Contacts of the helix formed by residues 208 - 218 (chain A) in PDB entry 1N3Y
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 TYR 208 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174A PHE* 4.0 4.0 - - - -
175A SER 3.0 14.6 + - - +
176A ASN* 3.6 35.4 - - + +
178A PHE* 4.0 8.2 - + + -
206A PHE* 3.5 28.2 - + + -
207A THR* 1.3 71.7 - - - +
209A THR* 1.3 56.1 + - - +
211A THR* 4.2 8.5 - - + -
212A ALA* 2.9 27.2 + - - +
244A GLU 3.3 26.2 - - - -
245A GLY* 3.5 20.4 + - - -
246A ASP* 3.0 32.8 - - - +
247A SER 5.8 0.9 - - - -
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Residues in contact with THR 209 (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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136A LEU* 5.5 0.2 - - + -
174A PHE* 3.6 21.6 - - + -
207A THR* 3.4 24.7 + - - +
208A TYR* 1.3 73.2 - - - +
210A ALA* 1.3 57.5 + - - +
212A ALA* 3.5 1.5 - - + +
213A ILE* 3.0 37.4 + - + +
237A VAL* 4.3 9.4 - - + -
239A THR* 4.6 5.1 + - + -
241A GLY 4.7 1.0 + - - -
243A LYS* 3.6 11.8 + - - +
246A ASP* 3.4 0.6 + - - -
250A TYR* 3.4 23.2 + - - +
281A GLU* 4.6 0.3 + - - -
285A ILE* 3.8 18.6 - - + -
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Residues in contact with ALA 210 (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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209A THR* 1.3 74.9 - - - +
211A THR* 1.3 66.8 + - - +
213A ILE* 3.2 4.1 + - - +
214A GLN 3.0 17.5 + - - -
243A LYS* 3.8 15.6 - - + +
246A ASP* 3.0 10.1 + - - +
248A LEU* 3.4 29.8 - - + +
249A ASP 4.1 10.8 - - - +
250A TYR* 4.1 12.5 - - + -
253A VAL* 3.6 16.1 - - + +
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Residues in contact with THR 211 (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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178A PHE* 3.3 26.5 - - + -
208A TYR* 3.9 8.2 - - + +
210A ALA* 1.3 75.4 - - - +
212A ALA* 1.3 57.3 + - - +
214A GLN* 3.2 7.4 + - - +
215A ASN* 2.9 37.1 + - - +
246A ASP* 2.7 31.3 + - - -
247A SER* 4.6 3.3 + - - -
248A LEU* 3.4 26.1 - - + +
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Residues in contact with ALA 212 (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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136A LEU* 3.9 13.5 - - + -
172A MET* 4.2 1.1 - - - +
174A PHE* 3.4 41.3 - - + -
178A PHE* 3.5 13.8 - - + -
208A TYR 2.9 15.1 + - - +
209A THR* 3.5 5.8 - - - +
211A THR* 1.3 77.0 - - - +
213A ILE* 1.3 61.3 + - - +
215A ASN* 3.2 3.8 + - - +
216A VAL* 3.0 25.8 + - - +
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Residues in contact with ILE 213 (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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136A LEU* 3.9 18.8 - - + -
209A THR* 3.0 27.1 + - + +
210A ALA 3.6 4.0 - - - +
212A ALA* 1.3 75.2 - - - +
214A GLN* 1.3 58.5 + - - +
216A VAL* 3.2 3.8 + - - +
217A VAL* 2.9 49.7 + - + +
235A LEU* 4.2 15.9 - - + -
237A VAL* 4.6 2.5 - - + -
250A TYR* 4.1 19.5 - - + -
253A VAL* 4.3 13.7 - - + -
254A ILE* 4.4 16.6 - - + -
257A ALA* 5.1 4.3 - - + -
264A ARG* 5.2 1.3 - - - -
285A ILE* 4.0 28.3 - - + -
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Residues in contact with GLN 214 (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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210A ALA 3.0 14.0 + - - +
211A THR* 3.4 14.2 - - - +
213A ILE* 1.3 77.1 - - - +
215A ASN* 1.3 71.6 + - - +
217A VAL* 4.6 1.6 - - - -
218A HIS* 3.0 50.5 + - + +
248A LEU* 3.1 30.5 - - - +
252A ASP 5.0 2.8 - - - +
253A VAL* 3.7 20.0 - - + +
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Residues in contact with ASN 215 (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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172A MET* 4.1 19.3 - - + +
178A PHE* 3.3 41.9 - - + +
211A THR* 2.9 23.6 + - - +
212A ALA 3.6 6.1 - - - +
214A GLN* 1.3 86.9 + - - +
216A VAL* 1.3 61.1 + - - +
218A HIS* 5.2 0.9 - - - -
219A ARG* 3.3 59.0 + - - +
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Residues in contact with VAL 216 (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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134A VAL* 3.8 25.8 - - + -
136A LEU* 3.8 20.9 - - + -
172A MET* 3.6 20.4 - - + -
212A ALA 3.0 14.7 + - - +
213A ILE* 3.6 7.6 - - - +
215A ASN* 1.3 76.4 - - - +
217A VAL* 1.3 64.6 - - + +
220A LEU* 3.0 41.5 + - + +
221A PHE* 4.0 22.7 + - + -
235A LEU* 4.1 13.0 - - + -
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Residues in contact with VAL 217 (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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213A ILE* 2.9 37.2 + - + +
214A GLN* 4.0 3.4 - - - +
216A VAL* 1.3 79.2 - - + +
218A HIS* 1.3 75.7 + - + +
219A ARG 3.6 0.5 + - - -
221A PHE* 4.6 11.0 + - - +
222A HIS* 5.1 3.3 + - - -
235A LEU* 4.9 6.3 - - + -
253A VAL 5.3 3.1 - - - +
256A MET* 4.7 6.1 - - + +
257A ALA* 4.0 25.8 - - + +
260A ALA* 5.0 3.4 - - + -
262A ILE* 3.7 33.6 - - + +
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Residues in contact with HIS 218 (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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214A GLN* 3.0 45.2 + - + +
215A ASN* 5.2 0.4 - - - -
217A VAL* 1.3 92.6 + - + +
219A ARG* 1.3 69.1 + - + +
222A HIS* 2.9 26.2 + - - -
253A VAL* 5.8 1.2 + - - -
256A MET* 3.4 46.1 - - + +
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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