Contacts of the helix formed by residues 143 - 159 (chain A) in PDB entry 6B9H
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 GLU 143 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18A THR* 6.5 1.3 - - - -
142A MET* 1.3 77.9 - - - +
144A GLU* 1.3 66.8 + - - +
145A SER* 3.9 17.7 + - - +
146A VAL* 3.1 17.6 + - + +
147A GLN* 3.0 18.0 + - - +
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Residues in contact with GLU 144 (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 MET 3.5 1.8 + - - +
143A GLU* 1.3 72.2 - - - +
145A SER* 1.3 63.5 + - - +
147A GLN* 3.1 11.2 + - - +
148A HIS* 2.9 25.1 + - - +
441B GLU* 2.6 37.3 + - + +
444B LEU* 3.8 13.2 - - + +
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Residues in contact with SER 145 (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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11A GLU* 5.3 3.0 - - - +
15A SER* 5.0 0.9 - - - -
143A GLU* 3.9 17.7 + - - +
144A GLU* 1.3 78.6 - - - +
146A VAL* 1.3 68.5 + - - +
148A HIS* 3.4 5.7 + - - +
149A VAL* 3.4 26.4 + - - +
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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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15A SER* 3.9 31.0 - - - +
18A THR* 4.3 21.8 - - + +
19A TRP* 5.3 0.2 - - + -
142A MET* 3.7 32.3 - - + -
143A GLU* 3.1 22.7 + - + +
145A SER* 1.3 82.6 + - - +
147A GLN* 1.3 66.6 + - - +
149A VAL* 3.1 3.3 + - - +
150A VAL* 2.9 38.2 + - + +
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Residues in contact with GLN 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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139A ILE* 3.4 23.8 - - + +
140A MET* 3.1 26.5 + - - +
142A MET* 2.9 23.1 + - + +
143A GLU 3.0 17.1 + - - +
144A GLU* 3.1 11.7 + - - +
146A VAL* 1.3 75.7 - - - +
148A HIS* 1.3 58.2 + - - +
150A VAL* 3.3 7.9 + - - +
151A MET* 2.8 30.7 + - - +
444B LEU* 3.8 26.0 - - + +
445B ALA* 5.2 0.7 + - - -
448B PHE* 3.6 24.5 - - + -
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Residues in contact with HIS 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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144A GLU 2.9 16.0 + - - +
145A SER* 3.9 7.2 - - - +
147A GLN* 1.3 78.6 - - - +
149A VAL* 1.3 63.7 + - + +
151A MET* 3.4 14.1 + - + +
152A THR* 3.0 36.9 + - - -
441B GLU* 4.1 17.3 + - - -
443B VAL* 6.2 0.7 - - + -
444B LEU* 3.8 22.8 - - + +
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Residues in contact with VAL 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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11A GLU* 3.3 52.7 - - + +
12A LEU* 3.9 21.0 - - + +
15A SER* 3.5 28.9 - - - +
16A LEU* 5.4 2.0 - - + -
145A SER 3.5 13.2 - - - +
146A VAL 3.1 3.0 + - - +
148A HIS* 1.3 76.1 - - + +
150A VAL* 1.3 61.2 + - - +
152A THR* 3.2 7.6 + - - -
153A ALA* 2.9 26.7 + - - +
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Residues in contact with VAL 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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15A SER* 5.2 0.4 - - - +
16A LEU* 3.9 21.5 - - + -
19A TRP* 5.2 6.7 - - + -
123A LEU* 4.0 9.9 - - + -
139A ILE* 3.9 33.7 - - + -
142A MET* 5.6 0.2 - - - -
146A VAL* 2.9 35.9 + - + +
147A GLN* 3.6 7.4 - - - +
149A VAL* 1.3 77.1 - - + +
151A MET* 1.3 56.8 + - - +
153A ALA* 3.2 7.5 + - - +
154A ILE* 2.9 54.7 + - + +
448B PHE* 4.2 0.9 - - + -
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Residues in contact with MET 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 GLN 2.8 17.8 + - - +
148A HIS* 3.4 18.6 - - + +
150A VAL* 1.3 75.2 - - - +
152A THR* 1.3 64.8 + - - +
154A ILE 3.3 0.7 + - - -
155A GLN* 2.9 50.9 + - - +
443B VAL* 5.5 6.3 - - + +
444B LEU* 3.7 23.6 - - + -
447B PHE* 3.6 52.3 - - + -
448B PHE* 4.0 4.9 - - + -
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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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12A LEU* 6.3 0.9 - - + -
148A HIS* 3.0 28.2 + - - -
149A VAL* 3.2 9.7 + - - -
151A MET* 1.3 76.3 - - - +
153A ALA* 1.3 62.8 + - - +
155A GLN* 3.3 20.1 + - - +
156A GLU* 3.1 24.9 + - + +
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Residues in contact with ALA 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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12A LEU* 3.9 23.7 - - + +
16A LEU* 4.8 3.4 - - + -
120A GLN* 3.1 25.6 + - + +
123A LEU* 3.8 17.9 - - + -
149A VAL 2.9 16.8 + - - +
150A VAL* 3.5 6.5 - - - +
152A THR* 1.3 78.1 - - - +
154A ILE* 1.3 56.1 + - - +
156A GLU* 3.4 0.8 + - - -
157A LEU* 3.0 29.0 + - - +
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Residues in contact with ILE 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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123A LEU* 3.8 16.4 - - + -
127A VAL* 4.0 28.3 - - + -
136A ILE* 5.8 0.2 - - + -
139A ILE* 5.0 1.3 - - + -
150A VAL* 2.9 36.8 + - + +
151A MET 3.8 3.4 - - - +
153A ALA* 1.3 72.3 - - - +
155A GLN* 1.3 69.1 + - - +
157A LEU* 3.2 9.2 + - + +
158A MET* 3.0 39.7 + - + +
447B PHE* 4.0 9.2 - - + -
448B PHE* 3.9 18.8 - - + -
451B LEU* 4.0 26.5 - - + -
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Residues in contact with GLN 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 MET* 2.9 50.8 + - - +
152A THR* 3.5 21.8 + - - +
154A ILE* 1.3 77.0 - - - +
156A GLU* 1.3 62.2 + - - +
158A MET* 4.0 3.2 - - - +
159A SER* 3.2 23.7 + - - -
447B PHE* 3.3 19.9 - - + -
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Residues in contact with GLU 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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12A LEU* 5.4 3.1 - - - +
96A ASN* 4.0 12.1 + - - +
117A ARG* 4.4 19.2 + - - -
120A GLN* 3.0 29.9 + - - +
152A THR* 3.1 15.1 + - + +
153A ALA* 3.7 2.0 - - - +
155A GLN* 1.3 78.0 - - - +
157A LEU* 1.3 63.4 + - - +
159A SER* 3.1 20.1 + - - +
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Residues in contact with LEU 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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94A GLN 3.4 5.9 - - - +
95A ILE* 4.4 16.8 - - + -
96A ASN* 2.8 35.3 + - - +
120A GLN* 3.5 36.3 - - + +
121A LEU* 6.0 1.1 - - + -
123A LEU* 4.3 7.9 - - + -
124A GLY* 3.6 27.8 - - - +
127A VAL* 4.8 1.8 - - + -
128A ASN* 4.2 4.0 - - - +
153A ALA 3.0 22.8 + - - +
154A ILE* 3.5 17.5 - - + +
156A GLU* 1.3 77.2 - - - +
158A MET* 1.3 80.9 + - + +
159A SER 3.4 0.2 - - - -
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Residues in contact with MET 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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94A GLN* 3.2 36.0 - - + +
127A VAL* 5.0 3.6 - - - +
128A ASN* 3.5 30.3 - - - +
154A ILE* 3.0 34.9 + - + +
155A GLN* 4.2 3.1 - - - +
157A LEU* 1.3 85.7 - - + +
159A SER* 1.3 65.4 + - - +
160A LYS* 3.9 0.9 + - - +
451B LEU* 4.8 15.5 - - + -
454B LYS* 5.4 15.0 - - + +
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Residues in contact with SER 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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94A GLN 5.2 1.0 - - - +
96A ASN* 3.6 27.7 + - - +
155A GLN 3.2 15.6 + - - -
156A GLU* 3.1 15.0 + - - +
157A LEU 4.1 0.2 - - - +
158A MET* 1.3 83.5 - - - +
160A LYS* 1.3 62.2 + - - +
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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