Contacts of the helix formed by residues 173 - 179 (chain B) in PDB entry 3N6J
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 HIS 173 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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169B VAL 4.7 0.9 - - - +
172B LYS* 1.3 80.9 - - - +
174B GLU* 1.3 82.8 + - + +
175B TRP* 2.8 14.7 + - - +
176B TYR* 3.0 36.0 + - + +
177B ASP* 3.7 5.5 + - - +
195B ALA* 3.4 28.9 - - - -
198B ASP* 2.7 32.8 + - + -
199B ARG* 3.7 30.0 + - + +
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Residues in contact with GLU 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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172B LYS 3.6 4.0 + - - -
173B HIS* 1.3 80.3 + - + +
175B TRP* 1.3 56.6 + - - +
177B ASP* 3.1 19.9 + - - +
178B ILE* 2.9 61.4 + - - +
191B GLU* 4.1 8.4 - - - +
195B ALA* 4.5 9.8 - - + +
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Residues in contact with TRP 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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152B LEU* 5.5 1.8 - - + -
173B HIS* 2.8 20.5 + - + +
174B GLU* 1.3 74.9 - - - +
176B TYR* 1.3 64.2 - + + +
178B ILE* 4.3 1.1 - - + -
179B ARG* 2.9 60.8 + - + +
192B LEU* 3.4 44.2 - - + -
195B ALA* 3.7 17.9 - - + +
196B SER* 3.5 23.3 - - - -
199B ARG* 4.8 4.3 - - + -
200B TYR* 3.4 27.4 + + - -
371B ILE* 2.7 57.1 + - + -
372B TRP* 4.0 24.9 - + - -
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Residues in contact with TYR 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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168B PRO* 3.9 2.8 - - - +
169B VAL* 3.1 39.5 + - + +
172B LYS* 4.3 18.8 - - + +
173B HIS* 3.0 26.1 + - + +
175B TRP* 1.3 75.8 - + + +
177B ASP* 1.3 64.9 + - - +
179B ARG* 3.6 27.0 + - - +
180B ARG* 4.4 9.7 - - - +
199B ARG* 2.7 49.6 + - + -
200B TYR* 3.9 8.1 - - - -
374B GLU* 2.5 45.9 + - - -
375B GLY* 4.5 9.1 - - - -
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Residues in contact with ASP 177 (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 PRO* 3.3 21.7 - - - +
169B VAL 3.1 14.6 + - - +
170B THR* 3.3 31.7 - - - +
173B HIS 3.7 2.3 + - - +
174B GLU* 3.1 25.9 + - - +
176B TYR* 1.3 82.4 - - - +
178B ILE* 1.3 68.5 + - + +
179B ARG 3.3 0.9 + - - -
180B ARG 3.5 5.5 + - - -
181B LYS* 3.4 28.8 + - - +
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Residues in contact with ILE 178 (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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155B VAL* 5.7 0.2 - - - +
174B GLU* 2.9 44.1 + - - +
175B TRP* 4.1 6.3 - - + +
177B ASP* 1.3 77.8 - - + +
179B ARG* 1.3 62.9 + - - +
180B ARG 3.3 0.7 - - - -
181B LYS* 3.4 39.0 + - + +
182B LYS 5.3 0.3 - - - +
183B ALA* 5.7 0.5 - - - +
191B GLU* 3.5 57.0 - - + +
192B LEU* 3.7 23.8 - - + +
195B ALA* 3.8 10.8 - - + -
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Residues in contact with ARG 179 (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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24B SER* 2.6 29.3 + - - -
155B VAL* 4.6 1.7 - - - +
166B GLN* 4.6 2.4 + - - -
169B VAL* 6.4 0.2 - - - +
175B TRP* 2.9 53.4 + - + +
176B TYR* 3.6 28.0 + - - +
178B ILE* 1.3 77.2 - - - +
180B ARG* 1.3 98.3 + - + +
181B LYS 3.3 6.0 + - - +
192B LEU* 4.6 4.3 - - - -
200B TYR* 4.5 0.2 + - - -
371B ILE 3.3 18.8 + - - -
372B TRP* 3.4 28.7 + - + +
374B GLU* 2.9 30.2 + - - +
375B GLY 4.4 7.5 + - - -
376B ASP* 4.4 5.1 - - - +
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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