Contacts of the helix formed by residues 200 - 211 (chain A) in PDB entry 2IL1
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 PHE 200 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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171A VAL* 4.4 16.4 - - + -
172A GLY* 4.5 11.0 - - - -
195A ALA* 3.5 33.0 - - + +
197A GLN* 3.0 31.9 + - + +
198A GLU 3.0 1.4 - - - -
199A ARG* 1.3 104.9 - - + +
201A ASN* 1.3 62.8 + - - +
202A SER 3.3 2.9 + - - -
203A ILE* 3.4 18.5 + - + +
204A THR* 3.1 28.4 + - + +
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Residues in contact with ASN 201 (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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195A ALA 5.5 0.9 - - - +
197A GLN 3.9 3.8 - - - +
198A GLU* 3.0 44.9 + - - +
199A ARG 3.4 0.2 - - - -
200A PHE* 1.3 77.1 - - - +
202A SER* 1.3 65.5 + - - +
204A THR* 3.3 7.5 + - - -
205A SER* 2.9 26.9 + - - -
231A LYS* 5.2 9.3 - - - +
232A TRP* 4.0 20.5 - - - -
235A MET* 3.7 34.3 - - - +
239A TYR* 5.7 1.1 - - - -
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Residues in contact with SER 202 (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 GLU 4.7 0.2 + - - -
199A ARG 4.6 6.7 + - - -
200A PHE 3.3 0.6 - - - -
201A ASN* 1.3 77.7 - - - +
203A ILE* 1.4 59.9 + - - +
205A SER* 2.5 27.0 + - - -
206A ALA* 4.3 0.9 + - - +
239A TYR* 5.5 3.6 - - - -
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Residues in contact with ILE 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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171A VAL* 3.3 60.6 - - + +
172A GLY* 4.3 7.0 - - - -
199A ARG 5.4 1.1 + - - +
200A PHE* 3.4 21.6 + - + +
202A SER* 1.4 79.1 - - - +
204A THR* 1.3 65.4 + - + +
205A SER 3.4 0.3 + - - -
206A ALA* 3.6 11.8 + - - +
207A TYR* 3.7 19.5 - - + +
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Residues in contact with THR 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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172A GLY 3.6 27.6 - - - +
173A VAL* 4.4 0.9 - - + -
194A THR* 4.0 24.0 - - - -
195A ALA 4.0 9.8 + - - +
200A PHE* 3.1 26.8 + - + +
201A ASN* 3.3 13.2 + - - -
203A ILE* 1.3 77.5 - - + +
205A SER* 1.3 64.6 + - - +
207A TYR* 3.0 24.6 + - - +
208A TYR* 3.3 21.7 + - - -
232A TRP* 5.8 1.4 - - - -
235A MET* 4.2 2.1 - - - +
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Residues in contact with SER 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A ASN 2.9 16.2 + - - -
202A SER* 2.5 21.5 + - - -
204A THR* 1.3 76.1 + - - +
206A ALA* 1.3 62.5 + - - +
208A TYR* 3.0 30.6 + - - +
209A ARG* 3.9 4.2 + - - +
235A MET* 4.5 0.2 - - - -
239A TYR* 3.6 48.1 + - - +
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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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202A SER 5.3 0.9 - - - +
203A ILE 3.6 13.1 + - - +
204A THR 3.1 0.2 + - - -
205A SER* 1.3 80.9 + - - +
207A TYR* 1.3 69.0 + - + +
208A TYR 3.5 0.7 + - - -
209A ARG* 3.8 12.3 + - - +
210A SER* 4.1 7.6 + - - -
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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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142A ILE* 3.4 29.3 - - + +
170A THR* 4.6 10.4 - - - +
171A VAL 5.1 1.0 + - - -
173A VAL* 3.5 41.7 - - + +
192A TRP* 3.6 49.7 - + + -
194A THR* 5.0 4.3 - - + -
203A ILE* 3.7 22.7 - - + -
204A THR 3.0 13.7 + - - +
206A ALA* 1.3 81.0 - - + +
208A TYR* 1.3 64.3 + - + +
209A ARG 3.4 0.2 - - - -
210A SER* 3.2 18.9 + - - -
211A ALA 3.5 2.8 + - - -
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Residues in contact with TYR 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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142A ILE* 3.7 23.3 - - + -
144A ILE* 3.4 42.0 - - + +
194A THR* 5.4 1.8 - - + -
204A THR* 3.3 28.1 + - - -
205A SER* 3.0 14.6 + - - +
207A TYR* 1.3 77.5 - - + +
209A ARG* 1.3 65.5 + - - +
211A ALA* 3.1 18.7 + - - +
214A ILE* 4.5 6.0 - - + +
232A TRP* 3.7 14.9 - - - -
235A MET* 3.7 58.9 - - + +
236A ILE* 4.0 6.1 - - + -
239A TYR* 3.6 17.7 - - + +
240A ALA* 3.9 15.2 - - - +
241A SER 4.3 0.3 + - - -
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Residues in contact with ARG 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 SER 3.9 3.2 + - - +
206A ALA* 3.8 9.2 + - - +
207A TYR 3.4 0.8 - - - -
208A TYR* 1.3 79.7 - - - +
210A SER* 1.3 61.5 + - - +
211A ALA 3.5 1.0 + - - +
239A TYR 3.5 16.1 + - - +
240A ALA 5.7 0.2 - - - -
241A SER* 2.9 29.3 + - - +
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Residues in contact with SER 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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140A GLN* 3.3 40.8 + - - +
192A TRP* 4.9 0.2 + - - -
206A ALA 4.1 4.1 + - - -
207A TYR* 3.2 24.8 + - - +
209A ARG* 1.3 79.8 - - - +
211A ALA* 1.3 61.5 + - - +
212A LYS* 3.4 10.2 + - - +
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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
----------------------------------------------------------
140A GLN* 3.7 9.2 - - - +
142A ILE* 3.7 33.0 - - + +
207A TYR 3.5 0.8 + - - +
208A TYR 3.1 18.0 + - - +
209A ARG 4.1 3.6 - - - +
210A SER* 1.3 80.2 + - - +
212A LYS* 1.3 60.6 + - - +
213A GLY 3.6 18.6 - - - +
214A ILE* 4.1 6.3 - - + -
241A SER* 4.4 5.2 + - - -
244A ALA* 4.0 13.2 - - - +
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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