Contacts of the helix formed by residues 143 - 156 (chain A) in PDB entry 3PEY
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 143 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118A ILE* 4.3 3.4 - - - -
119A GLN* 2.9 32.5 + - - +
141A GLY 3.5 1.4 + - - -
142A THR* 1.3 78.4 - - - +
144A LYS* 1.3 66.1 + - - +
145A THR 3.2 3.2 + - - -
146A ALA 3.5 4.9 + - - -
147A ALA* 3.5 4.5 + - - +
1000A ADP 3.0 31.7 + - - -
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Residues in contact with LYS 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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118A ILE* 4.4 4.0 - - + -
138A SER* 2.9 45.2 + - - +
139A GLN 2.9 8.5 + - - -
142A THR* 3.8 0.9 - - - +
143A GLY* 1.3 77.3 - - - +
145A THR* 1.3 63.1 + - - +
147A ALA* 3.0 16.2 + - - +
148A PHE* 3.2 20.4 + - + -
239A ASP* 5.4 2.5 - - - +
240A GLU* 5.9 0.7 - - - -
270A PHE* 3.7 35.7 - - + -
271A SER* 3.8 16.2 - - - +
272A ALA 3.8 11.0 - - - +
1000A ADP 2.8 27.3 + - - +
1001A MG 4.5 1.8 - - - -
1002A BEF 2.8 35.2 - - - -
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Residues in contact with THR 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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144A LYS* 1.3 79.0 - - - +
146A ALA* 1.3 58.5 + - - +
148A PHE* 3.7 21.8 - - + -
149A SER* 2.8 45.4 + - - +
174A LEU* 5.9 1.0 - - - +
177A GLN* 5.2 5.5 + - - +
178A THR* 4.2 16.4 + - + +
181A VAL* 3.9 29.4 - - + -
239A ASP* 4.9 1.0 + - - -
1000A ADP 2.7 32.1 + - - -
1001A MG 3.9 5.2 - - - -
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Residues in contact with ALA 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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94A PHE* 5.8 0.4 - - + -
112A PHE* 3.9 18.6 - - + -
119A GLN* 3.6 24.5 - - - +
143A GLY 3.5 2.4 + - - -
144A LYS 3.3 0.6 - - - -
145A THR* 1.3 79.2 - - - +
147A ALA* 1.3 62.5 + - - +
150A LEU* 2.9 34.3 + - + +
181A VAL* 5.2 1.7 - - + +
185A MET* 3.9 29.4 - - + -
1000A ADP 4.4 2.7 + - + +
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Residues in contact with ALA 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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118A ILE* 4.8 1.8 - - + +
119A GLN* 4.2 21.4 - - + +
122A ALA* 4.6 9.6 - - + -
123A LEU* 3.5 16.5 - - + +
126A LEU* 4.0 3.2 - - + +
143A GLY 3.5 9.1 + - - +
144A LYS* 3.0 11.3 + - - +
146A ALA* 1.3 80.5 - - - +
148A PHE* 1.3 59.3 + - - +
151A THR* 2.9 24.6 + - - -
270A PHE* 3.9 20.2 - - + -
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Residues in contact with PHE 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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126A LEU* 4.8 0.9 - - - -
144A LYS* 3.2 19.3 + - + -
145A THR* 3.7 25.1 - - + -
147A ALA* 1.3 78.3 - - - +
149A SER* 1.3 77.1 + - - +
151A THR* 3.3 6.3 + - - -
152A MET* 2.9 39.8 + - + +
167A CYS* 3.7 19.3 - - - -
178A THR* 3.9 11.0 - - + -
235A ILE* 6.2 0.2 - - + -
237A VAL* 3.8 25.0 - - + +
239A ASP* 3.6 42.8 - - + -
268A VAL* 4.6 2.5 - - + -
270A PHE* 3.8 35.9 - + + -
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Residues in contact with SER 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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145A THR* 2.8 38.3 + - - +
146A ALA* 4.1 4.5 - - - -
148A PHE* 1.3 82.5 - - - +
150A LEU* 1.3 64.6 + - - +
152A MET* 3.3 9.3 + - - +
153A LEU* 3.0 31.2 + - - +
181A VAL* 4.6 1.4 - - - +
182A VAL* 3.5 29.4 - - - +
185A MET* 4.3 11.7 - - - -
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Residues in contact with LEU 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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94A PHE* 4.3 8.7 - - + -
99A LEU* 4.2 11.9 - - + -
103A LEU* 4.2 26.1 - - + +
107A ILE* 3.7 31.4 - - + -
119A GLN* 6.3 0.2 - - + -
123A LEU* 4.1 31.6 - - + -
127A LEU* 5.1 0.4 - - - -
146A ALA* 2.9 25.7 + - + +
149A SER* 1.3 75.1 - - - +
151A THR* 1.3 58.1 + - - +
153A LEU* 3.5 7.3 + - + +
154A THR* 2.8 33.3 + - - -
185A MET* 3.5 29.8 - - + +
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Residues in contact with THR 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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123A LEU* 3.7 7.1 - - - +
126A LEU* 3.4 46.3 - - + +
127A LEU* 4.1 11.8 - - + +
147A ALA 2.9 15.2 + - - -
148A PHE* 3.3 11.8 + - - -
149A SER 3.1 0.6 - - - -
150A LEU* 1.3 75.3 - - - +
152A MET* 1.3 65.4 + - - +
154A THR* 3.1 2.3 + - - -
155A ARG* 3.0 35.3 + - + +
235A ILE* 3.6 22.7 - - + -
266A GLN* 4.3 1.3 - - - +
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Residues in contact with MET 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 PHE* 2.9 24.2 + - + +
149A SER* 3.3 12.1 + - - +
151A THR* 1.3 78.3 - - - +
153A LEU* 1.3 63.4 + - + +
155A ARG* 3.3 9.4 + - - +
156A VAL* 3.4 18.4 + - - +
165A ALA* 3.8 26.1 - - + +
166A ILE 4.2 1.3 - - - +
167A CYS* 3.7 37.7 - - + -
178A THR* 5.3 0.2 - - + -
182A VAL* 3.9 28.0 - - + -
211A VAL* 4.0 15.9 - - + -
213A VAL* 4.7 2.0 - - + -
235A ILE* 4.2 13.5 - - + -
237A VAL* 4.0 19.5 - - + -
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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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103A LEU* 4.0 24.1 - - + +
149A SER 3.0 23.7 + - - +
150A LEU* 3.9 6.5 - - + +
152A MET* 1.3 76.8 - - + +
154A THR* 1.3 63.6 + - - +
156A VAL* 3.4 11.9 + - - +
182A VAL* 4.0 29.4 - - + +
185A MET* 4.1 11.7 - - + -
186A GLY* 3.9 33.0 - - - +
191A ILE* 3.5 50.1 - - + +
211A VAL* 4.4 3.6 - - + -
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Residues in contact with THR 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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98A GLY 5.8 3.1 - - - +
99A LEU* 4.0 9.0 - - - +
100A ALA* 5.5 3.0 + - + +
103A LEU* 3.5 17.7 - - - +
127A LEU* 3.7 28.9 - - + +
150A LEU 2.8 23.3 + - - -
151A THR 3.1 4.0 + - - -
153A LEU* 1.3 79.7 - - - +
155A ARG* 1.3 65.4 + - + +
156A VAL 3.3 7.3 + - - +
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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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126A LEU 2.9 25.4 + - - -
127A LEU* 3.4 12.8 + - + +
128A HIS 2.9 23.8 + - - -
129A ASN* 2.8 25.1 + - - +
131A PRO* 3.8 17.9 - - - +
151A THR* 3.0 29.5 + - + +
152A MET 3.3 4.7 + - - +
154A THR* 1.3 79.3 - - - +
156A VAL* 1.3 62.5 - - - +
157A ASN* 3.3 4.2 + - - +
164A GLN* 5.5 0.7 - - - -
234A LYS* 3.9 29.7 - - + +
235A ILE* 4.2 18.4 - - + -
266A GLN* 2.9 23.4 + - - +
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Residues in contact with VAL 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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152A MET 3.4 17.4 + - - +
153A LEU 3.7 11.1 - - - +
154A THR 3.2 8.2 - - - +
155A ARG* 1.3 77.4 - - - +
157A ASN* 1.3 62.1 + - - +
158A PRO* 3.4 13.5 - - + +
164A GLN* 3.7 23.1 - - + +
165A ALA* 4.7 2.5 - - + -
191A ILE* 4.2 17.6 - - + +
210A GLN* 3.8 38.1 - - + +
211A VAL* 3.8 25.6 - - + -
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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