Contacts of the helix formed by residues 148 - 159 (chain A) in PDB entry 6MOL
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 HIS 148 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111A ALA 3.3 24.2 - - - -
112A ARG 3.2 16.8 + - - -
113A MET 3.5 15.8 + - - -
114A GLY* 3.5 15.5 + - - -
143A ALA* 3.3 7.6 + - + +
146A ALA* 3.4 25.0 - - + +
147A GLY* 1.3 77.5 + - - +
149A LEU* 1.3 65.5 + - - +
150A GLU 3.5 0.4 - - - +
151A ILE* 3.7 24.9 - - + +
152A VAL* 3.2 25.9 + - - +
184A ILE* 4.4 1.7 - - - +
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Residues in contact with LEU 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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147A GLY 3.9 3.8 + - - -
148A HIS* 1.3 73.0 - - - +
150A GLU* 1.3 63.6 + - + +
152A VAL* 3.1 5.6 + - + +
153A GLU* 3.0 39.7 + - + +
183A GLU* 3.5 43.7 - - + +
184A ILE* 3.7 20.2 - - + +
187A VAL* 4.1 14.1 - - + -
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Residues in contact with GLU 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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116A VAL* 3.9 33.5 - - + +
148A HIS 3.5 0.4 - - - -
149A LEU* 1.3 80.5 - - + +
151A ILE* 1.3 66.9 + - + +
153A GLU* 3.5 15.9 + - + +
154A VAL* 3.1 32.7 + - + +
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Residues in contact with ILE 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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111A ALA* 3.8 19.3 - - + -
114A GLY* 3.7 28.9 - - - +
116A VAL* 3.8 29.8 - - + +
119A VAL* 4.0 15.9 - - + -
143A ALA* 3.7 23.1 - - + -
148A HIS* 3.7 27.3 + - + +
149A LEU 3.3 0.6 - - - -
150A GLU* 1.3 77.0 - - + +
152A VAL* 1.3 61.1 + - - +
154A VAL* 3.3 5.9 + - - +
155A LEU* 2.9 37.6 + - + +
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Residues in contact with VAL 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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140A LEU* 3.9 18.4 - - + -
143A ALA* 3.9 26.5 - - + -
144A ALA* 4.5 4.5 - - + +
148A HIS 3.2 15.7 + - - +
149A LEU* 3.1 8.8 + - + +
151A ILE* 1.3 77.8 - - - +
153A GLU* 1.3 62.6 + - - +
155A LEU* 3.3 0.7 + - - +
156A LEU* 3.0 45.7 + - + +
184A ILE* 4.0 25.1 - - + -
187A VAL* 4.3 10.8 - - + -
188A LEU* 4.6 8.1 - - + -
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Residues in contact with GLU 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 LEU* 3.0 38.0 + - + +
150A GLU* 3.9 16.4 - - + +
152A VAL* 1.3 77.3 - - - +
154A VAL* 1.3 64.2 + - + +
156A LEU* 4.1 3.4 - - - -
157A LYS* 3.2 23.4 + - - +
187A VAL* 4.3 28.4 - - + +
191A TYR* 4.2 9.4 + - + +
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Residues in contact with VAL 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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116A VAL* 4.2 10.5 - - + -
119A VAL* 4.1 7.9 - - + -
120A GLU* 3.7 34.8 - - + +
123A LEU* 4.0 11.0 - - + -
150A GLU* 3.1 21.3 + - + +
151A ILE* 3.8 6.1 - - - +
152A VAL 3.2 0.2 - - - -
153A GLU* 1.3 77.9 - - + +
155A LEU* 1.3 66.0 + - - +
157A LYS* 3.2 5.6 + - - +
158A TYR* 3.0 52.5 + - + -
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Residues in contact with LEU 155 (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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107A LEU* 4.1 16.6 - - + -
111A ALA* 4.4 1.6 - - + -
119A VAL* 4.2 8.3 - - + -
123A LEU* 3.7 25.4 - - + -
129A VAL* 3.7 18.0 - - + +
139A PRO* 3.8 24.9 - - + +
140A LEU* 3.9 22.7 - - + +
143A ALA* 4.3 0.9 - - + -
151A ILE* 2.9 37.0 + - + +
152A VAL 3.9 2.5 - - - +
154A VAL* 1.3 76.8 - - - +
156A LEU* 1.3 61.5 + - - +
158A TYR* 3.2 1.7 + - - -
159A GLY 3.1 7.6 + - - -
160A ALA* 3.0 33.1 + - + +
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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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140A LEU* 3.7 26.5 - - + -
152A VAL* 3.0 39.9 + - + +
153A GLU 4.2 1.1 - - - +
155A LEU* 1.3 76.2 - - - +
157A LYS* 1.3 60.4 + - - +
159A GLY* 3.5 10.0 + - - -
160A ALA* 3.8 12.7 + - + +
162A VAL* 3.7 26.2 - - + -
187A VAL* 3.8 11.0 - - + +
188A LEU* 4.2 11.4 - - + -
191A TYR* 3.5 52.7 - - + -
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Residues in contact with LYS 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 GLU 3.2 18.8 + - - +
154A VAL* 3.2 8.3 + - - +
156A LEU* 1.3 79.7 - - - +
158A TYR* 1.3 64.2 + - + +
159A GLY* 4.7 0.2 - - - -
191A TYR* 4.0 10.9 + - - +
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Residues in contact with TYR 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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120A GLU* 4.0 20.2 + - + +
123A LEU* 3.6 55.9 - - + -
124A LYS* 4.3 10.5 + - - +
129A VAL* 4.4 8.8 - - + +
154A VAL* 3.0 43.6 + - + +
155A LEU 3.2 4.2 + - - +
157A LYS* 1.3 79.7 - - + +
159A GLY* 1.3 57.7 + - - +
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Residues in contact with GLY 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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129A VAL* 3.3 10.8 - - - +
130A ASN* 3.2 15.1 + - - +
155A LEU 3.1 1.0 + - - -
156A LEU 3.5 5.5 + - - -
157A LYS 3.3 4.2 - - - -
158A TYR* 1.3 80.8 - - - +
160A ALA* 1.3 69.2 + - - +
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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