1 + - - +
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Residues in contact with LYS 146 (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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138A TYR* 3.3 67.0 + - + +
139A HIS* 3.3 19.4 + - - +
141A LEU* 2.6 31.8 + - + +
142A GLY 2.9 15.1 + - - +
143A GLU* 3.6 31.7 + - - +
145A LYS* 1.3 73.9 - - - +
147A LEU* 1.3 57.5 + - - +
149A MET* 3.2 3.7 + - - +
150A LYS* 2.9 34.9 + - - +
192A PHE* 6.5 0.2 - - - -
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Residues in contact with LEU 147 (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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143A GLU* 3.0 37.8 + - + +
144A ASN* 3.6 9.9 - - - +
146A LYS* 1.3 72.9 - - - +
148A GLN* 1.3 65.9 + - - +
150A LYS* 3.3 28.3 + - + +
151A SER* 3.0 23.0 + - - -
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Residues in contact with GLN 148 (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 LEU* 3.8 18.1 - - + +
116A ARG* 5.8 1.0 - - - -
119A HIS* 3.9 40.1 + - + +
144A ASN* 3.0 36.9 + - - +
145A LYS* 3.2 29.6 + - - +
147A LEU* 1.3 74.8 - - + +
149A MET* 1.3 61.0 + - - +
151A SER* 2.6 24.7 + - - -
152A ILE* 3.1 13.0 + - - +
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Residues in contact with MET 149 (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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111A LEU* 4.4 6.7 - - + +
114A ALA* 6.3 0.4 - - + -
115A LEU* 3.6 24.4 - - + +
134A PHE* 3.6 33.4 - - + -
137A PHE* 3.8 28.5 - - + -
138A TYR* 4.3 8.5 - - + -
141A LEU* 4.4 3.8 - - + -
145A LYS 2.9 16.8 + - - +
146A LYS* 3.5 5.6 - - - +
148A GLN* 1.3 73.8 - - - +
150A LYS* 1.3 66.2 + - - +
152A ILE* 3.3 14.7 + - - +
153A VAL* 3.2 25.0 + - - +
158A LEU* 3.5 29.2 - - + -
193A MET* 4.0 10.8 - - + -
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Residues in contact with LYS 150 (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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138A TYR* 2.8 21.7 + - - -
143A GLU* 4.8 8.3 + - - -
146A LYS* 2.9 19.2 + - - +
147A LEU* 3.3 27.8 + - + +
149A MET* 1.3 76.0 - - - +
151A SER* 1.3 56.9 + - - +
153A VAL* 3.4 2.1 + - - +
154A LYS* 2.8 31.8 + - - +
192A PHE* 3.7 17.3 - - - +
193A MET* 3.6 28.7 - - + +
2001A NAG 6.5 0.9 - - + -
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Residues in contact with SER 151 (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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119A HIS* 5.4 4.0 - - - -
147A LEU 3.0 13.2 + - - -
148A GLN* 2.6 24.1 + - - -
150A LYS* 1.3 77.6 - - - +
152A ILE* 1.3 61.6 + - - +
154A LYS* 3.9 6.9 - - - +
155A ASN* 2.9 35.3 + - - +
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Residues in contact with ILE 152 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114A ALA 5.0 0.2 - - - -
115A LEU* 3.8 24.7 - - + +
118A LEU* 3.9 31.4 - - + -
119A HIS* 4.2 25.1 - - + +
148A GLN 3.1 11.2 + - - +
149A MET* 3.4 26.7 - - - +
151A SER* 1.3 84.9 + - - +
153A VAL* 1.3 57.8 + - - +
155A ASN* 2.7 23.4 - - - +
157A GLN* 3.0 38.2 + - + +
158A LEU* 3.1 11.7 + - + -
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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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149A MET* 3.2 18.0 + - + +
150A LYS 3.7 3.4 - - - +
152A ILE* 1.3 76.3 - - - +
154A LYS* 1.3 65.7 + - - +
156A GLY* 3.1 13.9 + - - -
158A LEU* 3.5 40.0 - - + +
160A PHE* 3.8 22.0 - - + -
193A MET* 3.8 28.0 - - - +
195A VAL* 4.0 29.3 - - + +
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Residues in contact with LYS 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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150A LYS 2.8 19.1 + - - +
151A SER* 3.9 5.6 - - - +
153A VAL* 1.3 82.0 - - - +
155A ASN* 1.3 58.4 + - - +
156A GLY 3.3 0.9 + - - -
193A MET 6.1 0.9 - - - +
194A ASN* 4.6 1.4 - - - +
195A VAL* 5.7 3.4 - - - -
2001A NAG 4.1 44.8 + - - +
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Residues in contact with ASN 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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122A PRO* 6.3 0.2 - - - +
125A LYS* 5.9 0.7 - - - -
151A SER* 2.9 19.7 + - - +
152A ILE* 2.7 24.9 - - - +
154A LYS* 1.3 75.8 - - - +
156A GLY* 1.3 56.7 + - - +
157A GLN* 2.9 36.7 + - - +
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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