Contacts of the helix formed by residues 147 - 162 (chain A) in PDB entry 5LUQ
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 PHE 147 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144A MSE 5.4 2.6 - - - +
146A GLU* 1.3 84.9 - - - +
148A LYS* 1.3 103.6 + - + +
149A ILE* 3.2 1.2 + - + +
150A GLY* 3.8 9.0 + - - +
151A GLU* 4.2 10.9 + - - +
186A PRO* 6.0 0.7 - - - +
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Residues in contact with LYS 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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147A PHE* 1.3 102.2 - - + +
149A ILE* 1.3 61.1 + - + +
150A GLY 3.2 2.5 - - - -
151A GLU* 3.9 13.7 - - + +
152A LEU* 2.9 36.8 + - + +
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Residues in contact with ILE 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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101A ALA 5.5 2.2 - - - +
102A PRO* 5.9 2.2 - - + -
105A VAL* 3.4 43.3 - - + -
108A LYS* 4.5 4.9 - - - +
144A MSE 5.1 4.7 - - - -
146A GLU* 3.2 49.6 - - + +
147A PHE 3.2 0.6 - - - -
148A LYS* 1.3 81.1 - - + +
150A GLY* 1.3 56.5 + - - +
152A LEU* 3.2 16.8 - - + +
153A PHE* 2.9 34.4 - - + -
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Residues in contact with GLY 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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144A MSE 3.5 28.6 - - - +
147A PHE 3.8 5.8 + - - -
148A LYS 3.2 0.6 - - - -
149A ILE* 1.3 78.4 - - - +
151A GLU* 1.3 59.7 + - - +
153A PHE* 3.3 13.6 - - - -
154A SER* 2.9 30.7 + - - -
184A VAL* 5.7 0.7 - - - -
186A PRO* 4.6 9.0 - - - -
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Residues in contact with GLU 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 PHE 4.2 8.1 + - - +
148A LYS* 3.5 15.8 + - + +
150A GLY* 1.3 74.8 - - - +
152A LEU* 1.3 65.3 + - - +
154A SER* 4.1 5.6 - - - -
155A LYS* 2.9 61.8 + - + +
186A PRO* 3.6 35.0 - - + +
187A SER* 5.8 0.3 + - - -
189A MSE 5.6 1.3 - - + -
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Residues in contact with LEU 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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105A VAL* 3.6 33.0 - - + +
108A LYS* 6.0 1.6 - - + -
109A ASN* 5.3 14.8 - - + +
148A LYS* 2.9 22.8 + - + +
149A ILE* 3.2 26.5 - - + +
150A GLY 3.3 0.2 - - - -
151A GLU* 1.3 77.7 - - - +
153A PHE* 1.3 82.6 + - + +
155A LYS* 5.0 1.3 - - - +
156A PHE* 3.1 24.2 + - + +
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Residues in contact with PHE 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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108A LYS* 3.2 39.3 - - + -
138A PHE* 3.5 24.7 - + + -
141A SER* 5.7 3.1 - - - -
144A MSE 3.5 27.1 - - - -
149A ILE* 2.9 27.1 - - + -
150A GLY* 3.3 14.6 - - - -
152A LEU* 1.3 88.1 - - + +
154A SER* 1.3 84.2 + - - +
155A LYS 3.3 2.4 + - - -
156A PHE* 3.3 11.0 + - + -
157A TYR* 2.9 45.7 + - + -
181A LEU* 4.2 19.5 - - + -
184A VAL* 5.2 3.6 - - + -
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Residues in contact with SER 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 GLY 2.9 23.3 + - - -
151A GLU* 4.1 4.5 - - - -
153A PHE* 1.3 81.9 - - - +
155A LYS* 1.3 64.1 + - - +
157A TYR* 4.0 0.9 - - - +
158A GLY 3.1 18.9 + - - -
181A LEU* 3.1 31.1 - - - +
186A PRO* 4.9 7.2 - - - +
189A MSE 2.9 39.5 - - - +
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Residues in contact with LYS 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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151A GLU* 2.9 52.5 + - + +
152A LEU* 5.0 1.8 - - - +
154A SER* 1.3 78.9 - - - +
156A PHE* 1.3 58.1 + - - +
158A GLY* 3.3 2.4 + - - -
159A GLU* 2.9 40.2 + - - +
189A MSE 4.1 18.7 - - + +
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Residues in contact with PHE 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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108A LYS 5.4 0.7 - - - -
109A ASN* 4.9 7.9 - - - -
112A THR* 2.9 44.0 - - + -
152A LEU* 3.1 24.8 + - + +
153A PHE* 3.3 19.8 + - + -
155A LYS* 1.3 76.6 - - - +
157A TYR* 1.3 98.6 + + - +
159A GLU* 3.1 24.0 - - - +
160A LEU* 2.8 42.2 + - + +
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Residues in contact with TYR 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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108A LYS 4.1 13.5 + - - -
111A CYS* 5.2 2.1 - - - +
112A THR* 4.1 9.2 + - - -
135A LEU* 5.6 6.3 - - + -
138A PHE* 3.1 53.2 - + + +
153A PHE* 2.9 33.1 + + + +
154A SER* 4.2 2.0 - - - +
156A PHE* 1.3 104.7 - + - +
158A GLY* 1.3 67.4 + - - +
160A LEU* 3.4 20.5 - - + +
161A ALA* 2.9 28.3 + - - +
173A LYS* 6.4 0.4 - - - -
177A LEU* 3.5 34.5 - - + +
178A LEU* 5.2 2.5 - - + -
181A LEU* 4.5 11.0 - - + -
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Residues in contact with GLY 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 SER 3.1 14.4 + - - -
155A LYS 3.6 4.9 - - - -
157A TYR* 1.3 75.8 - - - +
159A GLU* 1.3 56.7 + - - +
161A ALA* 4.5 4.0 - - - -
162A LEU* 3.0 45.3 + - - +
178A LEU* 4.6 8.8 - - - +
181A LEU* 5.3 0.6 - - - +
189A MSE 4.4 14.3 - - - +
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Residues in contact with GLU 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 LYS* 2.9 30.7 + - - +
156A PHE* 3.1 30.0 - - - +
157A TYR 3.0 0.6 - - - -
158A GLY* 1.3 78.5 - - - +
160A LEU* 1.3 62.2 + - - +
161A ALA 3.3 0.7 + - - -
162A LEU* 3.7 10.1 + - - +
163A LYS* 4.0 9.7 + - - +
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Residues in contact with LEU 160 (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 THR* 4.1 7.2 - - - +
115A TYR* 5.5 13.2 - - + -
119A ARG* 4.5 21.5 - - - +
156A PHE* 2.8 50.6 + - + +
157A TYR* 3.4 30.5 - - + +
159A GLU* 1.3 72.7 - - - +
161A ALA* 1.3 62.3 + - + +
163A LYS 2.9 19.9 - - - +
164A LYS* 3.1 23.1 - - + +
173A LYS* 5.2 12.1 - - - -
174A VAL* 6.2 2.9 - - + -
177A LEU* 5.1 6.3 - - + -
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Residues in contact with ALA 161 (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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157A TYR 2.9 18.4 + - - +
158A GLY 4.0 2.0 - - - +
160A LEU* 1.3 82.4 - - + +
162A LEU* 1.3 59.5 + - + +
163A LYS* 2.8 15.2 + - - -
164A LYS* 4.1 5.4 + - - +
174A VAL* 3.8 31.8 - - + +
177A LEU* 6.5 0.9 - - + -
178A LEU* 4.2 14.4 - - + -
200A PHE* 3.7 18.2 - - + -
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Residues in contact with LEU 162 (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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158A GLY* 3.0 32.1 + - - +
159A GLU* 3.7 5.4 + - - +
160A LEU 3.7 0.2 - - - -
161A ALA* 1.3 75.3 - - + +
163A LYS* 1.3 68.5 + - + +
178A LEU* 5.6 4.0 - - + -
193A ALA* 6.3 0.9 - - - -
196A LEU* 3.4 49.1 - - + -
200A PHE* 4.8 14.8 - - + -
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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