Contacts of the helix formed by residues 202 - 215 (chain A) in PDB entry 5EAA
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 LEU 202 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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201A THR* 1.3 74.5 - - - +
203A GLU* 1.3 67.2 + - + +
205A TRP* 3.2 10.9 + - + -
206A GLN* 3.0 45.6 + - + +
238A GLU* 4.0 50.0 - - + +
239A GLY 5.2 0.2 - - - +
242A ALA* 4.7 2.2 - - + -
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Residues in contact with GLU 203 (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 THR* 3.3 7.4 + - - +
202A LEU* 1.3 78.5 - - + +
204A GLN* 1.3 55.2 + - + +
206A GLN* 3.2 15.3 + - - +
207A THR* 2.7 38.2 + - - +
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Residues in contact with GLN 204 (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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168A LEU* 3.4 18.2 - - - +
170A PHE* 3.6 49.2 - - + +
199A ASP 4.5 0.4 + - - -
200A PRO* 3.2 16.3 - - + +
201A THR* 2.8 44.4 + - - +
203A GLU* 1.3 75.6 - - + +
205A TRP* 1.3 59.9 + - - +
207A THR* 3.7 1.8 - - - -
208A LEU* 2.8 35.3 + - - +
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Residues in contact with TRP 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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188A PHE* 3.8 32.5 - + + -
189A HIS 3.5 25.8 - - - -
190A GLY* 3.8 16.7 + - - -
199A ASP* 5.4 2.2 - - + +
200A PRO* 3.5 40.6 + - + +
201A THR 3.1 24.0 + - - -
202A LEU* 3.7 13.0 - - + +
204A GLN* 1.3 77.2 - - - +
206A GLN* 1.3 59.0 + - - +
208A LEU* 3.3 9.1 + - + -
209A ALA* 2.8 29.7 + - - +
221A PHE* 3.8 21.5 - + - -
238A GLU* 6.0 0.4 - - + -
239A GLY* 3.5 32.6 - - - +
242A ALA* 4.7 3.4 - - + -
243A PHE* 3.4 23.4 - + - -
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Residues in contact with GLN 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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202A LEU* 3.0 43.7 + - + +
203A GLU* 3.5 18.6 - - - +
205A TRP* 1.3 73.9 - - - +
207A THR* 1.3 65.3 + - - +
209A ALA* 3.3 7.7 + - - +
210A GLN* 3.1 24.3 + - - +
242A ALA* 4.4 11.6 - - + +
246A MET* 5.1 2.1 - - - +
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Residues in contact with THR 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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170A PHE* 4.0 23.9 - - + -
174A ILE* 5.0 8.1 - - + -
203A GLU* 2.7 23.2 + - - +
204A GLN* 3.8 5.3 - - - -
206A GLN* 1.3 78.3 - - - +
208A LEU* 1.3 61.7 + - - +
210A GLN* 3.3 7.4 + - + +
211A LEU* 3.0 27.5 + - + +
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Residues in contact with LEU 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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160A TYR* 6.4 0.2 - - + -
170A PHE* 3.8 20.0 - - + -
173A LEU* 3.8 32.3 - - + -
174A ILE* 4.7 7.2 - - + -
177A LEU* 5.0 4.9 - - + -
188A PHE* 4.2 26.9 - - + -
200A PRO* 4.7 10.1 - - + -
204A GLN 2.8 26.1 + - - +
205A TRP* 3.3 19.0 + - + +
207A THR* 1.3 77.6 - - + +
209A ALA* 1.3 61.1 + - - +
211A LEU* 4.0 10.0 - - + +
212A SER* 3.1 23.4 + - - -
217A TRP* 4.8 5.2 - - + -
243A PHE* 3.7 13.8 - - + -
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Residues in contact with ALA 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 TRP 2.8 16.3 + - - +
206A GLN* 3.4 9.9 - - - +
207A THR 3.1 0.4 - - - -
208A LEU* 1.3 76.0 - - - +
210A GLN* 1.3 65.1 + - - +
212A SER* 3.2 5.5 + - - -
213A VAL* 3.0 27.8 + - - +
242A ALA 4.2 7.9 - - - +
243A PHE* 3.6 27.6 - - + -
246A MET* 3.9 20.0 - - + -
247A HIS* 3.3 1.2 + - - -
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Residues in contact with GLN 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 GLN 3.1 13.1 + - - +
207A THR* 3.7 5.8 - - + +
209A ALA* 1.3 75.9 - - - +
211A LEU* 1.3 68.0 + - - +
213A VAL* 3.0 14.9 + - - +
214A GLU* 3.1 41.4 + - - +
246A MET* 3.6 24.2 - - + +
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Residues in contact with LEU 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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174A ILE* 4.0 31.9 - - + -
177A LEU* 5.4 0.2 - - + -
178A ASN* 4.4 9.4 - - - +
207A THR* 3.0 20.4 + - + +
208A LEU* 4.0 10.3 - - + +
210A GLN* 1.3 77.3 - - - +
212A SER* 1.3 63.0 + - - +
214A GLU* 3.3 6.4 + - + +
215A LYS* 3.0 45.5 + - + +
217A TRP* 3.6 28.7 - - + -
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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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186A VAL* 5.4 0.3 - - - +
188A PHE* 4.9 2.5 - - - -
208A LEU 3.1 15.7 + - - -
209A ALA 3.3 9.6 - - - -
210A GLN 3.1 0.6 - - - -
211A LEU* 1.3 77.2 - - - +
213A VAL* 1.3 61.7 + - - +
216A GLY* 3.2 18.0 + - - -
217A TRP* 3.1 48.1 + - - +
219A PRO* 4.0 7.3 - - - +
243A PHE* 4.1 7.1 - - - -
247A HIS* 3.4 21.8 - - - -
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Residues in contact with VAL 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 ALA 3.1 16.4 - - - +
210A GLN* 3.0 8.1 + - - +
212A SER* 1.3 79.8 - - - +
214A GLU* 1.3 72.8 + - - +
216A GLY* 3.5 7.4 + - - -
246A MET* 3.6 38.8 - - + +
247A HIS* 3.4 23.8 - - + +
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Residues in contact with GLU 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 GLN* 3.1 38.6 + - - +
211A LEU* 3.8 9.2 - - + +
213A VAL* 1.3 83.4 - - - +
215A LYS* 1.3 72.8 + - + +
216A GLY 3.6 0.5 + - - -
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Residues in contact with LYS 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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177A LEU 5.2 2.0 - - - +
178A ASN* 4.5 22.9 - - - +
180A ALA 5.2 5.8 - - - +
181A GLN 4.4 0.9 - - - -
182A ALA* 3.6 19.6 + - - +
211A LEU* 3.0 40.0 + - + +
214A GLU* 1.3 86.3 - - + +
216A GLY* 1.3 60.2 + - - +
217A TRP* 3.6 32.9 + - + +
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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