Contacts of the helix formed by residues 145 - 157 (chain H) in PDB entry 2Q5E
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 TYR 145 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143H ARG 3.3 1.0 + - - -
144H PRO* 1.3 96.4 - - + +
146H VAL* 1.3 59.2 + - - +
147H ASP 3.4 2.5 - - - -
148H GLU* 3.3 38.4 + - + +
149H PHE* 2.9 30.5 + - - +
242H ASP 4.0 10.3 - - - -
243H THR* 4.1 12.3 - - + +
245H LEU* 4.3 1.3 - - - -
246H LEU* 3.8 54.9 + - + +
249H ILE* 5.3 0.3 - - - +
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Residues in contact with VAL 146 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112H LEU* 3.9 31.0 - - + +
142H LYS* 3.8 31.0 - - + -
143H ARG 3.3 17.9 - - - +
144H PRO 3.2 1.6 - - - -
145H TYR* 1.3 77.9 - - - +
147H ASP* 1.3 56.9 + - - +
149H PHE* 3.2 2.8 + - + +
150H LEU* 2.8 44.1 + - + +
177H LEU* 3.8 26.5 - - + -
245H LEU* 3.6 17.0 - - + -
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Residues in contact with ASP 147 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142H LYS* 2.6 39.9 + - - -
146H VAL* 1.3 77.9 + - - +
148H GLU* 1.3 71.5 + - - +
150H LEU* 4.2 4.7 - - - +
151H ARG* 3.3 34.3 + - - +
177H LEU* 4.3 7.4 - - - +
179H ARG* 3.2 42.5 + - - +
180H CYS* 5.6 0.5 - - - -
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Residues in contact with GLU 148 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145H TYR* 3.3 51.3 + - + +
147H ASP* 1.3 84.2 - - - +
149H PHE* 1.3 66.9 + - - +
151H ARG* 4.0 6.5 - - - +
152H ARG* 3.3 22.5 + - - +
246H LEU* 5.0 4.9 - - + -
249H ILE* 3.8 13.2 - - + +
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Residues in contact with PHE 149 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106H ILE* 4.6 4.7 - - + -
112H LEU* 4.3 12.8 - - + -
145H TYR 2.9 19.2 + - - +
146H VAL 3.4 5.2 - - - +
148H GLU* 1.3 75.6 - - - +
150H LEU* 1.3 77.9 + - + +
152H ARG* 3.2 4.9 + - - +
153H MET* 3.1 60.0 + - + +
216H LEU* 3.7 31.6 - - + -
245H LEU* 3.4 44.4 - - + +
248H LEU* 4.3 8.3 - - + -
249H ILE* 3.8 15.7 - - + +
252H PHE* 4.1 16.8 - + - -
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Residues in contact with LEU 150 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106H ILE* 4.7 6.3 - - + -
112H LEU* 4.2 10.5 - - + -
146H VAL* 2.8 29.5 + - + +
147H ASP* 4.2 4.0 - - - +
149H PHE* 1.3 83.2 - - + +
151H ARG* 1.3 66.8 + - - +
153H MET* 3.1 4.9 + - + +
154H GLY 2.8 20.3 + - - -
177H LEU* 4.0 42.0 - - + +
178H ASP* 4.5 8.7 - - - +
179H ARG 5.7 0.2 - - - +
180H CYS* 6.1 1.1 - - + -
182H VAL* 3.6 20.8 - - + +
183H PHE* 3.8 35.2 - - + -
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Residues in contact with ARG 151 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147H ASP* 3.3 29.0 + - - +
148H GLU* 4.0 6.2 - - - +
150H LEU* 1.3 78.2 - - - +
152H ARG* 1.3 64.3 + - + +
154H GLY* 3.3 2.6 + - - -
155H GLU* 3.2 37.3 + - + +
179H ARG* 4.7 24.7 - - - +
180H CYS* 3.4 42.0 - - - -
182H VAL* 4.7 3.1 - - - +
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Residues in contact with ARG 152 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148H GLU 3.3 15.3 + - - +
149H PHE 3.2 4.6 + - - +
150H LEU 3.2 0.6 - - - -
151H ARG* 1.3 80.5 - - + +
153H MET* 1.3 59.6 + - + +
155H GLU* 2.4 57.0 + - - +
156H LEU* 3.2 46.7 + - + +
249H ILE* 3.5 28.0 - - + -
253H GLU* 3.3 32.3 + - - +
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Residues in contact with MET 153 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104H VAL* 3.9 19.1 - - + -
106H ILE* 4.4 6.3 - - + -
149H PHE* 3.1 49.6 + - + +
150H LEU* 3.1 8.4 + - + +
152H ARG* 1.3 73.7 - - + +
154H GLY* 1.3 56.9 + - - +
155H GLU 3.0 1.1 - - - -
156H LEU* 2.8 5.7 + - - +
157H PHE* 2.7 52.5 + - + +
159H CYS* 3.5 15.4 - - - -
249H ILE* 6.0 2.5 - - - -
252H PHE* 3.6 52.0 - - + -
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Residues in contact with GLY 154 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101H ARG* 3.0 19.4 + - - -
150H LEU 2.8 11.2 + - - -
151H ARG 3.6 4.9 - - - -
153H MET* 1.3 78.3 - - - +
155H GLU* 1.3 56.1 + - - +
157H PHE 3.9 2.2 - - - +
159H CYS* 4.0 2.2 - - - -
182H VAL* 3.3 31.2 - - - +
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Residues in contact with GLU 155 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101H ARG* 3.5 17.0 + - - +
151H ARG* 3.5 25.8 - - + +
152H ARG* 2.4 55.7 + - - +
154H GLY* 1.3 79.6 - - - +
156H LEU* 1.3 64.6 + - + +
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Residues in contact with LEU 156 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101H ARG* 3.6 18.2 - - - +
102H ILE 5.1 0.2 + - - -
152H ARG* 3.2 45.3 + - + +
153H MET* 2.8 3.5 + - - +
155H GLU* 1.3 87.3 - - + +
157H PHE* 1.3 83.4 + - + +
252H PHE* 5.6 0.7 - - + -
253H GLU* 3.9 38.1 - - + +
256H SER* 3.7 26.8 - - - +
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Residues in contact with PHE 157 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98H ASP* 3.8 2.1 - - - +
101H ARG* 3.2 20.4 + - - +
102H ILE* 3.6 39.0 - - + +
104H VAL* 3.2 29.2 - - + -
153H MET* 2.7 33.1 + - + +
154H GLY* 3.9 3.6 - - - +
156H LEU* 1.3 86.6 - - + +
158H GLU* 1.3 66.2 + - - +
159H CYS* 3.6 9.5 + - - -
214H LEU* 4.4 3.8 - - + -
252H PHE* 3.4 41.5 - + + -
255H LEU* 4.3 1.8 - - + -
256H SER* 3.3 38.6 - - - -
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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