Contacts of the helix formed by residues 209 - 222 (chain A) in PDB entry 1P4A
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 GLY 209 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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206A MET* 4.2 19.6 - - - +
207A LYS 3.6 1.2 - - - -
208A ALA* 1.3 78.6 - - - +
210A GLY* 1.3 64.6 + - - +
211A THR 3.3 2.7 - - - -
212A ILE* 3.5 4.1 + - - +
213A ASN* 3.0 34.4 + - - -
241A ARG 5.2 0.2 - - - -
242A LEU* 4.5 9.3 - - - +
604A PCP 2.8 12.6 + - - -
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Residues in contact with GLY 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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175A TYR* 3.7 8.4 - - - +
176A VAL* 3.4 27.4 - - - -
208A ALA* 3.5 3.8 + - - +
209A GLY* 1.3 78.3 - - - +
211A THR* 1.3 56.6 + - - +
213A ASN* 3.7 6.7 - - - +
214A GLY* 2.8 27.0 + - - -
604A PCP 3.4 5.1 + - - -
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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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137A VAL* 3.9 30.7 - - + -
175A TYR* 3.8 20.3 - - + +
176A VAL 4.1 0.2 + - - -
177A SER* 4.4 3.3 + - - -
186A MET* 3.5 9.2 - - + +
203A ASP* 5.0 2.0 - - - +
209A GLY 3.3 0.2 - - - -
210A GLY* 1.3 72.5 - - - +
212A ILE* 1.3 58.6 + - - +
214A GLY* 3.1 3.5 + - - -
215A MET* 2.9 31.6 + - + +
604A PCP 2.4 62.1 + - + +
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Residues in contact with ILE 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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201A ILE* 4.3 8.5 - - + -
203A ASP* 3.7 18.4 - - + +
206A MET* 3.4 33.7 - - + -
209A GLY* 3.5 8.6 + - - +
210A GLY 3.5 0.2 - - - -
211A THR* 1.3 78.4 - - - +
213A ASN* 1.3 58.1 + - - +
215A MET* 3.2 24.6 + - + +
216A ILE* 2.9 31.3 + - + +
229A ILE* 4.0 24.0 - - + -
231A VAL* 3.8 20.9 - - + -
242A LEU* 3.8 26.2 - - + -
246A TYR* 5.9 0.2 - - + -
604A PCP 5.0 0.4 + - - -
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Residues in contact with ASN 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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208A ALA 5.3 0.6 + - - -
209A GLY 3.0 26.5 + - - +
210A GLY* 3.8 6.9 - - - +
212A ILE* 1.3 72.3 - - - +
214A GLY* 1.3 61.7 + - - +
216A ILE* 3.4 12.5 + - - +
217A ASN* 2.9 39.5 + - - +
241A ARG 4.3 4.6 + - - -
242A LEU* 3.2 36.4 - - - +
243A VAL* 4.1 6.2 + - - +
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Residues in contact with GLY 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A ILE* 3.2 25.9 - - - +
175A TYR* 4.1 7.8 - - - +
186A MET* 3.4 11.9 - - - -
210A GLY 2.8 18.9 + - - -
211A THR 3.1 4.2 + - - -
213A ASN* 1.3 73.4 - - - +
215A MET* 1.3 56.6 + - - +
217A ASN* 3.1 5.0 + - - -
218A LEU* 2.8 26.2 + - - +
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Residues in contact with MET 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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135A MET* 3.9 28.1 - - - +
136A THR* 4.1 5.6 - - - -
137A VAL* 3.4 39.5 - - + +
159A VAL* 4.6 1.6 - - + -
186A MET* 3.4 11.4 - - - -
201A ILE* 3.7 37.9 - - + -
202A ILE 4.7 3.8 - - - +
203A ASP* 4.7 9.2 - - - +
211A THR* 2.9 15.2 + - + +
212A ILE* 3.2 30.3 + - + +
214A GLY* 1.3 74.3 - - - +
216A ILE* 1.3 57.7 + - - +
218A LEU* 3.3 5.7 + - - +
219A LEU* 2.9 32.6 + - - +
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Residues in contact with ILE 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A ILE* 4.0 16.2 - - + -
212A ILE* 2.9 32.5 + - + +
213A ASN* 3.7 16.4 - - - +
215A MET* 1.3 72.8 - - - +
217A ASN* 1.3 70.8 + - - +
219A LEU* 3.3 10.7 + - - +
220A ASP* 3.2 30.2 + - - +
226A VAL* 4.1 11.9 - - + -
229A ILE* 4.1 2.9 - - + -
242A LEU* 4.6 0.9 - - + -
243A VAL 3.9 6.7 - - - +
244A ASP* 3.4 42.4 - - + +
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Residues in contact with ASN 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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173A ILE* 4.0 18.6 - - + +
174A ASN 5.1 2.8 - - - +
213A ASN* 2.9 23.0 + - - +
214A GLY* 3.3 10.3 - - - +
216A ILE* 1.3 78.6 - - - +
218A LEU* 1.3 65.7 + - - +
220A ASP* 3.1 27.9 + - - +
221A GLU* 3.5 11.5 + - - +
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Residues in contact with LEU 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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135A MET* 5.0 3.8 - - + -
159A VAL* 3.8 41.7 - - + -
171A VAL* 3.6 38.4 - - + +
173A ILE* 3.1 29.9 - - + +
186A MET* 4.3 8.1 - - + +
187A SER 4.4 2.0 - - - -
188A LEU* 4.1 15.5 - - + -
214A GLY 2.8 15.4 + - - +
215A MET* 3.3 9.9 - - - +
217A ASN* 1.3 72.9 - - - +
219A LEU* 1.3 63.3 + - + +
221A GLU* 2.9 22.1 + - - +
222A PHE* 3.4 17.5 - - + -
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Residues in contact with LEU 219 (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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135A MET* 3.6 23.3 - - + -
193A MET* 3.3 29.8 - - + -
199A VAL* 3.7 34.8 - - + -
201A ILE* 3.9 14.1 - - + -
215A MET 2.9 15.3 + - - +
216A ILE* 3.5 9.0 - - - +
217A ASN 3.3 0.2 - - - -
218A LEU* 1.3 76.2 - - + +
220A ASP* 1.3 63.1 + - - +
222A PHE* 3.1 9.7 + - + +
224A ALA* 2.9 35.0 + - + +
225A ASN 4.4 3.1 - - - +
226A VAL* 3.9 26.7 - - + -
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Residues in contact with ASP 220 (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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216A ILE* 3.2 21.6 + - - +
217A ASN* 3.1 22.5 + - - +
219A LEU* 1.3 78.8 - - - +
221A GLU* 1.3 65.0 - - - +
223A ASN* 3.1 15.1 + - - +
224A ALA 4.5 7.6 - - - +
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Residues in contact with GLU 221 (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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171A VAL* 3.5 35.1 - - + +
172A SER 5.5 2.5 - - - +
173A ILE* 5.5 4.9 - - + -
195A THR* 5.7 0.3 - - - +
217A ASN 3.9 9.6 - - - +
218A LEU* 2.9 15.2 + - + +
220A ASP* 1.3 79.4 - - - +
222A PHE* 1.3 61.6 + - + +
223A ASN 3.4 0.8 + - - -
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Residues in contact with PHE 222 (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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171A VAL* 3.9 35.4 - - + -
188A LEU* 4.0 33.7 - - + -
189A ALA 4.0 7.0 - - - -
190A LYS* 3.9 19.5 - - + -
193A MET* 3.8 52.0 - - + -
194A LYS 4.8 0.4 - - - -
195A THR* 3.3 26.6 - - + -
196A GLY 3.1 15.9 + - - -
218A LEU* 3.4 19.1 - - + -
219A LEU 3.1 7.0 + - - +
221A GLU* 1.3 80.3 - - - +
223A ASN* 1.3 69.7 + - - +
224A ALA* 3.1 1.2 + - + +
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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