Contacts of the helix formed by residues 169 - 176 (chain B) in PDB entry 4NDH
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 GLN 169 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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164B MET 5.4 1.8 - - - +
165B GLY 4.5 1.7 - - - +
166B HIS* 2.9 37.5 + - - +
168B SER* 1.3 86.4 - - - +
170B GLY* 1.3 64.3 + - - +
171B LEU 3.4 1.6 - - - -
172B LYS* 3.3 12.2 + - + +
173B ILE* 3.1 37.1 + - + +
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Residues in contact with GLY 170 (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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166B HIS 4.0 2.4 + - - -
167B TRP 3.3 11.3 + - - -
168B SER 3.3 2.8 - - - -
169B GLN* 1.3 77.0 - - - +
171B LEU* 1.3 56.1 + - - +
173B ILE* 3.2 10.7 + - - +
174B SER* 2.9 32.7 + - - -
401B AMP 3.8 9.9 - - - -
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Residues in contact with LEU 171 (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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167B TRP 5.1 0.2 + - - -
168B SER 4.5 6.3 + - - +
169B GLN 3.4 0.6 - - - -
170B GLY* 1.3 74.6 - - - +
172B LYS* 1.3 57.9 + - - +
174B SER* 3.2 1.4 + - - -
175B MET* 2.9 36.5 + - + +
191B ILE* 3.7 22.7 - - + -
203B LEU* 4.1 6.5 - - + -
205B LEU* 4.5 10.8 - - + -
256B MET* 4.4 14.6 - - + -
260B HIS* 3.6 34.8 - - + +
401B AMP 3.6 55.3 + - + +
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Residues in contact with LYS 172 (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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168B SER 5.3 0.6 + - - +
169B GLN* 3.3 14.6 + - + +
170B GLY 3.3 0.6 - - - -
171B LEU* 1.3 78.2 - - - +
173B ILE* 1.3 65.3 + - + +
175B MET* 3.4 41.6 + - - +
176B GLN* 3.5 28.6 - - + +
207B TRP* 5.4 9.7 + - - -
258B HIS* 6.4 2.2 - - + -
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Residues in contact with ILE 173 (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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166B HIS 5.7 0.4 - - - +
169B GLN* 3.1 33.4 + - + +
170B GLY* 3.6 10.1 - - - +
172B LYS* 1.3 78.8 - - + +
174B SER* 1.3 64.4 + - - +
176B GLN* 3.1 17.3 + - - +
177B ASP* 3.3 12.0 + - + +
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Residues in contact with SER 174 (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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170B GLY 2.9 13.2 + - - -
171B LEU 3.6 4.3 - - - -
173B ILE* 1.3 75.4 - - - +
175B MET* 1.3 64.2 + - - +
177B ASP* 3.1 23.2 + - - +
180B MET* 3.6 23.3 - - - +
191B ILE* 4.3 8.6 - - - +
401B AMP 3.0 37.2 + - - -
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Residues in contact with MET 175 (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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171B LEU* 2.9 21.4 + - + +
172B LYS* 3.5 36.8 - - + +
174B SER* 1.3 75.6 - - - +
176B GLN* 1.3 59.2 + - + +
181B GLN* 2.8 26.7 + - - +
189B VAL* 3.5 26.3 - - + +
191B ILE* 4.4 11.1 - - - +
205B LEU* 3.6 37.0 - - + -
206B PRO 4.0 13.5 - - - +
207B TRP* 3.7 30.6 - - + -
260B HIS* 6.2 1.3 - - - -
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Residues in contact with GLN 176 (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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172B LYS* 3.5 29.0 - - + +
173B ILE* 3.1 10.0 + - - +
174B SER 3.1 1.2 - - - -
175B MET* 1.3 76.3 - - + +
177B ASP* 1.3 59.4 + - - +
178B PRO* 3.3 12.8 - - - +
181B GLN* 3.8 8.7 + - - +
207B TRP* 3.4 31.6 - - + -
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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