Contacts of the helix formed by residues 145 - 159 (chain A) in PDB entry 4PSQ
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 PRO 145 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113A THR* 3.8 38.1 - - + +
143A GLY 4.4 3.6 - - - +
144A LEU* 1.3 87.1 - - + +
146A PRO* 1.3 78.9 - - + +
147A GLU* 3.3 4.7 - - + +
148A ALA* 3.1 8.7 + - + +
149A GLN* 3.1 20.5 + - - +
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Residues in contact with PRO 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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145A PRO* 1.3 88.1 - - + +
147A GLU* 1.3 61.9 + - - +
149A GLN* 3.4 21.2 + - - +
150A LYS* 3.3 22.2 + - - +
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Residues in contact with GLU 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 PRO* 3.3 4.7 - - + +
146A PRO* 1.3 76.8 - - - +
148A ALA* 1.3 66.6 + - - +
150A LYS* 3.3 17.2 + - - +
151A ILE* 3.2 48.2 + - + +
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Residues in contact with ALA 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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110A ASP* 5.1 0.7 - - - +
113A THR* 3.9 11.0 - - - +
114A TYR* 3.8 36.3 - - + -
144A LEU* 3.8 16.8 - - + -
145A PRO* 3.1 14.7 + - + +
147A GLU* 1.3 77.5 - - - +
149A GLN* 1.3 59.0 + - - +
151A ILE* 3.2 3.9 + - - +
152A VAL* 2.8 36.4 + - - +
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Residues in contact with GLN 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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144A LEU* 2.7 42.1 + - + +
145A PRO* 3.1 20.9 + - - +
146A PRO* 3.4 19.0 - - - +
148A ALA* 1.3 75.1 - - - +
150A LYS* 1.3 63.0 + - - +
152A VAL* 4.0 2.3 - - - +
153A ARG* 3.1 27.6 + - - +
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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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146A PRO 3.3 9.0 + - - +
147A GLU* 3.3 22.5 + - - +
148A ALA 3.2 0.8 - - - -
149A GLN* 1.3 80.0 - - - +
151A ILE* 1.3 66.3 + - + +
153A ARG* 3.9 5.2 - - - +
154A GLN* 3.2 43.4 + - - +
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Residues in contact with ILE 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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108A ASP* 4.0 1.1 - - - +
114A TYR* 3.3 40.8 - - + +
147A GLU* 3.2 42.0 + - + +
148A ALA* 3.8 3.4 - - - +
150A LYS* 1.3 81.0 - - + +
152A VAL* 1.3 59.8 + - - +
154A GLN* 3.2 8.1 + - - +
155A ARG* 2.9 61.7 + - + +
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Residues in contact with VAL 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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114A TYR* 3.8 25.1 - - + -
116A VAL* 3.9 15.0 - - + -
136A VAL* 3.9 26.2 - - + -
144A LEU* 3.9 21.5 - - + -
148A ALA 2.8 20.5 + - - +
149A GLN* 4.0 3.6 - - - +
151A ILE* 1.3 74.7 - - - +
153A ARG* 1.3 57.4 + - - +
155A ARG* 3.1 2.3 + - - +
156A GLN* 2.8 55.9 + - + +
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Residues in contact with ARG 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 GLN 3.1 18.5 + - - +
150A LYS* 3.9 6.7 - - - +
151A ILE 3.3 0.2 - - - -
152A VAL* 1.3 76.9 - - - +
154A GLN* 1.3 61.6 + - - +
156A GLN* 3.5 12.3 + - - +
157A GLU* 3.2 46.7 + - - +
203A EDO 3.6 22.5 + - - +
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Residues in contact with GLN 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* 3.2 41.0 + - - +
151A ILE* 3.5 8.7 - - - +
152A VAL 3.2 0.6 - - - -
153A ARG* 1.3 80.4 - - - +
155A ARG* 1.3 83.1 + - - +
157A GLU* 3.3 10.4 + - - +
158A GLU* 3.0 51.3 + - + +
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Residues in contact with ARG 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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107A VAL* 4.1 5.2 - - + -
108A ASP* 2.6 41.9 + - + -
116A VAL* 4.4 21.3 - - + -
151A ILE* 2.9 39.9 + - + +
152A VAL 3.7 4.0 - - - +
154A GLN* 1.3 106.3 - - - +
156A GLN* 1.3 60.7 + - - +
158A GLU* 3.1 26.1 + - - +
159A LEU* 2.9 35.2 + - - +
205A EDO 3.6 17.0 - - - -
213A EDO 3.2 22.8 + - - -
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Residues in contact with GLN 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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28A ALA* 5.0 3.2 - - - +
116A VAL* 5.4 3.8 - - + +
136A VAL* 3.6 13.9 - - + +
152A VAL* 2.8 31.9 + - + +
153A ARG* 3.5 16.6 - - - +
155A ARG* 1.3 73.5 - - + +
157A GLU* 1.3 59.4 + - - +
159A LEU* 3.5 5.4 + - - +
161A LEU* 3.1 29.9 + - - +
162A ALA 4.4 2.0 - - - -
165A TYR* 3.3 58.6 - - + +
203A EDO 3.1 33.6 + - - -
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Residues in contact with GLU 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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2A ARG* 2.8 41.1 + - - +
153A ARG* 3.2 38.2 + - + +
154A GLN* 3.6 10.9 - - - +
155A ARG 3.2 0.2 - - - -
156A GLN* 1.3 79.2 - - + +
158A GLU* 1.3 56.3 + - + +
160A CYS* 3.0 16.3 + - - -
162A ALA* 3.9 24.5 - - + +
203A EDO 5.2 4.3 + - - -
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Residues in contact with GLU 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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2A ARG* 4.7 14.2 - - - +
3A ASP 4.8 2.6 - - - +
9A PHE* 3.3 20.8 - - - -
10A ARG* 6.1 0.9 - - - -
154A GLN* 3.0 47.5 + - + +
155A ARG* 3.1 28.1 + - - +
157A GLU* 1.3 72.7 - - + +
159A LEU* 1.3 57.7 + - - +
160A CYS* 3.1 10.9 + - - -
205A EDO 3.4 24.9 + - - -
213A EDO 4.5 1.7 + - - -
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Residues in contact with LEU 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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9A PHE* 3.6 36.5 - - + -
105A TRP* 6.2 0.2 - - + -
107A VAL* 4.2 15.0 - - + -
116A VAL* 4.2 20.2 - - + -
118A TYR* 4.0 28.1 + - + -
134A SER* 4.4 1.8 - - - +
155A ARG 2.9 20.0 + - - +
156A GLN 3.8 5.8 - - - +
157A GLU 3.2 0.4 - - - -
158A GLU* 1.3 75.7 - - - +
160A CYS* 1.3 69.8 + - - +
161A LEU* 3.5 16.9 + - + +
165A TYR* 3.9 19.1 - - - +
205A EDO 3.8 22.2 - - - -
209A EDO 5.1 3.3 - - - -
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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