Contacts of the helix formed by residues 161 - 172 (chain A) in PDB entry 6H2U
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 THR 161 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138A ASP* 4.8 5.6 + - - +
157A HIS* 4.3 1.7 - - - +
158A LYS* 2.7 43.9 + - + -
160A SER* 1.3 83.0 - - - +
162A ARG* 1.3 64.5 + - - +
163A GLU* 3.3 2.9 - - - -
164A HIS* 3.1 23.3 + - - +
165A VAL* 3.1 23.3 + - - +
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Residues in contact with ARG 162 (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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158A LYS 3.6 2.1 + - - -
159A SER* 3.2 22.5 + - - +
160A SER 3.4 1.2 - - - -
161A THR* 1.3 77.0 - - - +
163A GLU* 1.3 64.7 + - + +
165A VAL* 3.1 9.1 + - + +
166A GLN* 2.9 49.3 + - + +
178A ILE* 4.1 23.1 - - + +
181A GLU* 2.8 33.3 + - - +
203A ASP* 2.8 45.5 + - - +
205A ILE* 5.9 1.6 - - + -
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Residues in contact with GLU 163 (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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160A SER 5.3 0.6 + - - +
161A THR 3.3 0.6 - - - -
162A ARG* 1.3 79.3 - - + +
164A HIS* 1.3 57.7 + - - +
166A GLN* 3.4 16.2 + - - +
167A LYS* 3.0 29.0 + - - +
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Residues in contact with HIS 164 (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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135A LYS* 5.7 8.1 - - + +
139A MET* 4.0 31.2 - - + +
161A THR* 3.1 17.4 + - - +
163A GLU* 1.3 76.4 - - - +
165A VAL* 1.3 65.5 + - + +
167A LYS* 3.2 17.0 + - + +
168A LYS* 3.0 51.6 + - + +
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Residues in contact with VAL 165 (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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138A ASP* 5.4 0.2 - - - +
139A MET* 4.0 23.3 - - - -
142A LEU* 4.3 10.9 - - + +
157A HIS* 4.3 15.9 - - + +
161A THR* 3.1 28.2 + - - +
162A ARG* 3.1 8.6 + - - +
164A HIS* 1.3 75.9 - - + +
166A GLN* 1.3 57.0 + - - +
168A LYS* 3.4 2.1 + - - +
169A ALA* 3.0 28.6 + - - +
176A ILE* 4.0 7.6 - - + -
205A ILE* 4.1 9.6 - - + -
207A PHE* 3.7 34.1 - - + -
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Residues in contact with GLN 166 (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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162A ARG* 2.9 44.9 + - + +
163A GLU* 3.7 18.7 - - - +
165A VAL* 1.3 76.4 - - - +
167A LYS* 1.3 63.0 + - - +
169A ALA* 3.4 3.1 + - - +
170A ALA* 3.0 23.6 + - - +
176A ILE* 4.1 27.8 - - + +
178A ILE* 4.6 10.3 - - - +
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Residues in contact with LYS 167 (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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163A GLU 3.0 17.6 + - - +
164A HIS* 3.2 19.6 + - + +
166A GLN* 1.3 78.3 - - - +
168A LYS* 1.3 66.8 + - + +
170A ALA* 3.2 7.5 + - - +
171A GLU* 3.0 48.5 + - + +
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Residues in contact with LYS 168 (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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135A LYS* 6.2 3.3 - - - +
139A MET* 3.7 20.4 - - + -
164A HIS* 3.0 50.1 + - + +
165A VAL 3.9 1.8 - - - +
167A LYS* 1.3 78.9 - - + +
169A ALA* 1.3 58.2 + - - +
171A GLU* 2.6 30.2 + - - +
172A TRP* 2.8 71.6 + - + +
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Residues in contact with ALA 169 (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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165A VAL 3.0 17.0 + - - +
166A GLN 3.7 4.7 - - - +
168A LYS* 1.3 77.0 - - - +
170A ALA* 1.3 60.6 + - - +
172A TRP* 3.4 6.9 + - - -
173A LYS 3.0 3.6 + - - -
174A ILE* 3.0 51.7 + - + +
176A ILE* 4.0 27.6 - - + -
207A PHE* 4.8 8.1 - - + -
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Residues in contact with ALA 170 (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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166A GLN 3.0 14.4 + - - +
167A LYS* 3.2 11.0 + - - +
169A ALA* 1.3 77.9 - - - +
171A GLU* 1.3 61.9 + - + +
173A LYS* 3.2 19.1 + - - +
174A ILE 5.1 1.3 - - - -
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Residues in contact with GLU 171 (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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167A LYS* 3.0 40.8 + - + +
168A LYS* 2.6 39.9 + - - +
170A ALA* 1.3 76.2 - - + +
172A TRP* 1.3 66.6 + - + +
173A LYS* 3.2 10.6 + - - +
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Residues in contact with TRP 172 (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 MET* 4.1 18.6 - - + -
142A LEU* 4.0 19.1 - - + -
143A LYS* 4.2 43.8 - - + +
146A LEU* 3.6 30.5 - - + -
168A LYS* 2.8 59.6 + - + +
169A ALA* 4.0 4.9 - - - +
170A ALA 3.3 0.2 - - - -
171A GLU* 1.3 81.9 - - + +
173A LYS* 1.3 69.7 + - - +
174A ILE* 3.4 20.3 + - + +
207A PHE* 6.5 0.2 - + - -
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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