Contacts of the helix formed by residues 204 - 216 (chain A) in PDB entry 2Y01
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 ASN 204 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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181A TRP 2.8 26.2 + - - +
182A TRP* 2.8 18.8 + - - +
183A ARG 2.7 27.3 + - - +
184A ASP* 3.9 22.2 - - - +
203A THR* 1.3 79.9 + - - +
205A ARG* 1.3 62.3 + - - +
206A ALA* 3.1 12.0 + - - +
207A TYR* 2.8 29.2 + - - +
208A ALA* 3.3 16.8 + - - +
501A 2CV 3.3 27.7 + - - +
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Residues in contact with ARG 205 (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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184A ASP* 4.9 5.5 + - - +
186A ASP* 5.0 9.7 + - - -
204A ASN* 1.3 72.0 - - - +
206A ALA* 1.3 66.1 + - - +
208A ALA* 3.4 2.5 + - - +
209A ILE* 3.0 28.4 + - - +
313A ASN 4.5 0.2 + - - -
314A VAL* 2.6 64.6 + - + +
317A ARG* 3.3 29.1 - - - +
501A 2CV 5.0 4.9 + - - -
503A 2CV 2.9 39.6 + - - -
157B ARG* 5.8 0.2 - - - -
401B Y01 3.8 34.5 + - + +
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Residues in contact with ALA 206 (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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204A ASN* 3.1 9.2 + - - +
205A ARG* 1.3 78.5 - - - +
207A TYR* 1.3 58.1 + - - +
209A ILE 3.4 0.2 + - - -
210A ALA* 2.8 33.8 + - - +
501A 2CV 4.1 9.6 - - + +
160B VAL* 3.7 15.7 - - + -
164B THR* 3.5 25.1 - - - +
401B Y01 3.1 29.5 + - + +
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Residues in contact with TYR 207 (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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122A VAL* 4.1 11.6 - - - +
173A SER* 4.9 1.6 + - - -
176A PRO* 3.8 24.1 - - + +
177A ILE* 3.7 24.5 - - + +
181A TRP 3.9 10.8 - - - +
182A TRP* 3.8 24.7 - - + +
201A PHE* 3.7 29.3 - + - -
203A THR* 4.0 15.3 - - + -
204A ASN* 2.8 19.2 + - - +
206A ALA* 1.3 73.9 - - - +
208A ALA* 1.3 61.2 + - - +
211A SER* 2.7 59.3 + - - -
501A 2CV 3.9 33.8 - - + +
601A Y00 4.0 3.4 - - - -
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Residues in contact with ALA 208 (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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203A THR* 3.8 11.9 + - - +
204A ASN 3.3 12.5 + - - +
205A ARG* 3.6 7.9 - - - +
207A TYR* 1.3 82.6 - - - +
209A ILE* 1.3 60.8 + - - +
211A SER* 3.7 4.4 + - - -
212A SER* 2.8 31.9 + - - -
310A ASN* 4.5 20.4 - - - +
311A ILE* 4.5 2.0 - - - +
314A VAL* 3.9 18.6 - - + -
601A Y00 4.9 1.6 - - - +
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Residues in contact with ILE 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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205A ARG 3.0 19.5 + - - +
206A ALA 4.0 2.0 - - - +
208A ALA* 1.3 74.7 - - - +
210A ALA* 1.3 59.2 + - - +
212A SER* 3.6 0.9 - - - -
213A ILE* 3.0 56.1 + - + +
311A ILE* 4.5 17.0 - - + -
314A VAL* 3.6 34.1 - - + -
315A PHE* 5.0 9.9 - - + -
503A 2CV 4.6 7.4 - - + -
401B Y01 3.7 44.2 - - + +
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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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206A ALA 2.8 22.4 + - - +
207A TYR 3.9 0.4 - - - +
209A ILE* 1.3 72.7 - - - +
211A SER* 1.3 57.6 + - - +
213A ILE* 3.3 4.4 + - - +
214A ILE* 2.9 37.0 + - - +
501A 2CV 3.8 27.6 - - + -
164B THR* 4.3 5.6 - - + -
168B ILE* 4.4 9.0 - - + -
401B Y01 3.8 20.3 - - + +
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Residues in contact with SER 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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122A VAL* 5.6 2.0 - - - -
172A VAL* 5.9 2.0 - - - -
207A TYR* 2.7 54.1 + - - -
208A ALA 3.7 1.4 + - - -
210A ALA* 1.3 71.1 - - - +
212A SER* 1.3 57.6 + - - +
214A ILE* 4.7 0.7 - - - -
215A SER* 2.7 43.7 + - - +
501A 2CV 4.0 11.8 - - - +
601A Y00 3.2 30.5 + - - -
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Residues in contact with SER 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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208A ALA 2.8 21.3 + - - -
209A ILE 3.6 2.9 - - - -
211A SER* 1.3 80.5 + - - +
213A ILE* 1.3 57.9 + - - +
216A PHE* 2.8 28.9 + - - +
217A TYR* 3.0 19.7 + - - -
307A PHE* 3.7 13.0 - - - -
310A ASN* 3.0 23.7 + - - +
311A ILE* 3.8 21.6 - - - +
601A Y00 4.3 4.0 - - - -
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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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209A ILE* 3.0 41.4 + - + +
210A ALA* 3.8 4.3 - - - +
212A SER* 1.3 77.1 - - - +
214A ILE* 1.3 64.1 + - + +
217A TYR* 3.6 20.4 + - + -
218A ILE* 3.1 54.0 + - + +
311A ILE* 5.7 2.2 - - + -
401B Y01 4.3 42.4 - - + -
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Residues in contact with ILE 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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126A THR* 5.4 0.3 - - - +
130A GLU* 5.3 1.2 - - - +
172A VAL* 3.5 38.2 - - + +
210A ALA* 2.9 20.7 + - + +
211A SER* 4.3 2.5 - - - +
213A ILE* 1.3 83.0 - - + +
215A SER* 1.3 61.9 + - - +
218A ILE* 4.8 0.2 - - - -
219A PRO* 3.8 4.3 - - - +
401A Y01 3.7 33.7 - - + +
501A 2CV 4.0 15.3 - - + -
168B ILE* 3.9 39.7 - - + -
401B Y01 4.4 26.9 - - + -
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Residues in contact with SER 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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122A VAL* 4.0 10.8 - - - +
125A VAL* 5.3 3.2 - - - +
126A THR* 2.9 36.7 + - - +
129A ILE* 3.2 24.3 - - - +
172A VAL* 3.5 15.1 - - - +
211A SER* 2.7 27.1 + - - -
212A SER 4.6 0.2 - - - -
214A ILE* 1.3 74.8 - - - +
216A PHE* 1.3 58.3 + - - +
219A PRO* 3.5 6.0 - - - +
307A PHE* 5.5 1.1 - - - -
601A Y00 4.2 12.3 + - - -
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Residues in contact with PHE 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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125A VAL* 4.9 5.6 - - + -
129A ILE* 4.4 6.8 - - + +
212A SER 2.8 16.3 + - - +
214A ILE 3.5 1.4 - - - -
215A SER* 1.3 76.6 - - - +
217A TYR* 1.3 71.7 + + - +
218A ILE 3.3 2.0 + - - -
219A PRO* 3.3 3.5 - - - +
220A LEU* 2.8 62.9 + - + +
299A PHE* 4.3 16.2 - + - -
300A THR 5.0 1.1 - - - -
303A TRP* 3.7 20.6 - - + -
304A LEU* 3.7 43.7 - - + -
307A PHE* 3.5 49.4 - + + -
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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