Contacts of the helix formed by residues 166 - 175 (chain B) in PDB entry 3NAY
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 166 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2B MP6 4.0 37.5 + - + +
164B ASN 4.0 0.2 + - - -
165B GLY* 1.3 73.2 - - - -
167B LEU* 1.3 63.2 + - - +
168B LEU* 3.9 17.6 - - - +
169B LYS* 3.1 29.4 + - + +
170B TYR* 3.4 10.2 - - - -
208B PRO 4.0 2.2 - - - +
209B GLU* 3.4 49.6 - - - +
211B ILE 3.7 5.6 - - - -
212B LEU* 4.3 2.9 - - + +
213B LEU* 4.4 0.7 - - - -
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Residues in contact with LEU 167 (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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165B GLY 4.1 0.6 + - - -
166B GLU* 1.3 71.9 - - - +
168B LEU* 1.4 60.8 + - - +
170B TYR* 3.1 7.0 + - + +
171B ILE* 3.1 24.0 + - + +
177B PHE* 4.4 14.8 - - + -
185B TYR* 5.2 15.0 - - + -
189B ILE* 4.8 5.6 - - + -
208B PRO* 3.6 14.1 - - + +
211B ILE* 2.8 55.6 + - + +
213B LEU* 4.0 20.7 - - + +
219B ILE* 6.2 0.9 - - + -
271B ILE* 4.3 8.1 - - + -
275B LEU* 3.9 29.4 - - + -
358B LEU* 6.2 0.9 - - + -
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Residues in contact with LEU 168 (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 GLU* 3.1 8.9 - - - +
167B LEU* 1.4 74.2 - - - +
169B LYS* 1.3 59.8 + - - +
171B ILE* 3.4 7.1 + - + -
172B ARG* 3.0 72.6 + - + +
208B PRO* 3.3 28.6 + - + +
209B GLU* 4.0 31.6 - - + +
248B TYR* 5.4 1.1 - - - +
274B GLN* 4.0 23.3 - - - +
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Residues in contact with LYS 169 (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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2B MP6 4.4 11.5 + - - -
163B LYS 5.1 0.4 + - - -
164B ASN* 3.1 34.9 + - - +
165B GLY* 3.7 9.0 - - - +
166B GLU* 3.1 22.4 + - + +
168B LEU* 1.3 77.5 - - - +
170B TYR* 1.3 72.9 + - + +
172B ARG* 3.6 6.3 + - - +
173B LYS* 3.0 36.2 + - + +
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Residues in contact with TYR 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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164B ASN* 2.9 46.2 + - - +
166B GLU 3.4 14.8 - - - -
167B LEU* 3.1 8.7 + - + +
169B LYS* 1.3 88.1 - - - +
171B ILE* 1.4 58.5 + - - +
172B ARG 3.1 1.1 - - - -
173B LYS* 3.9 26.7 - - + -
174B ILE* 2.9 38.7 + - + +
177B PHE* 4.1 10.8 - - + -
213B LEU* 3.4 25.6 - - + -
217B MET* 4.2 9.6 - - + -
358B LEU* 3.7 31.2 - - + -
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Residues in contact with ILE 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 LEU* 3.1 15.3 + - + +
168B LEU* 3.4 10.3 + - + +
170B TYR* 1.4 73.7 - - - +
172B ARG* 1.4 56.9 + - + +
175B GLY* 3.0 30.6 + - - +
177B PHE* 4.0 11.7 - - + -
208B PRO* 3.7 36.8 - - + -
271B ILE* 5.5 0.4 - - + +
274B GLN* 3.9 36.6 - - + +
275B LEU* 3.8 33.0 - - + -
278B GLY* 3.8 24.0 - - - +
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Residues in contact with ARG 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 LEU* 3.0 57.6 + - + +
169B LYS* 3.6 6.9 - - - +
171B ILE* 1.4 77.6 - - + +
173B LYS* 1.3 64.9 + - - +
175B GLY* 4.2 3.1 + - - -
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Residues in contact with LYS 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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169B LYS* 3.0 31.0 + - + +
170B TYR* 3.9 26.1 - - + +
172B ARG* 1.3 74.4 - - - +
174B ILE* 1.4 81.7 + - + +
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Residues in contact with ILE 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 TYR* 2.9 11.3 + - + +
173B LYS* 1.4 101.6 - - + +
175B GLY* 1.3 60.3 + - - +
176B SER 3.7 3.3 + - - +
177B PHE* 3.5 42.2 - - + -
358B LEU* 4.3 22.2 - - + +
359B THR 3.7 8.3 - - - +
360B ALA* 3.6 48.7 - - + +
362B LEU* 5.9 1.6 - - - +
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Residues in contact with GLY 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 ILE* 3.0 24.1 + - - +
172B ARG 4.2 2.9 + - - -
173B LYS 3.8 0.8 - - - -
174B ILE* 1.3 75.6 - - - +
176B SER* 1.3 65.2 + - - -
177B PHE* 3.3 18.2 - - - -
275B LEU 4.0 2.3 - - - +
278B GLY* 4.2 13.7 - - - -
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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