Contacts of the helix formed by residues 188 - 196 (chain B) in PDB entry 3N1Y
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 ARG 188 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122B ALA* 6.6 0.2 - - - -
182B ASP 5.5 3.5 + - - -
183B VAL 3.4 23.6 + - - -
184B GLY* 2.9 24.0 + - - +
187B LYS* 1.3 91.7 - - + +
189B GLU* 1.3 66.8 + - - +
190B ARG 3.3 2.9 - - - -
191B ASP* 3.2 15.3 + - + +
192B VAL* 3.2 28.2 + - + +
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Residues in contact with GLU 189 (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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122B ALA* 4.7 3.1 - - - +
126B THR* 2.7 46.7 + - - +
127B PRO* 3.5 19.3 - - + +
129B ARG* 3.1 29.8 + - - +
130B TYR* 3.8 4.0 - - + -
184B GLY 4.2 0.5 - - - +
185B PHE* 3.6 9.1 - - - -
186B GLY* 2.8 45.9 + - - -
187B LYS 3.6 1.0 - - - -
188B ARG* 1.3 74.0 - - - +
190B ARG* 1.3 57.8 + - - +
192B VAL* 3.2 2.6 + - - +
193B TRP* 2.9 31.7 + - - +
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Residues in contact with ARG 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A ASN* 3.5 23.8 + - - +
18A TRP* 3.4 17.2 - - + +
19A THR* 3.2 23.8 + - - +
41A MET* 4.8 8.1 - - - -
45A GLU* 4.3 15.6 + - - -
129B ARG* 4.5 1.8 - - - +
130B TYR* 3.5 28.6 + - + +
187B LYS 4.9 3.5 + - - +
188B ARG 3.3 1.0 - - - -
189B GLU* 1.3 77.3 - - - +
191B ASP* 1.3 61.5 + - - +
193B TRP* 3.8 1.1 - - - +
194B GLU* 2.8 52.8 + - + +
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Residues in contact with ASP 191 (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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187B LYS 5.2 2.7 + - - +
188B ARG* 3.2 16.1 + - + +
190B ARG* 1.3 81.0 - - - +
192B VAL* 1.3 62.1 + - + +
194B GLU* 4.6 6.2 - - - +
195B ASN* 2.8 50.4 + - - +
196B ASP 3.8 0.2 + - - -
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Residues in contact with VAL 192 (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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122B ALA 4.4 10.5 - - - +
123B ARG* 3.7 15.7 - - + +
127B PRO* 3.8 7.0 - - + -
188B ARG* 3.2 25.6 - - + +
189B GLU* 3.2 7.5 + - - +
191B ASP* 1.3 77.8 - - + +
193B TRP* 1.3 61.0 + - - +
196B ASP* 2.8 50.5 + - + +
199B TRP* 3.6 29.2 - - + +
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Residues in contact with TRP 193 (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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18A TRP* 3.3 51.0 - + + -
127B PRO* 4.5 6.9 - - + +
130B TYR* 3.7 39.7 - + + +
131B LEU* 4.0 27.8 - - + -
189B GLU 2.9 16.7 + - - +
190B ARG 3.8 2.2 - - - +
192B VAL* 1.3 77.3 - - - +
194B GLU* 1.3 60.8 + - + +
199B TRP* 3.7 43.9 - + + +
200B GLN* 2.9 18.9 + - - -
202B PHE* 4.5 0.7 - - + -
203B ARG* 3.4 49.8 - - + -
206B ILE* 4.0 19.3 - - + -
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Residues in contact with GLU 194 (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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18A TRP* 3.5 2.7 - - + -
19A THR* 2.9 32.2 + - - -
21A LYS* 5.3 3.3 - - - +
190B ARG* 2.8 58.8 + - - +
191B ASP* 4.7 5.0 - - - +
193B TRP* 1.3 85.5 - - + +
195B ASN* 1.3 73.6 + - - +
200B GLN* 3.4 7.8 + - - +
203B ARG* 2.8 40.6 + - - +
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Residues in contact with ASN 195 (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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191B ASP* 2.8 48.9 + - - +
194B GLU* 1.3 91.2 + - - +
196B ASP* 1.3 62.0 + - - +
197B PRO* 3.3 9.7 - - - +
200B GLN* 3.8 5.1 - - - +
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Residues in contact with ASP 196 (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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123B ARG* 2.7 48.7 + - - +
191B ASP 3.8 0.2 + - - -
192B VAL* 2.8 41.2 + - + +
195B ASN* 1.3 72.0 - - - +
197B PRO* 1.3 64.0 - - - +
198B ALA* 2.8 30.8 + - - +
199B TRP* 2.8 23.7 + - + -
200B GLN* 3.0 13.0 + - - -
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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