Contacts of the helix formed by residues 140 - 150 (chain B) in PDB entry 2HT6
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 140 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136B LYS* 3.5 6.5 - - + +
139B ASN* 1.3 86.0 - - + +
141B TRP* 1.3 58.7 + - - +
142B LEU 2.6 19.5 + - - -
143B HIS* 2.6 34.1 + - + +
144B ASP* 3.9 14.4 + - - +
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Residues in contact with TRP 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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193A SER* 3.9 24.9 - - - -
194A ASP* 3.6 40.6 - - + +
196A VAL* 3.8 3.8 - - + +
221A SER* 4.6 3.4 - - - -
224A VAL* 4.1 28.5 - - + +
226A HIS* 3.6 41.1 - + + -
139B ASN 4.4 9.4 + - - -
140B GLU* 1.3 80.6 - - - +
142B LEU* 1.3 87.7 + - + +
143B HIS 3.2 0.2 - - - -
144B ASP* 3.2 12.5 + - - +
145B HIS* 2.9 45.0 + + + +
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Residues in contact with LEU 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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226A HIS* 4.2 8.1 - - + +
132B MET* 3.5 54.3 - - + +
134B GLU* 4.4 13.0 - - + +
136B LYS* 3.3 21.1 - - - +
139B ASN 4.7 1.8 - - - +
140B GLU 2.6 4.6 + - - -
141B TRP* 1.3 112.7 - - + +
143B HIS* 1.3 59.5 + - - +
145B HIS* 3.5 5.2 - - + +
146B CYS* 2.9 34.9 + - - -
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Residues in contact with HIS 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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132B MET 5.5 0.4 + - - -
133B TRP* 3.5 50.7 + + + -
134B GLU 2.7 32.3 + - - -
135B ASN* 4.7 5.7 + - - -
136B LYS* 4.0 20.0 + - + +
140B GLU* 2.6 26.7 + - + +
142B LEU* 1.3 73.3 - - - +
144B ASP* 1.3 65.4 + - - +
146B CYS 3.3 2.3 + - - -
147B MET* 3.1 29.3 + - - +
174B GLN* 4.9 10.1 - - - +
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Residues in contact with ASP 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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196A VAL* 3.6 23.5 - - + +
197A ARG* 5.7 7.1 - - - -
140B GLU* 3.9 21.5 + - - +
141B TRP* 3.2 10.4 + - - +
143B HIS* 1.3 79.0 - - - +
145B HIS* 1.3 64.2 + - - +
147B MET* 3.5 7.9 + - - +
148B GLN* 3.2 25.5 + - - +
174B GLN* 6.0 0.2 + - - -
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Residues in contact with HIS 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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193A SER* 4.4 14.4 + - - -
196A VAL* 3.9 11.1 - - + +
199A ARG* 4.4 10.0 + - - -
203A VAL* 5.4 0.2 - - + -
219A GLU* 4.3 18.2 - - + -
226A HIS* 5.5 3.6 - + - -
77B ARG* 5.9 2.1 + - - -
130B LEU* 4.7 3.2 - - - +
132B MET* 3.8 33.6 - - + +
141B TRP* 2.9 32.8 + + + +
142B LEU* 3.5 9.4 - - + +
144B ASP* 1.3 75.8 - - - +
146B CYS* 1.3 65.6 + - - +
148B GLN* 3.1 7.8 + - - +
149B VAL* 3.0 55.0 + - + +
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Residues in contact with CYS 146 (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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79B VAL* 4.0 8.0 - - + +
80B LEU 5.4 1.6 - - - -
81B ILE* 4.7 7.2 - - + -
130B LEU* 5.1 7.2 - - - -
132B MET* 3.7 38.6 - - - -
133B TRP* 3.7 26.7 - - + -
142B LEU 2.9 23.6 + - - +
143B HIS 3.5 4.9 - - - +
145B HIS* 1.3 76.6 - - - +
147B MET* 1.3 51.7 + - - +
148B GLN 3.4 0.3 + - - -
149B VAL* 3.8 11.4 + - - +
150B GLY 3.9 3.1 + - - -
153B TYR* 2.6 33.8 + - - -
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Residues in contact with MET 147 (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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81B ILE* 4.6 13.2 - - - -
133B TRP* 4.0 18.4 - - + -
143B HIS 3.1 18.7 + - - +
144B ASP* 3.9 9.9 - - - +
145B HIS 3.2 0.2 - - - -
146B CYS* 1.3 71.2 - - - +
148B GLN* 1.3 56.9 + - - +
153B TYR* 3.1 15.3 + - - -
171B LEU* 4.2 1.1 - - - +
174B GLN* 3.2 37.9 - - + +
175B LEU* 3.1 50.6 - - + +
178B ALA* 4.2 15.8 - - + +
179B ARG* 2.9 27.5 + - - +
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Residues in contact with GLN 148 (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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159A ILE* 5.2 0.4 - - - +
193A SER 5.4 0.6 + - - -
196A VAL* 3.1 47.4 + - + +
199A ARG* 3.0 42.9 - - - +
144B ASP 3.2 13.4 + - - +
145B HIS* 3.1 9.1 + - - +
147B MET* 1.3 78.6 - - - +
149B VAL* 1.3 62.5 + - + +
178B ALA* 6.0 0.9 - - + -
179B ARG* 2.9 29.4 + - - +
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Residues in contact with VAL 149 (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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199A ARG* 5.6 1.1 - - - +
203A VAL* 3.3 35.4 - - + +
77B ARG* 3.5 27.8 - - - +
130B LEU* 3.5 28.7 - - + -
145B HIS* 3.0 39.2 + - + +
146B CYS* 3.9 6.3 - - - +
148B GLN* 1.3 82.7 - - + +
150B GLY* 1.3 67.4 + - - +
151B ASP* 3.8 4.3 + - - +
179B ARG* 3.7 0.2 - - - -
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Residues in contact with GLY 150 (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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77B ARG* 3.7 9.6 - - - -
79B VAL* 3.7 17.5 - - - -
149B VAL* 1.3 81.7 - - - +
151B ASP* 1.3 64.5 + - - +
152B ALA 3.4 1.6 - - - -
153B TYR* 3.1 21.2 + - - -
179B ARG* 2.2 32.9 + - - -
184B ILE* 4.8 0.3 - - - +
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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