Contacts of the helix formed by residues 147 - 159 (chain A) in PDB entry 1REC
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 THR 147 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130A PHE* 4.0 4.9 - - - -
145A GLU 3.4 0.4 - - - -
146A ASN* 1.3 91.9 + - - +
148A PRO* 1.3 75.5 - - + +
149A GLU* 3.5 15.4 - - - +
150A LYS* 3.1 34.2 + - + +
151A ARG* 3.0 23.2 + - - +
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Residues in contact with PRO 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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123A LEU* 3.8 7.0 - - + -
126A VAL* 3.6 13.9 - - + +
127A THR* 3.4 40.2 - - + +
130A PHE* 4.0 26.2 - - + -
147A THR* 1.3 83.7 - - - +
149A GLU* 1.3 71.5 + - - +
151A ARG 3.4 0.2 + - - -
152A ALA* 2.9 31.2 + - - +
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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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123A LEU* 3.8 23.3 - - + +
147A THR* 3.5 15.8 - - - +
148A PRO* 1.3 97.5 - - - +
150A LYS* 1.3 56.1 + - + +
152A ALA* 4.0 1.1 - - - +
153A GLU* 2.9 38.9 + - + +
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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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143A GLU* 2.7 44.0 + - - +
144A ASP* 3.6 19.2 - - - +
146A ASN* 2.7 29.0 + - - +
147A THR* 3.1 28.9 + - - +
149A GLU* 1.3 74.1 - - + +
151A ARG* 1.3 66.6 + - - +
153A GLU* 3.3 6.3 + - - +
154A LYS* 3.0 25.1 + - - +
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Residues in contact with ARG 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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126A VAL* 3.3 29.4 - - + -
130A PHE* 4.1 11.0 - - + -
133A ILE* 6.1 0.4 - - - +
141A LEU* 3.9 24.7 - - - +
145A GLU* 3.3 44.9 + - - +
147A THR 3.0 16.3 + - - +
148A PRO 3.7 2.2 - - - +
150A LYS* 1.3 78.5 - - - +
152A ALA* 1.3 60.9 + - - +
154A LYS* 3.6 5.7 - - - +
155A ILE* 3.1 27.0 + - + +
184A ARG* 3.6 19.8 + - - +
185A LEU* 3.3 41.9 + - - +
187A GLN 5.3 3.8 + - - -
193A VAL* 5.4 13.1 - - - +
197A LEU* 5.9 1.2 - - - +
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Residues in contact with ALA 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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119A LYS* 5.3 8.1 - - + +
122A VAL* 4.2 16.1 - - + +
123A LEU* 3.9 37.7 - - + +
126A VAL* 4.3 3.3 - - + +
148A PRO 2.9 19.2 + - - +
149A GLU* 4.0 3.6 - - - +
151A ARG* 1.3 74.5 - - - +
153A GLU* 1.3 59.2 + - + +
155A ILE* 3.3 6.4 + - - +
156A TRP* 2.9 29.0 + - - +
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Residues in contact with GLU 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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119A LYS* 2.8 39.5 + - - +
149A GLU* 2.9 31.6 + - + +
150A LYS* 3.7 6.3 - - - +
152A ALA* 1.3 73.2 - - + +
154A LYS* 1.3 56.4 + - - +
156A TRP* 3.2 7.7 + - - +
157A GLY* 2.7 32.9 + - - -
163A ASP* 4.5 2.6 - - - +
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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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144A ASP* 2.7 33.4 + - + +
145A GLU* 2.5 40.1 + - + -
150A LYS 3.0 17.7 + - - +
151A ARG* 3.6 6.1 - - - +
152A ALA 3.3 0.2 - - - -
153A GLU* 1.3 75.7 - - - +
155A ILE* 1.3 63.2 - - - +
157A GLY* 3.1 3.5 + - - -
158A PHE* 2.9 54.7 + - + -
181A GLU* 4.3 5.5 + - - -
184A ARG* 3.9 6.4 - - - +
185A LEU* 3.9 13.2 - - + -
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Residues in contact with ILE 155 (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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109A TYR* 5.0 0.7 - - - +
122A VAL* 4.0 22.0 - - + -
126A VAL* 3.8 23.8 - - + -
151A ARG 3.1 15.4 + - - +
152A ALA 3.5 5.8 - - - +
154A LYS* 1.3 77.8 - - - +
156A TRP* 1.3 66.8 + - + +
158A PHE* 3.1 13.2 + - - +
159A PHE* 3.2 36.4 + - + -
167A LEU* 6.0 0.4 - - + -
182A ILE* 5.5 1.8 - - + -
185A LEU* 3.5 50.5 - - + +
186A ILE* 4.1 17.7 - - + -
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Residues in contact with TRP 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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117A ILE 3.4 25.4 - - - -
119A LYS* 3.5 46.8 - - + +
122A VAL* 4.0 28.5 - - + -
152A ALA 2.9 17.7 + - - +
153A GLU* 3.6 9.4 - - - +
155A ILE* 1.3 77.6 - - + +
157A GLY* 1.3 60.5 + - - +
159A PHE* 3.3 6.8 + + + +
160A GLY 3.2 4.2 + - - -
161A LYS* 3.0 65.0 + - + +
162A LYS 2.8 23.3 + - - -
163A ASP* 3.9 4.2 - - - +
165A ASP 3.2 24.2 - - - -
167A LEU* 4.1 28.9 - - + -
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Residues in contact with GLY 157 (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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153A GLU 2.7 14.8 + - - -
154A LYS* 3.1 4.7 + - - -
156A TRP* 1.3 75.9 - - - +
158A PHE* 1.3 58.8 + - - +
160A GLY* 3.0 18.9 + - - -
161A LYS 4.8 4.7 - - - -
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Residues in contact with PHE 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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154A LYS* 2.9 50.4 + - + -
155A ILE* 3.1 7.8 + - - +
157A GLY* 1.3 75.6 - - - +
159A PHE* 1.3 61.8 + - - +
160A GLY* 3.1 1.4 + - - -
179A ASN* 3.6 28.0 - - - -
181A GLU* 4.1 21.5 - - + -
182A ILE* 3.8 24.0 - - + +
185A LEU* 3.6 20.4 - - + -
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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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155A ILE* 3.2 39.4 + - + -
156A TRP* 3.7 10.5 - + + +
157A GLY 3.2 0.2 - - - -
158A PHE* 1.3 76.2 - - - +
160A GLY* 1.3 62.6 + - - +
161A LYS* 3.8 24.3 - - + -
167A LEU* 3.5 34.3 - - + -
171A GLU* 3.5 29.7 - - + +
172A PHE* 3.9 12.8 - + - -
175A GLY* 4.1 11.4 - - - -
176A THR* 4.2 13.9 - - + -
182A ILE* 3.7 33.0 - - + -
186A ILE* 4.9 1.8 - - + -
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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