Contacts of the helix formed by residues 145 - 157 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143A ARG 3.1 1.2 + - - -
144A PRO* 1.3 91.8 - - + +
146A VAL* 1.3 52.5 + - - +
147A ASP 3.1 2.9 - - - -
148A GLU* 3.1 31.5 + - + +
149A PHE* 2.7 36.5 + - - +
242A ASP 3.8 17.3 - - - -
243A THR* 4.1 10.1 - - + +
245A LEU* 4.4 2.2 - - + -
246A LEU* 3.6 61.1 - - + +
249A ILE* 6.0 1.8 - - + -
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Residues in contact with VAL 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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112A LEU* 3.9 37.0 - - + +
142A LYS* 4.0 25.8 - - + -
143A ARG 3.3 18.4 + - - +
144A PRO 3.3 1.0 - - - -
145A TYR* 1.3 77.5 - - - +
147A ASP* 1.3 56.6 + - - +
148A GLU* 3.9 0.2 + - - -
149A PHE* 3.7 1.2 - - + +
150A LEU* 2.8 39.1 + - + +
177A LEU* 3.9 33.0 - - + -
245A LEU* 3.8 15.3 - - + -
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Residues in contact with ASP 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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142A LYS* 3.0 31.2 + - - -
145A TYR 3.1 0.4 - - - -
146A VAL* 1.3 80.1 - - - +
148A GLU* 1.3 74.9 + - - +
150A LEU* 3.6 5.5 + - - +
151A ARG* 3.3 24.1 + - - +
177A LEU* 4.0 12.3 - - - +
179A ARG* 2.7 58.2 + - - +
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Residues in contact with GLU 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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145A TYR* 3.2 41.3 - - + +
147A ASP* 1.3 84.1 + - - +
149A PHE* 1.3 61.8 + - - +
151A ARG* 3.3 26.5 + - - +
152A ARG* 3.2 24.6 + - - +
179A ARG* 5.5 1.6 + - - -
249A ILE* 4.4 9.9 - - + +
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Residues in contact with PHE 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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106A ILE* 4.3 10.5 - - + -
112A LEU* 4.5 6.7 - - + -
145A TYR 2.7 21.8 + - - +
146A VAL 3.7 3.4 - - - +
148A GLU* 1.3 74.0 - - - +
150A LEU* 1.3 73.6 + - + +
151A ARG 3.2 0.3 + - - -
152A ARG* 3.5 1.9 + - - +
153A MET* 3.0 65.2 + - + +
216A LEU* 3.7 31.2 - - + -
245A LEU* 3.6 50.5 - - + +
248A LEU* 4.4 9.0 - - + -
249A ILE* 3.8 19.6 - - + +
252A PHE* 4.3 14.6 - + - -
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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
----------------------------------------------------------
106A ILE* 4.3 15.5 - - + -
112A LEU* 4.3 7.4 - - + -
146A VAL* 2.8 40.6 + - + +
147A ASP* 4.2 6.1 - - - +
148A GLU 3.3 0.2 - - - -
149A PHE* 1.3 88.1 - - + +
151A ARG* 1.3 57.1 + - - +
153A MET* 3.8 2.8 - - + +
154A GLY 3.0 23.6 + - - -
177A LEU* 4.3 17.5 - - + +
178A ASP* 4.7 11.7 - - - +
182A VAL* 3.1 29.1 - - + +
183A PHE* 4.1 35.9 - - + -
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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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147A ASP 3.3 16.1 + - - +
148A GLU* 3.8 28.9 + - - +
149A PHE 3.2 0.8 - - - -
150A LEU* 1.3 73.4 - - - +
152A ARG* 1.3 68.7 + - - +
154A GLY* 3.2 4.7 + - - -
155A GLU* 3.2 36.8 + - + +
179A ARG* 5.1 10.7 - - - +
180A CYS* 4.7 24.2 - - + -
182A VAL* 4.2 7.1 - - + +
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Residues in contact with ARG 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 GLU 3.2 12.3 + - - +
149A PHE 3.9 2.7 - - - +
151A ARG* 1.3 81.1 - - - +
153A MET* 1.3 65.8 + - + +
155A GLU* 2.7 53.8 + - - +
156A LEU* 3.2 39.3 + - + +
249A ILE* 4.3 21.3 - - + -
253A GLU* 2.6 41.2 + - - +
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Residues in contact with MET 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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104A VAL* 4.1 15.3 - - + -
106A ILE* 4.9 5.8 - - + -
149A PHE* 3.0 61.4 + - + +
150A LEU* 3.8 6.1 - - - +
151A ARG 3.3 0.4 - - - -
152A ARG* 1.3 76.4 - - - +
154A GLY* 1.3 57.4 + - - +
156A LEU* 2.9 5.5 + - - +
157A PHE* 2.8 53.0 + - + +
159A CYS* 3.6 17.0 - - - -
182A VAL* 5.0 0.2 - - + -
249A ILE* 5.9 2.5 - - - -
252A PHE* 3.4 47.3 - - + -
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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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101A ARG* 2.8 21.4 + - - -
150A LEU 3.0 14.3 + - - -
151A ARG 3.2 5.1 + - - -
153A MET* 1.3 74.9 - - - +
155A GLU* 1.3 57.1 + - - +
157A PHE 4.4 0.2 - - - -
159A CYS* 3.9 3.9 - - - -
182A VAL* 3.9 20.4 - - - -
184A ARG* 3.2 19.4 + - - -
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Residues in contact with GLU 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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101A ARG* 3.3 19.7 + - - +
151A ARG* 3.2 26.9 + - + +
152A ARG* 2.7 53.9 + - - +
154A GLY* 1.3 77.0 - - - +
156A LEU* 1.3 61.6 + - - +
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Residues in contact with LEU 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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101A ARG* 3.8 17.8 - - - +
152A ARG* 3.2 55.8 + - + +
153A MET* 2.9 5.9 + - - -
155A GLU* 1.3 82.9 - - - +
157A PHE* 1.3 84.5 + - + +
252A PHE* 4.9 1.1 - - + -
253A GLU* 4.0 22.0 - - + +
256A SER* 4.0 31.1 - - - +
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Residues in contact with PHE 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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101A ARG* 3.0 22.7 + - - +
102A ILE* 3.5 37.5 - - + +
104A VAL* 3.4 26.9 - - + -
153A MET* 2.8 35.6 + - + +
154A GLY 4.0 1.9 - - - +
156A LEU* 1.3 95.2 - - + +
158A GLU* 1.3 62.2 + - - +
159A CYS* 3.5 10.0 + - - -
184A ARG* 4.0 4.0 + - - -
214A LEU* 4.4 4.0 - - + -
252A PHE* 3.4 41.5 - + + -
255A LEU* 4.4 2.2 - - + -
256A SER* 3.4 31.4 - - - -
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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