Contacts of the helix formed by residues 199 - 206 (chain A) in PDB entry 1RL3
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 199 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163A ILE* 4.0 0.7 - - - -
171A ASN 4.6 1.8 - - - -
172A PHE* 3.9 5.0 - - - -
198A PHE* 1.3 78.6 - - - +
200A GLU* 1.3 61.0 + - - +
203A LEU* 3.2 23.6 + - - +
209A ARG* 3.2 20.2 + - - -
401A PCG 2.6 37.4 + - - -
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Residues in contact with GLU 200 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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172A PHE* 3.6 14.8 - - + -
198A PHE* 3.5 4.4 - - - -
199A GLY* 1.3 75.9 + - - +
201A LEU* 1.3 74.2 + - + +
203A LEU* 3.1 7.5 + - - +
204A ILE* 2.8 48.5 + - + +
229A TYR* 3.1 30.5 - - + +
237A THR* 5.2 0.4 - - + -
241A ARG* 2.7 37.5 + - - +
260A TRP* 3.5 12.1 + - - -
401A PCG 2.7 19.2 + - - -
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Residues in contact with LEU 201 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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199A GLY 3.6 0.4 - - - -
200A GLU* 1.3 107.6 + - + +
202A ALA* 1.3 65.2 + - - +
204A ILE* 3.2 0.8 + - - -
205A TYR* 2.7 52.1 + - + +
207A THR* 4.4 4.9 - - + +
210A ALA* 5.5 3.6 - - + -
241A ARG* 3.8 12.1 - - - +
260A TRP* 4.1 9.0 - - + -
263A LEU* 5.4 4.0 - - + -
401A PCG 3.2 57.9 - - + +
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Residues in contact with ALA 202 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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169A GLY* 4.1 14.4 - - - +
200A GLU 3.2 0.4 + - - -
201A LEU* 1.3 73.7 - - - +
203A LEU* 1.3 59.3 + - + +
206A GLY* 2.4 38.5 + - - -
207A THR 3.3 26.7 - - - +
208A PRO* 4.9 0.4 - - + -
209A ARG* 3.6 26.0 - - + +
401A PCG 2.6 24.3 + - - +
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Residues in contact with LEU 203 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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169A GLY* 3.4 36.8 - - - -
171A ASN 3.7 7.4 - - - +
172A PHE* 3.4 35.9 - - + +
199A GLY 3.2 19.5 - - - +
200A GLU* 3.4 4.3 - - - +
202A ALA* 1.3 78.1 - - - +
204A ILE* 1.3 60.3 + - - +
206A GLY* 4.2 3.4 + - - -
209A ARG* 4.4 3.1 - - - +
226A ARG* 3.4 34.5 + - + +
229A TYR* 4.0 19.1 - - + -
230A ARG* 2.9 31.2 + - + +
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Residues in contact with ILE 204 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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200A GLU* 2.8 36.6 + - + +
201A LEU 3.8 2.2 - - - +
202A ALA 2.8 0.8 + - - -
203A LEU* 1.3 74.8 - - - +
205A TYR* 1.3 82.3 + - + +
206A GLY 3.4 0.2 - - - -
229A TYR* 3.7 35.0 - - + +
230A ARG* 3.6 17.5 + - - -
234A MET* 3.8 14.6 - - + -
237A THR* 4.3 8.7 - - + -
238A LEU* 3.3 44.6 - - + -
241A ARG* 5.0 2.2 - - - +
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Residues in contact with TYR 205 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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201A LEU* 2.7 47.2 + - + -
204A ILE* 1.3 95.4 - - + +
206A GLY* 1.3 68.7 + - - +
207A THR* 3.0 23.7 + - + +
238A LEU* 3.4 19.2 - - + +
241A ARG* 5.4 5.3 + - - -
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Residues in contact with GLY 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 ALA 2.4 23.8 + - - -
203A LEU* 4.2 3.0 + - - -
204A ILE 3.4 2.4 - - - -
205A TYR* 1.3 71.2 - - - +
207A THR* 1.3 55.5 + - - -
208A PRO* 4.3 2.5 - - - +
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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