Contacts of the helix formed by residues 134 - 146 (chain B) in PDB entry 6DU3
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 134 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132B ARG 3.4 0.6 + - - -
133B PRO* 1.3 86.2 - - + +
135B VAL* 1.3 58.3 + - - +
136B ASP 3.2 3.7 + - - +
137B GLU* 3.3 26.7 + - - +
138B PHE* 2.8 28.7 + - - +
231B ASP 3.8 8.6 + - - -
232B THR* 3.8 23.5 - - - +
234B LEU* 4.6 0.9 - - - -
235B HIS* 3.8 36.6 + + + +
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Residues in contact with VAL 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B LEU* 3.9 37.5 - - + +
131B LYS* 3.7 34.5 - - + -
132B ARG 3.2 18.2 - - - +
133B PRO 3.0 3.0 + - - -
134B HIS* 1.3 77.3 - - - +
136B ASP* 1.3 60.9 + - - +
138B PHE* 3.1 1.0 + - - +
139B LEU* 2.8 35.0 + - + +
166B LEU* 3.8 23.6 - - + -
234B LEU* 3.8 14.4 - - + -
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Residues in contact with ASP 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B LYS* 2.7 35.5 + - - -
134B HIS* 3.2 1.7 - - - -
135B VAL* 1.3 76.6 - - - +
137B GLU* 1.3 67.3 + - - +
139B LEU* 3.4 3.2 + - - +
140B GLN* 3.0 26.6 + - - +
166B LEU* 4.2 12.8 - - - +
168B LYS* 3.3 35.4 + - - +
169B TRP* 4.0 10.9 + - + +
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Residues in contact with GLU 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134B HIS* 3.3 27.9 + - + +
136B ASP* 1.3 78.1 - - - +
138B PHE* 1.3 62.7 + - - +
140B GLN* 3.7 5.3 - - - +
141B ARG* 3.1 25.1 + - + +
235B HIS* 3.1 37.9 + - - -
238B LEU* 3.9 17.5 - - + +
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Residues in contact with PHE 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B ILE* 4.6 5.6 - - + -
101B LEU* 4.1 24.2 - - + -
134B HIS 2.8 17.4 + - - +
135B VAL* 3.1 7.6 + - - +
137B GLU* 1.3 78.3 - - - +
139B LEU* 1.3 69.9 + - + +
141B ARG* 3.9 1.0 - - - +
142B MET* 2.9 67.3 + - + +
205B LEU* 3.5 32.1 - - + -
234B LEU* 3.5 43.3 - - + +
237B LEU* 4.8 2.2 - - + -
238B LEU* 3.8 16.6 - - + +
241B PHE* 4.0 14.6 - + - -
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Residues in contact with LEU 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B ILE* 4.3 12.1 - - + -
101B LEU* 4.2 9.2 - - + -
135B VAL* 2.8 25.0 + - + +
136B ASP* 4.2 2.9 - - - +
138B PHE* 1.3 86.4 - - + +
140B GLN* 1.3 57.5 + - - +
142B MET* 3.9 3.3 - - + +
143B GLY* 2.8 26.5 + - - -
166B LEU* 4.0 33.9 - - + +
167B ASP* 4.7 14.1 - - + +
169B TRP* 4.8 6.1 - - + -
171B ALA* 3.5 22.3 - - + +
172B PHE* 3.9 38.6 - - + -
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Residues in contact with GLN 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136B ASP 3.0 19.7 + - - +
137B GLU* 3.7 6.1 - - - +
139B LEU* 1.3 78.9 - - - +
141B ARG* 1.3 63.0 + - - +
143B GLY* 3.4 1.7 + - - -
144B GLU* 3.1 43.6 + - - +
169B TRP* 3.4 58.6 - - + +
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Residues in contact with ARG 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137B GLU* 3.1 15.5 + - + +
140B GLN* 1.3 76.9 + - - +
142B MET* 1.3 66.3 - - - +
144B GLU* 2.5 57.9 + - - +
145B LEU* 3.1 37.4 + - + +
238B LEU* 3.8 25.4 - - + -
242B GLU* 2.7 42.1 + - - +
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Residues in contact with MET 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93B VAL* 4.1 15.5 - - + -
95B ILE* 4.7 7.0 - - + -
138B PHE* 2.9 65.2 + - + +
139B LEU* 3.9 6.1 - - + +
141B ARG* 1.3 75.8 - - - +
143B GLY* 1.3 57.7 + - - +
145B LEU* 4.7 2.7 - - - -
146B PHE* 3.0 59.1 + - + +
148B CYS* 3.2 20.2 - - - -
238B LEU* 4.3 7.2 - - + -
241B PHE* 3.7 39.3 - - + -
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Residues in contact with GLY 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90B LYS* 4.9 0.2 + - - -
139B LEU 2.8 18.2 + - - -
140B GLN 3.4 3.1 + - - -
141B ARG 3.1 0.2 - - - -
142B MET* 1.3 77.3 - - - +
144B GLU* 1.3 59.3 + - - +
146B PHE 3.6 0.2 - - - +
148B CYS* 3.9 1.5 - - - -
171B ALA* 3.8 15.0 - - - -
173B ARG* 2.9 41.4 + - - -
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Residues in contact with GLU 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90B LYS* 3.8 17.9 + - - +
140B GLN* 3.1 39.4 + - - +
141B ARG* 2.5 51.4 + - - +
143B GLY* 1.3 79.1 - - - +
145B LEU* 1.3 62.6 + - - +
146B PHE 3.6 0.2 + - - -
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Residues in contact with LEU 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90B LYS* 3.5 18.3 - - - +
91B ILE 4.9 0.3 + - - -
141B ARG* 3.1 61.0 + - + +
142B MET* 4.9 2.2 - - - -
144B GLU* 1.3 77.8 - - + +
146B PHE* 1.3 90.8 + - + +
238B LEU* 5.3 1.3 - - + +
241B PHE* 4.5 3.8 - - + +
242B GLU* 4.0 28.9 - - - +
245B SER* 4.0 23.1 - - - +
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Residues in contact with PHE 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B LYS* 4.3 6.2 - - - +
91B ILE* 3.3 34.1 - - + +
93B VAL* 3.3 20.6 - - + -
142B MET* 3.0 50.7 + - + +
143B GLY 3.6 1.4 - - - +
144B GLU 3.5 0.4 - - - -
145B LEU* 1.3 95.6 - - + +
147B GLU* 1.3 60.1 + - - +
148B CYS* 3.4 7.4 + - - -
173B ARG* 2.9 30.2 + - - -
203B LEU* 4.4 4.5 - - + -
241B PHE* 3.4 40.4 - + + -
245B SER* 3.6 26.9 - - - -
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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