Contacts of the helix formed by residues 200 - 211 (chain A) in PDB entry 4J1O
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 PRO 200 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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198A SER 3.6 8.3 - - - +
199A LEU* 1.3 88.9 - - + +
201A SER* 1.3 67.3 + - - +
202A ARG* 4.1 30.1 - - + +
203A ASP* 2.9 29.0 + - - +
204A ALA* 3.2 7.1 + - - +
227A GLU* 4.8 5.8 - - - +
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Residues in contact with SER 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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199A LEU 3.8 1.4 + - - -
200A PRO* 1.3 70.9 - - - +
202A ARG* 1.3 63.2 + - - +
204A ALA* 3.8 1.1 - - - +
205A LEU* 2.9 35.6 + - - +
222A CYS* 4.1 16.6 - - - -
227A GLU* 4.2 17.9 + - - +
230A ALA* 5.6 0.9 - - - +
231A ILE* 3.4 27.2 - - - +
234A ARG* 6.2 0.4 - - - -
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Residues in contact with ARG 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 PRO* 4.1 20.7 - - + +
201A SER* 1.3 78.9 - - - +
203A ASP* 1.3 90.4 + - - +
205A LEU* 3.8 10.0 - - - +
206A ARG* 3.3 23.4 + - - +
209A ARG* 5.1 1.2 + - - -
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Residues in contact with ASP 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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168A ARG 5.6 0.5 - - - +
170A VAL* 3.7 41.5 + - + +
199A LEU* 4.5 10.2 - - + +
200A PRO* 2.9 23.5 + - + +
202A ARG* 1.3 119.9 + - - +
204A ALA* 1.3 61.7 + - - +
205A LEU 3.3 0.2 - - - -
206A ARG* 3.3 9.1 + - - +
207A LEU* 3.0 28.9 + - - +
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Residues in contact with ALA 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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199A LEU* 4.1 12.6 - - + +
200A PRO 3.2 10.6 + - - +
201A SER 3.2 5.6 + - - +
203A ASP* 1.3 74.4 - - - +
205A LEU* 1.3 65.9 + - - +
207A LEU* 3.4 5.1 + - - +
208A SER* 3.2 23.2 + - - -
218A LEU* 4.2 8.0 - - + +
221A PRO* 4.0 22.0 - - + -
222A CYS* 4.1 5.6 - - - -
231A ILE* 3.9 24.7 - - + -
235A VAL* 4.7 2.4 - - - +
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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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201A SER* 2.9 30.3 + - - +
202A ARG* 3.8 9.6 - - - +
204A ALA* 1.3 76.9 - - - +
206A ARG* 1.3 56.9 + - - +
208A SER* 4.0 1.4 - - - -
209A ARG* 2.9 40.9 + - - +
231A ILE* 4.4 11.9 - - + -
234A ARG* 3.7 71.3 - - + +
235A VAL* 4.2 13.4 - - + +
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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
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170A VAL* 3.6 30.0 - - - +
171A GLU* 3.8 30.5 + - - +
174A ILE* 3.8 8.6 - - + +
202A ARG 3.3 13.3 + - - +
203A ASP* 3.7 10.9 + - - +
204A ALA 3.3 0.6 - - - -
205A LEU* 1.3 77.3 - - - +
207A LEU* 1.3 67.1 + - - +
209A ARG* 3.6 25.1 - - - +
210A GLU* 2.9 55.9 + - - +
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Residues in contact with LEU 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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165A ILE* 3.7 28.3 - - + -
170A VAL* 4.8 4.9 - - + -
173A ASP 5.4 0.4 - - - -
174A ILE* 3.8 30.3 - - + +
177A VAL* 4.4 16.8 - - + -
193A VAL* 4.1 6.1 - - + -
199A LEU* 4.4 6.1 - - + -
203A ASP 3.0 17.6 + - - +
204A ALA 3.8 4.0 - - - +
205A LEU 3.4 0.2 - - - -
206A ARG* 1.3 78.4 - - - +
208A SER* 1.3 62.1 + - - +
211A CYS* 3.5 25.0 + - - +
216A PHE* 3.9 21.0 - - + -
218A LEU* 3.8 26.2 - - + -
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Residues in contact with SER 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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204A ALA 3.2 12.5 + - - -
205A LEU 4.1 2.5 - - - -
207A LEU* 1.3 77.2 - - - +
209A ARG* 1.3 66.7 + - - +
211A CYS 3.1 12.1 + - - -
212A PRO* 3.8 2.8 - - - +
216A PHE* 4.3 2.5 - - - -
218A LEU* 5.0 4.5 - - - -
234A ARG 5.7 0.4 - - - -
235A VAL* 3.5 32.8 - - - +
236A GLN* 3.6 10.4 + - - +
237A HIS* 2.7 40.9 + - - -
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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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202A ARG 5.1 1.4 + - - -
205A LEU* 2.9 28.5 + - - +
206A ARG* 3.6 47.1 + - - +
208A SER* 1.3 76.1 - - - +
210A GLU* 1.3 69.4 + - + +
211A CYS 3.5 0.3 + - - -
212A PRO* 3.6 10.0 - - - +
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Residues in contact with GLU 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 ILE* 3.5 17.4 - - + +
178A ARG* 3.4 34.0 + - - +
206A ARG* 2.9 57.7 + - + +
209A ARG* 1.3 88.8 + - - +
211A CYS* 1.3 64.6 + - - +
212A PRO* 3.4 6.6 - - - +
213A GLU* 4.0 6.2 - - - +
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Residues in contact with CYS 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* 4.2 25.4 - - - -
177A VAL* 5.0 2.5 - - - -
178A ARG* 4.2 7.6 - - - -
207A LEU* 3.5 25.1 + - - +
208A SER 3.1 3.2 + - - -
210A GLU* 1.3 86.2 - - - +
212A PRO* 1.3 66.2 - - - +
213A GLU* 3.1 8.7 - - - -
214A ILE* 3.1 29.4 + - + +
216A PHE* 3.8 15.5 - - + -
237A HIS* 3.0 18.7 + - - -
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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