Contacts of the helix formed by residues 203 - 215 (chain A) in PDB entry 5AJO
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 203 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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176A ASP* 2.8 15.4 + - - -
202A GLU* 1.3 79.6 - - - +
204A LEU* 1.3 65.0 + - - -
205A MET 3.4 2.9 + - - -
206A ARG 3.6 0.6 + - - -
207A SER* 2.7 32.9 + - - -
329A ASP 4.4 1.8 - - - -
330A VAL* 3.6 28.8 - - - +
0B ALA* 4.6 0.7 - - - -
1B GLY 5.7 0.2 - - - -
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Residues in contact with LEU 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A THR* 4.0 4.0 - - - +
203A GLY* 1.3 70.7 - - - -
205A MET* 1.3 75.1 - - + +
207A SER* 3.3 2.2 + - - -
208A ARG* 2.8 74.5 + - - +
224A ASP* 5.5 0.4 - - - +
324A TYR* 4.5 1.1 - - - +
329A ASP 5.0 1.2 + - - -
330A VAL* 4.9 4.7 + - - +
334A GLU* 4.0 21.3 - - + +
0B ALA* 3.8 19.7 - - - +
1B GLY 3.6 22.2 + - - +
2B THR* 3.4 36.1 - - + +
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Residues in contact with MET 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A GLY 3.4 0.8 - - - -
204A LEU* 1.3 92.0 - - + +
206A ARG* 1.3 63.5 + - - +
208A ARG 3.3 1.2 + - - -
209A VAL* 3.1 26.7 + - - +
324A TYR* 3.6 46.4 - - + -
325A ASP 4.7 1.8 - - - +
326A MET* 5.5 0.2 - - - -
328A MET* 3.6 49.4 - - + +
329A ASP 5.0 3.8 + - - +
332A GLY 3.7 22.9 - - - +
333A GLY 4.0 6.1 - - - +
334A GLU* 4.0 20.0 - - + +
337A GLU* 5.4 5.6 - - - +
338A ILE 6.2 0.2 - - - -
380A ASN* 3.8 5.6 - - - +
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Residues in contact with ARG 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A GLU* 2.9 58.9 + - + +
203A GLY 3.6 2.0 + - - -
205A MET* 1.3 76.3 - - - +
207A SER* 1.3 62.8 + - - +
209A VAL* 3.3 4.3 + - - +
210A ARG* 3.1 20.4 + - - +
325A ASP 5.0 0.7 - - - +
326A MET* 2.8 80.4 + - + +
327A MET* 4.3 8.9 - - - +
328A MET 3.3 21.9 + - - +
329A ASP* 5.5 0.2 - - - +
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Residues in contact with SER 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A THR* 3.7 22.0 - - - -
174A VAL* 3.8 21.1 - - - +
176A ASP* 3.3 12.3 + - - +
198A ASN* 3.0 23.6 + - - +
202A GLU* 4.1 0.7 - - - +
203A GLY 2.7 25.4 + - - -
204A LEU 3.6 3.6 - - - -
206A ARG* 1.3 76.4 - - - +
208A ARG* 1.3 57.7 + - - +
210A ARG* 3.1 7.1 + - - +
211A GLY 3.0 22.9 + - - -
0B ALA* 4.5 0.7 - - - -
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Residues in contact with ARG 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A VAL* 4.6 3.8 + - - -
143A THR* 3.7 20.1 + - + +
204A LEU* 2.8 45.9 + - + +
205A MET 3.3 0.6 + - - +
207A SER* 1.3 74.1 - - - +
209A VAL* 1.3 59.2 + - - +
211A GLY 3.3 1.3 + - - +
212A ALA* 2.8 32.3 + - - +
222A PHE* 3.5 39.1 - - + +
223A LEU 4.1 11.5 + - - -
224A ASP* 4.9 0.8 + - - +
308A GLY 2.7 24.7 + - - -
309A GLY* 2.8 29.7 + - - -
311A PHE* 3.7 10.1 - - - -
318A PHE* 5.2 0.2 - - - -
324A TYR* 3.2 40.2 + - + -
2B THR* 4.6 2.2 - - - +
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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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205A MET 3.1 15.1 + - - +
206A ARG 3.3 2.9 + - - +
208A ARG* 1.3 76.3 - - - +
210A ARG* 1.3 58.8 + - - +
212A ALA* 3.8 5.1 - - - +
213A ASP* 2.8 48.5 + - - +
318A PHE* 4.5 2.5 - - + -
323A LYS* 4.2 19.5 - - + +
324A TYR* 3.8 34.8 - - + +
326A MET* 3.6 35.4 - - + -
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Residues in contact with ARG 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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174A VAL* 4.6 3.6 - - + -
196A LEU* 3.9 39.2 - - + +
197A ARG 3.0 16.4 + - - +
198A ASN* 2.9 25.9 + - - -
206A ARG 3.1 11.5 + - - +
207A SER* 3.1 11.4 + - - +
209A VAL* 1.3 78.0 - - - +
211A GLY* 1.3 63.1 + - - +
213A ASP* 3.4 7.5 + - - +
214A ALA* 3.2 21.5 + - - +
326A MET* 6.0 0.2 - - - +
1593A SO4 2.5 37.8 + - - -
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Residues in contact with GLY 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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141A VAL* 4.0 15.7 - - - -
172A ILE* 3.6 15.9 - - - +
174A VAL* 4.0 17.9 - - - +
196A LEU* 4.4 2.2 - - - -
207A SER 3.0 13.4 + - - -
208A ARG 3.3 2.4 + - - -
210A ARG* 1.3 76.8 - - - +
212A ALA* 1.3 60.7 + - - +
214A ALA* 3.1 4.7 + - - +
215A ALA* 3.1 18.4 + - - +
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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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141A VAL* 4.3 1.4 - - - +
208A ARG 2.8 20.9 + - - +
209A VAL 3.8 2.2 - - - +
211A GLY* 1.3 72.9 - - - +
213A ASP* 1.3 64.7 + - - +
215A ALA* 3.2 15.8 + - - +
220A LEU* 3.8 26.9 - - + -
222A PHE* 4.4 3.4 - - + -
315A LYS* 4.1 11.9 - - + +
318A PHE* 3.6 30.3 - - + -
319A GLU* 4.9 3.7 - - + +
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Residues in contact with ASP 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* 2.8 33.8 + - - +
210A ARG* 3.7 7.8 - - - +
212A ALA* 1.3 80.8 - - - +
214A ALA* 1.3 57.8 + - - +
215A ALA 3.6 3.5 + - - +
318A PHE* 5.9 0.2 - - - -
319A GLU* 5.3 4.4 - - - +
323A LYS* 3.2 31.8 + - - +
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Residues in contact with ALA 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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170A GLU* 4.2 1.9 - - - +
172A ILE* 4.1 6.6 - - + +
194A ARG* 4.0 22.1 + - - +
196A LEU* 3.9 20.2 - - + -
210A ARG 3.2 11.7 + - - +
211A GLY 3.1 10.0 + - - +
213A ASP* 1.3 76.7 - - - +
215A ALA* 1.3 63.6 + - - +
216A GLN* 3.4 10.6 + - - +
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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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139A SER* 3.6 23.8 - - - +
141A VAL* 5.1 0.7 - - + -
170A GLU* 3.4 7.0 - - - -
172A ILE* 3.9 2.7 - - + -
211A GLY 3.1 10.3 + - - +
212A ALA 3.2 16.2 + - - +
213A ASP 4.4 2.8 - - - +
214A ALA* 1.3 77.6 - - - +
216A GLN* 1.3 59.9 + - - +
217A ALA 4.5 0.9 - - - +
220A LEU* 3.7 18.8 - - + -
315A LYS* 3.0 24.0 + - + +
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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