Contacts of the helix formed by residues 199 - 212 (chain A) in PDB entry 1H4R
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 ALA 199 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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197A GLY 3.5 5.1 + - - -
198A ARG* 1.3 79.6 - - - +
200A ARG* 1.3 61.2 + - - +
201A ASP* 3.3 18.8 - - - +
202A GLU* 3.0 19.1 + - + +
203A ALA* 2.9 25.7 + - - +
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Residues in contact with ARG 200 (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 4.0 11.0 - - - +
148A ALA* 3.2 34.7 + - + +
149A LYS* 4.4 9.8 + - - +
150A TYR 5.3 0.4 - - - -
151A GLY* 4.5 15.5 - - - +
198A ARG 3.7 1.3 + - - +
199A ALA* 1.3 72.7 - - - +
201A ASP* 1.3 63.8 + - - +
203A ALA* 3.2 5.1 + - - +
204A GLU* 3.2 29.2 + - - +
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Residues in contact with ASP 201 (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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112A GLU* 3.8 39.3 - - + +
115A GLN* 4.1 17.0 - - - +
199A ALA* 3.4 18.0 - - - +
200A ARG* 1.3 74.7 - - - +
202A GLU* 1.3 76.7 + - - +
204A GLU* 3.4 13.1 + - - +
205A MET* 3.2 20.6 + - - +
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Residues in contact with GLU 202 (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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198A ARG* 2.8 44.3 + - - +
199A ALA* 3.0 18.7 + - + +
201A ASP* 1.3 93.0 + - - +
203A ALA* 1.3 60.5 + - - +
205A MET* 3.2 8.0 + - - +
206A GLU* 2.9 32.0 + - - +
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Residues in contact with ALA 203 (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 TYR* 3.7 37.7 - - + +
147A GLN* 3.8 22.7 - - + -
148A ALA* 3.9 4.3 - - - +
198A ARG* 3.8 8.5 - - + +
199A ALA 2.9 12.0 + - - +
200A ARG 3.2 8.7 + - - +
202A GLU* 1.3 73.4 - - - +
204A GLU* 1.3 66.7 + - - +
206A GLU* 3.2 0.9 + - - +
207A TYR* 3.0 22.7 + - - +
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Residues in contact with GLU 204 (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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115A GLN* 5.2 5.2 - - + +
116A HIS* 2.7 50.8 + - - +
119A PHE* 3.3 38.9 - - + -
148A ALA* 3.5 22.4 - - + +
200A ARG* 3.2 15.7 + - - +
201A ASP* 3.7 12.8 - - - +
202A GLU 3.2 0.4 - - - -
203A ALA* 1.3 78.0 - - - +
205A MET* 1.3 60.6 + - - +
207A TYR* 3.3 4.5 + - - +
208A LEU* 3.0 27.0 + - - +
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Residues in contact with MET 205 (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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105A ALA* 3.9 19.1 - - - +
106A GLU* 3.8 37.5 - - + +
109A LEU* 4.1 4.3 - - + +
115A GLN* 3.7 42.8 - - + +
201A ASP 3.2 13.3 + - - +
202A GLU* 3.2 10.7 + - - +
204A GLU* 1.3 74.1 - - - +
206A GLU* 1.3 65.6 + - - +
208A LEU* 3.2 17.6 + - + -
209A LYS* 2.9 38.8 + - + +
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Residues in contact with GLU 206 (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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106A GLU* 4.9 2.3 - - - +
144A TYR* 3.6 36.8 + - + -
198A ARG* 4.6 19.9 + - - +
202A GLU* 2.9 21.7 + - + +
203A ALA 3.2 2.4 + - - +
205A MET* 1.3 78.0 - - - +
207A TYR* 1.3 60.8 + - - +
209A LYS* 3.0 39.8 + - - +
210A ILE* 3.2 30.5 + - - +
1315A SO4 4.4 8.5 + - - +
213B ASP* 5.8 0.3 - - - +
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Residues in contact with TYR 207 (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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119A PHE* 3.6 25.8 - + + -
122A VAL* 4.5 2.7 - - + -
123A LYS* 3.3 53.9 - - + +
126A ILE* 3.8 19.8 - - + +
127A LEU* 5.5 0.7 - - - +
141A LEU* 3.3 61.3 - - + +
142A ALA* 4.7 0.4 - - - -
144A TYR* 4.2 7.5 - - + +
145A ALA* 4.2 6.1 - - + -
203A ALA 3.0 12.3 + - - +
204A GLU 3.3 9.6 - - - +
206A GLU* 1.3 76.7 - - - +
208A LEU* 1.3 68.7 + - + +
210A ILE 3.2 2.8 + - - -
211A ALA* 2.9 30.8 + - + -
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Residues in contact with LEU 208 (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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105A ALA* 4.5 7.6 - - + -
109A LEU* 4.2 14.4 - - + -
115A GLN 3.6 25.1 - - - +
118A PHE* 4.0 17.0 - - + +
119A PHE* 3.9 23.6 - - - +
122A VAL* 4.0 22.2 - - + -
204A GLU 3.0 15.3 + - - +
205A MET* 3.2 24.7 + - + +
207A TYR* 1.3 82.6 - - + +
209A LYS* 1.3 56.6 + - - +
211A ALA* 4.3 1.8 - - - -
212A GLN* 2.9 35.6 + - - +
217A TYR* 4.8 9.6 - - + +
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Residues in contact with LYS 209 (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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105A ALA* 5.7 0.4 - - + -
106A GLU* 3.6 41.8 + - + +
205A MET* 2.9 33.3 + - + +
206A GLU* 3.0 41.8 + - - +
207A TYR 3.2 0.2 - - - -
208A LEU* 1.3 76.6 - - - +
210A ILE* 1.3 62.8 + - + +
212A GLN* 3.4 29.7 + - - +
213A ASP* 3.8 13.3 - - - +
213B ASP* 5.8 2.2 + - - -
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Residues in contact with ILE 210 (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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137A ALA* 5.0 10.1 - - + +
140A LEU* 3.7 27.4 - - + -
141A LEU* 3.4 28.5 - - + -
144A TYR* 3.6 30.3 - - + -
206A GLU* 3.2 16.2 + - + +
207A TYR 3.2 6.4 + - - +
209A LYS* 1.3 77.7 - - + +
211A ALA* 1.3 62.6 + - - +
213A ASP* 3.2 19.0 + - - +
214A LEU* 3.8 10.5 + - + +
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Residues in contact with ALA 211 (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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122A VAL* 3.7 29.4 - - + -
126A ILE* 5.1 1.8 - - + -
131A ILE* 5.3 0.2 - - - +
141A LEU* 4.5 3.6 - - + -
207A TYR* 2.9 27.6 + - + +
208A LEU* 3.9 5.4 - - - +
210A ILE* 1.3 79.1 - - - +
212A GLN* 1.3 56.5 + - - +
214A LEU* 3.0 41.8 + - + +
217A TYR* 3.4 12.3 - - + +
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Residues in contact with GLN 212 (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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102A PRO 4.9 2.3 - - - +
103A GLU 4.1 7.6 + - - +
104A ASN* 3.9 13.9 + - - +
105A ALA* 3.0 38.2 + - + +
106A GLU* 5.0 1.0 - - - +
208A LEU 2.9 17.1 + - - +
209A LYS* 3.4 27.0 + - - +
211A ALA* 1.3 77.2 - - - +
213A ASP* 1.3 70.2 + - - +
214A LEU 3.3 3.5 + - - +
217A TYR* 3.5 41.3 + - + +
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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