Contacts of the helix formed by residues 148 - 162 (chain A) in PDB entry 2P4G
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 148 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144A PRO* 4.3 12.5 - - - +
146A ASN 3.7 6.6 + - - -
147A ASN* 1.3 77.7 + - - +
149A GLU* 1.3 64.0 + - - +
150A GLN* 4.2 8.1 - - - +
151A TRP* 3.2 22.3 + - - +
152A ASP* 3.1 26.9 + - - +
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Residues in contact with GLU 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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147A ASN* 4.2 0.8 - - - +
148A SER* 1.3 69.6 - - - +
150A GLN* 1.3 59.4 + - - +
151A TRP 3.3 0.2 - - - -
152A ASP* 3.5 12.8 - - - +
153A GLN* 3.0 40.3 + - - +
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Residues in contact with GLN 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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148A SER* 4.8 7.8 - - - -
149A GLU* 1.3 74.0 - - - +
151A TRP* 1.3 56.5 + - - +
153A GLN* 3.1 10.3 + - - +
154A ARG* 2.8 74.0 + - - +
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Residues in contact with TRP 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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116A LYS 3.2 20.3 + - - -
117A SER* 3.7 16.4 - - - +
118A LEU* 3.4 11.9 - - + +
141A THR* 3.1 36.4 + - + -
142A GLN 3.3 22.3 + - - -
143A GLN* 3.8 21.3 - - - -
144A PRO* 3.6 21.1 - - + -
148A SER* 3.2 21.8 + - - +
150A GLN* 1.3 75.9 - - - +
152A ASP* 1.3 72.6 + - - +
154A ARG* 3.1 6.0 + - - +
155A LEU* 2.8 62.4 + - + +
167A VAL* 3.9 17.0 - - + -
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Residues in contact with ASP 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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143A GLN* 5.2 2.9 + - - -
144A PRO* 5.5 0.7 - - - +
147A ASN* 5.8 3.2 + - - +
148A SER 3.1 17.1 + - - +
149A GLU* 3.5 15.6 - - - +
151A TRP* 1.3 93.8 - - - +
153A GLN* 1.3 57.7 + - + +
155A LEU* 3.5 6.8 - - - +
156A GLN* 3.0 27.7 + - - +
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Residues in contact with GLN 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 GLU* 3.0 29.8 + - - +
150A GLN* 3.1 7.8 + - - +
152A ASP* 1.3 75.1 - - + +
154A ARG* 1.3 61.4 + - + +
156A GLN* 3.4 7.2 + - - +
157A LYS* 3.0 36.4 + - + +
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Residues in contact with ARG 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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117A SER* 2.9 43.0 + - - +
118A LEU* 3.5 27.8 - - + +
119A TYR* 3.8 27.5 - - - +
122A PHE* 4.8 1.0 - - - -
150A GLN* 2.8 55.3 + - - +
151A TRP* 3.5 4.0 - - - +
153A GLN* 1.3 76.7 - - + +
155A LEU* 1.3 66.1 + - - +
157A LYS* 3.2 10.7 + - + +
158A LEU* 3.0 26.9 + - - +
281A EDO 3.8 16.4 + - - +
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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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118A LEU* 3.7 16.9 - - + +
151A TRP* 2.8 48.2 + - + +
152A ASP* 3.5 6.5 - - - +
154A ARG* 1.3 72.2 - - - +
156A GLN* 1.3 63.1 + - - +
158A LEU* 3.1 7.7 + - - +
159A ILE* 2.9 42.0 + - + +
165A VAL* 3.6 38.4 - - + -
167A VAL* 4.4 11.9 - - + -
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Residues in contact with GLN 156 (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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152A ASP 3.0 14.6 + - - +
153A GLN* 3.6 11.7 - - - +
154A ARG 3.2 0.2 - - - -
155A LEU* 1.3 76.5 - - - +
157A LYS* 1.3 51.7 + - - +
159A ILE* 3.1 21.0 + - - +
160A ASP* 2.5 77.0 + - - +
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Residues in contact with LYS 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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122A PHE* 3.7 17.9 - - + -
153A GLN* 3.0 25.2 + - + +
154A ARG* 3.2 12.5 + - + +
156A GLN* 1.3 74.5 - - + +
158A LEU* 1.3 64.0 + - - +
160A ASP* 3.2 10.5 + - - +
161A VAL* 3.1 26.0 + - - +
281A EDO 3.6 30.1 - - - -
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Residues in contact with LEU 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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118A LEU* 3.8 34.3 - - + +
120A PHE* 3.9 17.7 - - + -
122A PHE* 3.7 19.3 - - + -
127A PHE* 3.6 33.2 - - + -
139A VAL* 4.5 2.7 - - + -
154A ARG 3.0 18.2 + - - +
155A LEU* 3.4 7.0 - - - +
157A LYS* 1.3 75.5 - - - +
159A ILE* 1.3 64.1 + - - +
161A VAL* 3.1 7.0 + - - +
162A GLY 3.1 5.0 + - - -
163A VAL* 3.0 33.1 + - + -
165A VAL* 3.9 24.2 - - + -
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Residues in contact with ILE 159 (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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155A LEU* 2.9 43.0 + - + +
156A GLN* 3.4 26.0 - - - +
158A LEU* 1.3 75.0 - - - +
160A ASP* 1.3 59.8 + - - +
162A GLY* 2.8 21.1 + - - -
163A VAL 4.3 10.8 - - - +
165A VAL* 4.9 5.4 - - + -
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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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129A PRO* 5.2 2.4 - - - +
156A GLN* 2.5 57.8 + - - +
157A LYS* 3.6 9.4 - - - +
159A ILE* 1.3 75.6 - - - +
161A VAL* 1.3 61.7 + - + +
162A GLY 3.3 0.2 - - - -
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Residues in contact with VAL 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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122A PHE* 3.7 25.1 - - + -
127A PHE* 3.6 26.0 - - + +
128A SER 4.6 1.4 - - - +
129A PRO* 3.5 41.8 - - + +
157A LYS 3.1 13.1 + - - +
158A LEU* 3.3 15.0 - - - +
160A ASP* 1.3 80.2 - - + +
162A GLY* 1.3 57.9 + - - +
163A VAL* 3.8 16.3 + - + +
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Residues in contact with GLY 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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136A SER* 5.0 0.4 - - - -
159A ILE 2.8 15.8 + - - -
160A ASP 3.3 0.8 - - - -
161A VAL* 1.3 78.8 - - - +
163A VAL* 1.3 64.3 + - - +
164A GLU 3.5 0.9 + - - -
285A EDO 3.0 24.3 + - - -
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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