Contacts of the helix formed by residues 142 - 158 (chain A) in PDB entry 2HPD
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 142 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A VAL* 1.3 94.0 - - + +
143A GLU* 1.4 62.3 + - - +
145A MET* 3.3 2.5 + - + +
146A THR* 2.7 40.3 + - - +
270A SER* 4.5 1.6 + - - +
274A SER* 3.5 19.3 - - - +
440A LYS* 4.1 28.3 - - + +
441A PRO* 3.1 33.0 - - + +
443A GLY 4.7 2.2 - - - +
444A PHE* 3.5 15.9 - - + +
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Residues in contact with GLU 143 (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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140A GLU* 3.4 39.4 - - + +
141A VAL 3.2 0.6 + - - -
142A PRO* 1.4 92.7 - - - +
144A ASP* 1.3 61.3 + - - +
146A THR* 3.4 6.7 + - - -
147A ARG* 3.2 42.0 + - - +
440A LYS* 4.5 11.1 + - - -
442A GLU* 4.7 4.5 - - - +
443A GLY* 5.5 5.7 + - - -
444A PHE 5.1 0.3 - - - +
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Residues in contact with ASP 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A LEU* 3.8 16.7 - - + +
129A LYS* 2.9 24.0 + - - -
130A TRP* 3.0 30.4 + - + +
139A ILE* 4.0 8.7 - - - +
140A GLU* 3.2 14.4 + - - +
141A VAL 4.3 1.6 - - - +
143A GLU* 1.3 75.5 - - - +
145A MET* 1.3 60.9 + - - +
147A ARG* 2.7 36.4 + - - +
148A LEU* 3.0 28.1 + - - +
165A PHE* 3.8 8.2 - - + -
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Residues in contact with MET 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A LEU* 4.1 13.0 - - + -
130A TRP* 3.3 40.2 - - + -
141A VAL* 3.0 33.9 + - + +
142A PRO 3.8 2.0 - - - +
144A ASP* 1.3 78.2 - - - +
146A THR* 1.4 59.9 + - - +
148A LEU* 3.5 11.2 + - - +
149A THR* 3.1 20.4 + - - +
270A SER* 3.3 29.1 - - - +
273A LEU* 3.8 33.0 - - + +
274A SER* 3.7 14.1 - - - +
413A VAL* 4.9 0.2 - - - -
417A MET* 4.1 13.9 - - + +
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Residues in contact with THR 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A PRO* 2.7 22.9 + - - +
143A GLU* 3.4 5.8 + - - -
144A ASP 3.3 0.2 - - - -
145A MET* 1.4 71.6 - - - +
147A ARG* 1.4 62.0 + - - +
149A THR* 3.3 5.7 + - - +
150A LEU* 3.0 36.7 + - + +
178A VAL* 6.5 0.9 - - + -
266A HIS* 3.9 27.8 - - + +
267A GLU* 5.5 3.3 - - + +
270A SER* 3.0 15.9 + - - +
440A LYS* 5.7 4.2 - - - +
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Residues in contact with ARG 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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129A LYS* 3.8 9.8 - - - +
140A GLU* 5.3 6.9 + - - +
143A GLU* 3.2 34.5 + - - +
144A ASP* 2.7 44.1 + - - +
146A THR* 1.4 74.7 - - - +
148A LEU* 1.3 63.8 + - - +
150A LEU* 4.2 3.1 - - - +
151A ASP* 3.2 31.0 + - - +
164A SER* 3.8 36.0 + - - -
165A PHE* 3.7 21.7 - - + +
167A ARG 4.5 7.1 + - - -
168A ASP* 4.1 18.8 + - - +
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Residues in contact with LEU 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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119A MET 5.8 0.2 - - - +
122A ILE* 3.7 22.0 - - + +
123A ALA* 3.8 29.2 - - - -
126A LEU* 4.0 18.4 - - + -
144A ASP 3.0 16.1 + - - +
145A MET* 3.7 10.8 - - - +
146A THR 3.3 0.2 - - - -
147A ARG* 1.3 78.3 - - - +
149A THR* 1.3 53.4 + - + +
152A THR* 2.6 38.0 + - - +
165A PHE* 3.9 6.0 - - + -
273A LEU* 3.9 19.1 - - + -
409A GLU* 4.2 11.0 - - - +
413A VAL* 3.7 33.9 - - + -
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Residues in contact with THR 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 MET 3.1 17.3 + - - +
146A THR* 3.3 5.2 + - - -
148A LEU* 1.3 81.2 - - + +
150A LEU* 1.3 63.1 + - - +
152A THR* 3.2 1.2 + - - -
153A ILE* 3.1 32.5 + - - +
265A GLY 4.7 0.7 - - - -
266A HIS* 2.8 29.9 + - - +
269A THR* 3.9 20.6 - - + +
270A SER* 3.7 23.1 - - - +
273A LEU* 4.6 1.8 - - + -
409A GLU* 4.0 14.8 - - - +
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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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146A THR* 3.0 35.9 + - + +
147A ARG* 4.2 3.8 - - - +
149A THR* 1.3 70.6 + - - +
151A ASP* 1.3 69.4 + - - +
153A ILE* 4.2 0.9 - - - +
154A GLY 2.9 19.8 + - - -
162A PHE* 3.6 11.5 - - + -
164A SER* 4.8 1.3 - - - +
174A ILE* 3.6 47.3 - - + -
177A MET* 3.9 16.6 - - + -
178A VAL* 5.7 1.6 - - + -
262A LEU* 4.2 16.4 - - + +
266A HIS* 3.8 32.1 - - + +
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Residues in contact with ASP 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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122A ILE* 3.8 28.0 - - + +
125A GLN* 5.0 2.9 + - - -
147A ARG 3.2 14.7 + - - +
150A LEU* 1.3 83.3 - - - +
152A THR* 1.3 60.9 + - - +
154A GLY* 3.9 0.2 - - - -
155A LEU* 3.1 25.8 + - - +
160A TYR 4.9 1.2 - - - +
161A ARG* 6.0 0.8 - - - -
162A PHE* 3.4 17.8 + - - +
163A ASN* 3.4 13.9 + - - -
164A SER* 2.6 45.2 + - - -
165A PHE* 4.4 8.6 + - - -
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Residues in contact with THR 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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118A MET 4.9 0.9 - - - +
119A MET* 3.8 35.5 + - + -
122A ILE* 3.6 20.8 - - - +
148A LEU* 2.6 26.4 + - - +
149A THR 3.2 2.7 + - - -
151A ASP* 1.3 74.5 - - - +
153A ILE* 1.3 59.7 + - - +
155A LEU* 3.3 1.9 + - - +
156A CYS* 2.8 36.7 + - - +
405A PHE* 4.3 9.0 - - + -
409A GLU* 3.4 26.0 + - - +
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Residues in contact with ILE 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 THR* 3.1 21.2 + - - +
150A LEU 4.2 1.6 - - - +
152A THR* 1.3 73.7 - - - +
154A GLY* 1.3 58.2 + - - +
157A GLY* 2.6 38.2 + - - +
158A PHE* 4.7 1.0 - - + -
233A LEU* 6.5 0.9 - - + -
261A PHE* 3.7 32.5 - - + +
262A LEU* 3.7 23.1 - - + +
265A GLY* 3.7 34.3 - - - +
266A HIS* 3.9 8.1 - - + +
269A THR* 6.1 0.4 - - - -
405A PHE* 4.2 23.8 - - + -
472A HEM 4.6 9.0 - - + -
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Residues in contact with GLY 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 LEU 2.9 17.9 + - - -
151A ASP 3.9 1.1 - - - -
153A ILE* 1.3 75.3 - - - +
155A LEU* 1.3 55.3 + - - +
158A PHE* 3.0 44.5 + - - -
159A ASN 3.3 5.2 + - - -
160A TYR 3.3 14.3 + - - -
162A PHE* 3.8 13.5 - - - -
262A LEU* 4.3 1.9 - - - +
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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 MET* 3.9 40.0 - - + +
121A ASP* 4.5 4.5 - - + -
122A ILE* 4.0 22.2 - - + -
151A ASP 3.1 16.2 + - - +
152A THR* 4.0 2.7 - - - +
154A GLY* 1.3 74.4 - - - +
156A CYS* 1.3 63.6 + - - +
159A ASN* 3.1 50.2 + - - +
160A TYR 3.7 5.8 + - - +
161A ARG* 3.9 49.1 - - + +
232A ASP* 4.0 1.7 - - - +
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Residues in contact with CYS 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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115A TYR* 4.0 28.6 - - + -
118A MET* 3.7 32.5 - - - -
119A MET* 4.2 2.0 - - - -
152A THR* 2.8 32.3 + - - +
153A ILE 4.3 0.4 - - - +
155A LEU* 1.3 72.9 - - - +
157A GLY* 1.3 57.7 + - - +
231A ASP 4.6 0.3 - - - +
232A ASP* 3.2 7.3 - - - -
233A LEU* 2.9 29.2 + - + +
405A PHE* 3.8 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
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A ILE* 2.6 27.4 + - - -
156A CYS* 1.3 74.2 - - - +
158A PHE* 1.3 64.0 + - - +
159A ASN 3.7 0.2 - - - -
232A ASP* 3.7 1.2 - - - +
233A LEU* 3.3 18.5 + - - +
234A LEU* 2.9 28.8 + - - +
258A ILE* 5.0 3.8 - - - +
261A PHE* 5.4 5.4 - - - -
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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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153A ILE* 4.7 0.7 - - + -
154A GLY* 3.0 23.5 + - - -
157A GLY* 1.3 80.3 - - - +
159A ASN* 1.3 72.7 + - - +
160A TYR* 3.2 27.8 + + + +
162A PHE* 3.9 22.0 - + - -
173A PHE* 5.4 0.9 - + - -
215A LEU* 4.8 9.2 - - + -
216A VAL* 5.3 6.3 - - + -
219A ILE* 3.6 34.8 - - + +
223A ARG* 3.3 10.7 + - - -
232A ASP* 3.2 9.9 - - - -
234A LEU* 4.0 18.6 - - + -
258A ILE* 3.9 35.7 - - + -
262A LEU* 4.4 13.2 - - + -
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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