Contacts of the helix formed by residues 145 - 155 (chain A) in PDB entry 1QS0
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 145 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143A ASP 3.9 1.6 + - - -
144A VAL* 1.3 75.3 - - - +
146A LEU* 1.3 62.5 + - - +
147A VAL* 3.3 12.3 + - - +
148A GLU* 3.2 43.1 + - - +
149A MSE 3.2 22.3 + - - +
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Residues in contact with LEU 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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86A LYS* 4.0 21.5 - - + +
90A PHE* 3.8 16.8 - - + -
140A MSE 3.8 37.7 - - + -
144A VAL 3.2 3.5 + - - +
145A SER* 1.3 71.6 + - - +
147A VAL* 1.3 58.3 + - - +
149A MSE 3.4 8.3 + - - +
150A ILE* 3.0 36.1 + - - +
361A PHE* 6.1 0.4 - - + -
364A ALA* 4.1 34.1 - - + +
365A VAL* 4.3 11.7 - - + -
368A ALA* 3.6 15.3 - - + -
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Residues in contact with VAL 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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145A SER* 3.2 9.5 + - - +
146A LEU* 1.3 78.6 - - + +
148A GLU* 1.3 61.2 + - + +
151A CYS* 3.0 40.2 + - - -
158A ARG* 5.9 2.2 - - + -
368A ALA* 4.0 15.3 - - + +
371A GLU* 3.0 40.4 - - + +
372A ALA* 3.9 13.3 - - - +
375A TYR* 5.2 6.5 - - + -
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Residues in contact with GLU 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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144A VAL* 5.3 6.0 - - + +
145A SER* 3.2 28.5 + - - +
147A VAL* 1.3 77.6 - - + +
149A MSE 1.3 67.9 + - + +
151A CYS* 4.4 4.7 - - - -
152A GLN* 3.3 15.8 + - - +
158A ARG* 5.6 3.1 - - + +
160A PRO* 3.7 31.8 - - + +
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Residues in contact with MSE 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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90A PHE* 4.1 20.6 - - + -
136A GLN* 4.4 12.1 - - + -
139A LEU* 3.6 40.8 - - + -
140A MSE 4.2 20.0 - - - +
144A VAL* 4.3 17.5 - - + +
145A SER 3.2 20.6 + - - +
146A LEU* 3.7 13.0 - - - +
147A VAL 3.3 0.2 - - - -
148A GLU* 1.3 77.6 - - - +
150A ILE* 1.3 63.1 + - - +
152A GLN* 3.1 15.0 + - - +
153A LEU* 3.1 17.2 + - - +
170A TYR* 3.8 37.3 - - + +
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Residues in contact with ILE 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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90A PHE* 3.5 20.9 - - + -
94A MSE 3.3 33.9 - - + -
103A MSE 4.9 0.7 - - + -
146A LEU 3.0 17.8 + - - +
149A MSE 1.3 76.8 - - - +
151A CYS* 1.3 62.2 + - - +
153A LEU* 2.9 12.6 + - - +
154A LEU* 3.0 23.6 + - + +
365A VAL* 4.3 3.4 - - + +
368A ALA* 3.7 11.4 - - + -
369A GLN* 3.5 41.1 - - + +
372A ALA* 3.5 21.1 - - + -
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Residues in contact with CYS 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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147A VAL* 3.0 32.1 + - - +
148A GLU* 3.7 6.5 - - - +
149A MSE 3.3 0.2 - - - -
150A ILE* 1.3 75.5 - - - +
152A GLN* 1.3 52.3 + - - +
154A LEU 3.0 1.9 + - - -
155A SER* 2.8 30.5 + - - -
156A ASN* 3.3 33.6 + - - +
158A ARG* 3.6 44.9 - - - +
159A ASP* 3.7 2.8 - - - +
372A ALA* 3.8 16.8 - - - -
375A TYR* 4.6 1.3 - - - -
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Residues in contact with GLN 152 (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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148A GLU 3.3 8.8 + - - +
149A MSE 3.1 10.6 + - - +
151A CYS* 1.3 78.0 - - - +
153A LEU* 1.3 67.9 + - - +
154A LEU 3.1 1.1 + - - -
155A SER* 3.5 5.9 + - - -
159A ASP* 3.0 31.8 + - - +
160A PRO* 4.1 7.8 - - + +
161A LEU* 3.9 28.2 - - + +
165A GLN 3.6 12.6 + - - +
166A LEU 3.0 25.5 + - - -
167A PRO* 4.2 3.1 - - - +
168A ILE 3.1 21.7 + - - -
169A MSE 4.2 2.8 - - - +
170A TYR* 3.7 18.7 - - + -
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Residues in contact with LEU 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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90A PHE* 4.0 8.7 - - + -
94A MSE 3.1 28.0 - - + -
103A MSE 3.4 34.8 - - + +
104A SER* 4.5 1.4 + - - -
106A TYR* 3.9 19.5 - - + -
149A MSE 3.3 11.2 - - - +
150A ILE 2.9 8.9 + - - +
152A GLN* 1.3 82.9 - - - +
154A LEU* 1.3 58.6 + - - +
167A PRO* 3.8 17.9 - - + +
168A ILE* 3.1 38.6 - - + +
170A TYR* 3.3 24.9 - - + +
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Residues in contact with LEU 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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102A LYS* 2.9 37.2 - - + +
103A MSE 4.3 13.5 - - + +
150A ILE* 3.0 30.9 + - + +
151A CYS 3.0 0.2 + - - -
153A LEU* 1.3 80.4 - - - +
155A SER* 1.3 69.6 + - - +
156A ASN* 3.3 37.1 - - - +
167A PRO* 6.1 0.2 - - - -
369A GLN* 5.9 0.4 - - + -
372A ALA* 4.2 6.3 - - + -
373A GLU* 4.3 15.3 - - + +
376A GLY 3.9 7.0 - - - +
377A THR* 4.3 25.7 - - + +
378A LEU* 4.6 10.0 - - - +
383A ILE* 5.4 0.7 - - - +
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Residues in contact with SER 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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151A CYS 2.8 4.4 + - - -
152A GLN 3.5 6.8 + - - -
154A LEU* 1.3 82.4 - - - +
156A ASN* 1.3 61.6 + - - +
159A ASP* 3.4 17.2 + - - -
163A GLY* 3.9 21.4 + - - -
165A GLN 4.4 6.9 + - - -
167A PRO* 5.2 6.8 - - - +
378A LEU* 5.8 3.4 - - - -
383A ILE* 3.6 13.0 - - - +
384A PRO* 2.9 21.4 - - - +
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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