Contacts of the helix formed by residues 200 - 216 (chain A) in PDB entry 3K5M
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 SER 200 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A LEU* 3.8 9.2 - - - -
198A VAL* 3.3 8.4 - - - +
199A ALA* 1.3 76.1 - - - +
201A ARG* 1.3 60.3 - - - +
202A PRO* 3.0 25.1 - - - +
203A GLN* 2.8 47.4 + - - +
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Residues in contact with ARG 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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160A THR* 4.9 4.0 - - - +
164A GLU* 3.5 41.9 + - - +
165A LEU* 2.6 50.1 + - + +
166A TYR* 4.8 7.5 - - - -
181A LEU* 3.3 29.2 - - + +
200A SER* 1.3 72.2 - - - +
202A PRO* 1.3 71.6 - - + +
204A LEU* 2.9 28.1 + - + +
205A LEU* 3.8 5.2 + - - +
236A HIS* 4.0 18.1 + - + -
240A TYR* 3.5 22.1 + - - +
321A PHE* 5.4 0.6 - - - -
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Residues in contact with PRO 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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200A SER* 3.0 18.4 - - - +
201A ARG* 1.3 94.5 - - + +
203A GLN* 1.3 60.7 + - + +
205A LEU* 3.2 16.7 + - + +
206A GLU* 3.2 18.1 + - - +
240A TYR* 4.1 32.8 - - + -
242A LEU* 3.8 23.1 - - + +
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Residues in contact with GLN 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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198A VAL* 3.6 14.3 - - + +
199A ALA* 2.8 24.7 - - - +
200A SER* 2.8 46.9 + - - +
202A PRO* 1.3 78.0 - - + +
204A LEU* 1.3 63.7 + - - +
206A GLU* 3.0 31.4 + - + +
207A LYS* 3.0 18.8 + - + +
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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
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165A LEU* 4.0 32.1 - - + -
166A TYR 4.2 15.3 - - - +
167A CYS* 4.6 2.5 - - - +
168A ILE* 4.1 17.2 - - + +
179A TYR* 3.7 39.0 - - + +
180A MET 4.0 4.3 - - - +
181A LEU* 4.5 6.1 - - + -
198A VAL* 3.5 25.8 - - + -
200A SER 4.4 0.7 - - - +
201A ARG* 2.9 22.8 + - + +
203A GLN* 1.3 78.6 - - - +
205A LEU* 1.3 61.7 + - - +
207A LYS* 3.3 7.1 + - - +
208A LEU* 3.1 21.7 + - - +
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Residues in contact with LEU 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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165A LEU* 4.5 6.5 - - + -
168A ILE* 4.7 0.4 - - + -
201A ARG 4.6 5.4 - - - +
202A PRO* 3.2 10.1 + - + +
204A LEU* 1.3 78.9 - - - +
206A GLU* 1.3 56.8 + - - +
208A LEU* 3.1 13.8 + - + +
209A ASN* 2.8 38.1 + - - +
233A LEU* 3.7 35.7 - - + +
236A HIS* 4.0 11.4 - - + -
237A ALA* 3.6 41.7 - - + +
240A TYR* 4.9 2.9 - - + -
242A LEU* 4.2 21.8 - - + +
243A PRO 5.4 1.6 - - - +
244A LEU* 4.5 10.1 - - + -
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Residues in contact with GLU 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 PRO* 3.2 18.6 - - - +
203A GLN* 3.0 26.4 + - + +
205A LEU* 1.3 77.0 - - - +
207A LYS* 1.3 65.4 + - + +
209A ASN* 3.2 10.0 + - - +
210A ALA* 3.0 23.3 + - - +
242A LEU* 4.0 18.1 - - + +
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Residues in contact with LYS 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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179A TYR* 3.7 41.3 + - + -
196A GLU* 2.5 33.0 + - - +
197A TYR 4.7 5.9 + - - -
198A VAL* 3.9 16.5 - - + +
203A GLN* 3.0 16.6 + - + +
204A LEU* 3.7 5.6 - - - +
206A GLU* 1.3 79.9 - - + +
208A LEU* 1.3 52.9 + - - +
210A ALA* 3.2 7.2 + - + +
211A TRP* 2.7 36.0 + - - +
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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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155A ILE* 4.5 4.5 - - + -
168A ILE* 3.9 26.9 - - + -
170A LEU* 3.8 29.2 - - + -
179A TYR* 4.7 3.8 - - + -
204A LEU 3.1 10.2 + - - +
205A LEU* 3.1 10.3 + - + +
207A LYS* 1.3 77.4 - - - +
209A ASN* 1.3 66.5 + - - +
211A TRP* 3.3 3.7 + - - +
212A PHE* 3.0 42.2 + - + +
233A LEU* 3.8 29.4 - - + -
244A LEU* 3.9 22.0 - - + -
246A LEU* 4.3 10.5 - - + -
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Residues in contact with ASN 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 LEU* 2.8 20.2 + - - +
206A GLU* 3.6 10.5 - - - +
208A LEU* 1.3 77.5 - - - +
210A ALA* 1.3 58.6 + - - +
212A PHE* 3.3 2.4 + - - +
213A ALA* 2.9 29.7 + - - +
242A LEU* 5.3 2.6 - - - +
243A PRO 3.0 18.0 - - - +
244A LEU* 3.6 13.9 - - - +
245A ARG* 2.6 58.5 + - + +
246A LEU* 4.4 1.0 - - - +
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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 GLU 3.0 14.1 + - - +
207A LYS* 3.4 12.1 - - + +
209A ASN* 1.3 74.8 - - - +
211A TRP* 1.3 65.0 + - - +
213A ALA* 3.2 7.3 + - - +
214A ASN* 2.8 27.1 + - - +
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Residues in contact with TRP 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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153A VAL* 3.5 38.6 - - + -
170A LEU* 3.8 23.6 - - + -
172A GLY 3.6 23.1 - - - -
173A CYS* 4.0 6.3 - - - -
175A GLN* 3.8 17.0 + - + +
177A ILE* 4.0 17.9 - - + +
179A TYR* 3.4 22.0 + - - +
207A LYS 2.7 20.2 + - - +
208A LEU 3.8 3.8 - - - +
210A ALA* 1.3 72.4 - - - +
212A PHE* 1.3 68.7 + + - +
214A ASN* 4.7 0.9 - - - -
215A TYR* 2.7 79.9 + + + +
217A PRO* 4.0 14.8 - - + -
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Residues in contact with PHE 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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153A VAL* 4.0 18.8 - - + -
155A ILE* 5.5 5.2 - - + -
170A LEU* 5.4 2.0 - - + -
208A LEU* 3.0 37.5 + - + +
209A ASN 3.6 3.8 - - - +
211A TRP* 1.3 89.8 - + - +
213A ALA* 1.3 58.2 + - - +
216A ASP* 2.9 28.8 + - - -
217A PRO* 3.9 13.7 - - + -
220A ILE* 3.5 33.9 - - + -
245A ARG 4.0 10.3 - - - +
246A LEU* 3.6 41.1 - - + -
272A ARG* 3.2 35.0 + - - +
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Residues in contact with ALA 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 ASN 2.9 17.7 + - - +
210A ALA* 3.6 7.0 - - - +
212A PHE* 1.3 80.5 - - - +
214A ASN* 1.3 62.5 + - - +
216A ASP* 4.3 7.3 + - - +
250A ASN* 4.0 21.1 - - - +
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Residues in contact with ASN 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 ALA 2.8 19.4 + - - +
211A TRP* 3.9 1.6 - - - +
213A ALA* 1.3 76.2 - - - +
215A TYR* 1.3 91.5 + - + +
216A ASP* 4.6 2.4 - - - +
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Residues in contact with TYR 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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151A LYS* 4.4 12.0 + - - +
173A CYS* 3.9 18.6 - - + +
175A GLN* 3.3 38.5 + - + -
211A TRP* 2.7 78.5 + + + +
214A ASN* 1.3 96.9 + - + +
216A ASP* 1.3 68.5 + - - +
217A PRO* 3.5 2.1 - - - -
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Residues in contact with ASP 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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31A PRO* 3.8 18.1 - - - +
151A LYS* 4.4 11.3 + - - +
212A PHE 2.9 15.7 + - - +
213A ALA 4.6 5.6 - - - +
214A ASN 4.6 4.7 - - - +
215A TYR* 1.3 75.2 - - - +
217A PRO* 1.3 68.5 - - - +
218A ASP* 3.6 0.7 + - - +
248A ARG* 2.9 31.3 + - - +
272A ARG* 2.6 31.2 + - - +
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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