Contacts of the helix formed by residues 207 - 220 (chain A) in PDB entry 4MYF
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 207 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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203A VAL 2.9 12.9 + - - +
204A ARG* 3.5 5.9 + - - -
205A LYS 3.3 3.8 + - - -
206A LYS* 1.3 78.6 - - - +
208A ALA* 1.3 59.6 + - - -
209A VAL 3.4 2.2 - - - -
210A ALA* 3.3 4.0 + - - -
211A ALA* 2.9 26.3 + - - +
252A GLU* 6.0 0.2 - - - -
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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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175A PHE* 3.8 3.6 - - - -
203A VAL* 3.6 24.9 + - + -
207A GLY* 1.3 71.7 - - - +
209A VAL* 1.3 59.4 + - + +
211A ALA* 3.8 1.9 - - - +
212A LEU* 2.9 29.3 + - - +
248A LEU* 4.7 0.7 - - + -
252A GLU* 3.9 42.1 + - + +
256A MET* 4.2 17.2 - - + +
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Residues in contact with VAL 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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207A GLY 3.4 0.2 - - - -
208A ALA* 1.3 75.1 - - + +
210A ALA* 1.3 60.5 + - - +
212A LEU* 3.3 4.3 + - - -
213A GLU* 2.9 41.9 + - - +
255A ASP* 3.5 45.3 - - + +
256A MET* 4.3 4.0 - - + +
259A LEU* 3.6 22.9 - - + +
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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 LYS* 3.5 27.6 - - + +
207A GLY* 3.3 3.6 + - - +
209A VAL* 1.3 79.1 - - - +
211A ALA* 1.3 61.5 + - - +
213A GLU* 3.3 17.2 + - - +
214A ASP* 3.1 26.9 + - - +
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Residues in contact with ALA 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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175A PHE* 3.6 21.5 - - + -
198A MET* 3.9 7.0 - - + +
202A GLU* 6.1 0.9 - - + -
203A VAL* 4.0 21.5 - - + -
206A LYS* 4.2 21.0 - - + +
207A GLY 2.9 17.0 + - - +
208A ALA 3.8 3.4 - - - +
210A ALA* 1.3 76.9 - - - +
212A LEU* 1.3 58.3 + - - +
214A ASP* 3.2 7.6 + - - +
215A ALA* 2.9 23.0 + - - +
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Residues in contact with LEU 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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135A ILE* 3.4 33.9 - - + -
175A PHE* 3.5 12.3 - - + -
208A ALA 2.9 18.5 + - - +
209A VAL* 3.3 4.7 + - - +
211A ALA* 1.3 74.3 - - - +
213A GLU* 1.3 59.4 + - - +
215A ALA* 3.1 2.0 + - + -
216A PHE* 2.8 56.8 + - + -
225A PHE* 3.9 15.5 - - + -
256A MET* 3.6 46.7 - - + +
259A LEU* 3.8 7.4 - - + -
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Residues in contact with GLU 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 VAL* 2.9 26.8 + - - +
210A ALA* 3.4 16.0 - - - +
212A LEU* 1.3 75.6 - - - +
214A ASP* 1.3 64.9 + - - +
216A PHE* 3.3 8.1 + - + +
217A GLY* 3.0 18.7 + - - -
259A LEU* 3.5 29.6 - - + +
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Residues in contact with ASP 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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198A MET* 4.1 14.8 - - + -
206A LYS* 2.8 35.1 + - - +
210A ALA* 3.1 14.6 + - - +
211A ALA 3.2 8.5 + - - +
213A GLU* 1.3 76.3 - - - +
215A ALA* 1.3 62.5 + - - +
217A GLY* 3.1 11.4 + - - -
218A LEU* 3.2 17.2 + - + +
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Residues in contact with ALA 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 ILE* 3.8 28.5 - - + -
173A VAL* 4.1 10.3 - - + +
175A PHE* 4.0 3.4 - - + -
198A MET* 3.9 22.6 - - - +
211A ALA 2.9 13.1 + - - +
212A LEU* 3.1 9.6 + - + +
214A ASP* 1.3 77.6 - - - +
216A PHE* 1.3 57.9 + - - +
218A LEU* 2.9 6.9 + - - +
219A THR* 2.9 30.1 + - - +
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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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135A ILE* 4.1 5.4 - - + -
212A LEU* 2.8 56.9 + - + +
213A GLU* 3.8 6.1 - - - +
215A ALA* 1.3 73.6 - - - +
217A GLY* 1.3 57.8 + - - +
219A THR* 3.3 13.7 + - - +
220A GLY* 3.0 27.7 + - - +
223A THR* 4.0 12.6 - - + -
225A PHE* 3.8 22.0 - + - -
259A LEU* 4.1 9.9 - - + -
260A ALA* 3.9 17.9 - - + -
263A THR* 3.9 28.0 - - + -
265A THR* 5.2 5.1 + - - +
266A VAL* 3.7 24.5 - - + -
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Residues in contact with GLY 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 GLU 3.0 13.3 + - - -
214A ASP* 3.5 6.5 - - - -
215A ALA 3.1 0.6 - - - -
216A PHE* 1.3 77.7 - - - +
218A LEU* 1.3 61.8 + - - +
220A GLY* 4.0 7.0 + - - -
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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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170A LYS 3.9 3.0 - - - +
171A ARG* 3.6 20.5 - - - +
173A VAL* 4.0 12.6 - - + -
196A HIS* 3.8 45.5 - - + +
198A MET* 3.7 29.4 - - + -
214A ASP* 3.5 8.3 - - + +
215A ALA 2.9 6.7 + - - +
217A GLY* 1.3 78.8 - - - +
219A THR* 1.3 65.1 + - - +
220A GLY* 3.3 0.9 + - - -
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Residues in contact with THR 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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133A GLY* 3.4 8.8 - - - -
134A VAL 3.5 31.9 - - - +
135A ILE* 4.1 10.5 - - + +
171A ARG* 2.9 38.7 + - - +
173A VAL* 4.0 13.7 - - + -
215A ALA 2.9 15.1 + - - +
216A PHE* 3.3 18.5 + - - -
218A LEU* 1.3 75.7 - - - +
220A GLY* 1.3 62.6 + - - +
223A THR* 2.8 28.7 + - + +
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Residues in contact with GLY 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A ARG* 4.5 2.5 - - - -
216A PHE* 3.0 16.4 + - - +
217A GLY 4.3 6.3 - - - -
218A LEU 3.3 2.2 - - - -
219A THR* 1.3 75.7 + - - +
221A LYS* 1.3 61.4 + - - -
223A THR* 2.9 16.3 + - - -
265A THR* 3.5 19.0 + - - -
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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