Contacts of the helix formed by residues 138 - 151 (chain H) in PDB entry 6PB4
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 ASP 138 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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572 G 3.3 30.1 - - - +
136H PHE 3.7 3.8 + - - -
137H LEU* 1.3 81.8 - - - +
139H VAL* 1.3 55.1 + - - +
140H THR* 3.0 16.9 + - - +
141H GLY* 2.7 29.1 + - - -
142H ARG* 3.8 5.8 - - - +
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Residues in contact with VAL 139 (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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572 G 5.1 13.8 + - - -
582 A 5.2 8.7 - - - +
138H ASP* 1.3 71.2 - - - +
140H THR* 1.3 51.9 + - - +
142H ARG* 2.8 40.4 + - + +
143H ILE* 2.6 50.1 + - + +
176H VAL* 6.1 1.1 - - + -
178H CYS* 5.5 10.8 - - - -
182H THR* 4.3 15.7 - - + -
183H VAL* 5.8 0.9 - - + +
186H ILE* 3.6 21.8 - - + -
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Residues in contact with THR 140 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138H ASP* 2.8 22.4 + - - +
139H VAL* 1.3 73.6 - - - +
141H GLY* 1.3 58.3 + - - +
143H ILE* 3.4 3.8 + - - +
144H ALA* 2.9 27.1 + - + +
186H ILE* 3.5 32.3 - - + +
189H MET* 4.9 11.0 - - - -
190H LEU* 4.8 15.8 - - + +
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Residues in contact with GLY 141 (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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137H LEU* 3.3 34.8 - - - +
138H ASP* 2.7 13.3 + - - -
140H THR* 1.3 78.3 - - - +
142H ARG* 1.3 58.3 + - - +
144H ALA* 3.1 10.0 - - - +
145H GLN* 2.9 25.1 + - - +
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Residues in contact with ARG 142 (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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572 G 4.6 9.9 + - - -
133H ASN 4.1 6.7 - - - +
134H LEU* 4.8 17.1 + - - +
137H LEU* 2.7 32.1 + - + +
138H ASP* 3.5 4.4 + - - +
139H VAL* 2.8 54.9 + - + +
141H GLY* 1.3 73.6 - - - +
143H ILE* 1.3 59.1 + - - +
145H GLN* 3.0 33.6 + - - +
146H THR* 2.5 26.5 + - - -
176H VAL* 4.9 17.0 - - + +
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Residues in contact with ILE 143 (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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139H VAL* 2.6 25.3 + - + +
140H THR 3.7 3.6 - - - +
142H ARG* 1.3 72.7 - - + +
144H ALA* 1.3 56.7 + - - +
146H THR* 3.5 7.1 - - - -
147H LEU* 2.9 36.0 + - + +
172H ILE* 6.5 0.7 - - + -
176H VAL* 5.9 5.4 - - + -
183H VAL* 3.8 39.0 - - + +
186H ILE* 3.4 43.1 - - + -
187H LEU* 5.4 5.2 - - + +
190H LEU* 3.9 24.9 - - + -
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Residues in contact with ALA 144 (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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140H THR* 2.9 16.5 + - + +
141H GLY* 3.1 16.2 - - - +
142H ARG 3.1 0.4 - - - -
143H ILE* 1.3 76.4 - - - +
145H GLN* 1.3 63.1 + - - +
147H LEU* 3.1 15.3 - - - +
148H LEU* 3.0 25.9 + - - +
190H LEU* 5.6 4.7 - - + -
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Residues in contact with GLN 145 (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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129H GLU* 4.3 14.6 - - - +
130H LYS* 5.3 4.9 + - - +
133H ASN* 2.7 49.7 - - - +
134H LEU 5.0 0.2 - - - +
137H LEU* 4.2 1.8 - - + +
141H GLY 2.9 13.2 + - - +
142H ARG* 3.0 42.5 + - - +
144H ALA* 1.3 76.0 - - - +
146H THR* 1.3 66.8 + - - +
148H LEU* 3.6 9.0 - - - +
149H ASN* 3.0 30.7 + - - +
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Residues in contact with THR 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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142H ARG 2.5 24.1 + - - -
143H ILE* 3.5 8.2 - - - -
145H GLN* 1.3 77.0 - - - +
147H LEU* 1.3 64.4 + - - +
149H ASN* 2.5 30.4 + - - +
150H LEU* 2.9 31.5 + - + +
172H ILE* 3.9 11.7 - - + -
175H ILE* 4.5 7.9 - - + -
176H VAL* 3.1 34.7 - - + +
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Residues in contact with LEU 147 (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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143H ILE* 2.9 28.6 + - + +
144H ALA* 3.1 33.9 - - - +
146H THR* 1.3 75.4 - - - +
148H LEU* 1.3 66.3 + - + +
150H LEU* 4.6 7.2 - - - -
151H ALA* 3.2 21.8 + - - +
165H ILE* 4.3 10.0 - - + +
187H LEU* 5.2 3.8 - - + -
190H LEU* 4.8 15.0 - - + -
195H LEU* 6.0 1.3 - - + -
196H ILE* 3.6 39.7 - - + -
202H THR* 5.3 2.2 - - - +
204H VAL* 4.2 16.3 - - + +
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Residues in contact with LEU 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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144H ALA 3.0 19.2 + - - +
145H GLN* 3.6 9.0 - - - +
147H LEU* 1.3 81.1 - - + +
149H ASN* 1.3 61.2 + - + +
151H ALA* 2.9 24.2 + - + +
152H LYS* 3.2 31.2 + - + +
204H VAL* 5.9 7.9 - - + -
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Residues in contact with ASN 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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126H VAL* 6.0 3.8 - - - +
145H GLN* 3.0 25.4 + - - +
146H THR* 2.5 25.5 + - - +
148H LEU* 1.3 78.3 - - + +
150H LEU* 1.3 83.2 + - - +
152H LYS* 2.9 12.0 + - + +
153H GLN* 2.9 29.2 + - - +
175H ILE* 5.9 1.1 - - - +
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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
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146H THR* 2.9 32.1 + - + +
147H LEU* 4.6 2.7 - - - +
149H ASN* 1.3 95.6 + - - +
151H ALA* 1.3 58.6 + - - +
152H LYS 3.1 2.5 + - - -
153H GLN* 3.2 47.6 + - - +
155H ASP* 4.0 1.4 - - - +
156H ALA* 3.9 3.3 - - - +
165H ILE* 3.4 29.4 - - + +
167H ILE* 5.8 6.2 - - + +
172H ILE* 3.9 29.2 - - + -
175H ILE* 4.1 25.1 - - + -
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Residues in contact with ALA 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 LEU 3.2 19.2 + - - +
148H LEU* 2.9 10.8 + - + +
150H LEU* 1.3 75.1 - - - +
152H LYS* 1.3 65.4 + - - +
156H ALA* 4.1 2.2 - - - -
163H MET* 3.0 49.0 - - + +
165H ILE* 3.9 13.4 - - + +
204H VAL* 4.1 15.9 - - + -
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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