Contacts of the helix formed by residues 233 - 243 (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 LEU 233 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135A LEU* 3.6 29.4 - - + +
136A PHE* 4.2 25.8 - - + -
139A LEU* 4.7 8.7 - - + -
147A ILE* 4.0 22.0 - - + -
151A MET* 6.1 0.7 - - - -
172A PHE* 4.2 13.9 - - + -
224A ILE* 4.8 7.0 - - + -
229A TYR* 2.6 51.2 + - + +
232A ILE* 1.3 79.2 - - - +
234A MET* 1.3 62.9 + - - +
235A GLY 3.6 0.2 - - - -
236A SER* 3.6 7.7 + - - +
237A THR* 3.1 25.8 + - - +
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Residues in contact with MET 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A ILE* 3.8 23.8 - - + -
229A TYR* 2.9 19.3 + - + -
230A ARG* 3.1 77.3 + - + +
232A ILE 3.8 0.2 - - - -
233A LEU* 1.3 68.5 - - - +
235A GLY* 1.3 58.6 + - - +
237A THR* 2.7 10.3 + - - -
238A LEU* 2.6 62.7 + - + +
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Residues in contact with GLY 235 (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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230A ARG 4.6 2.4 + - - -
232A ILE 5.2 1.4 + - - -
233A LEU 3.6 0.8 - - - -
234A MET* 1.3 80.2 - - - +
236A SER* 1.3 62.2 + - - +
238A LEU* 3.5 5.2 + - - +
239A ARG* 3.0 41.2 + - - +
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Residues in contact with SER 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A LEU* 4.3 12.1 + - - +
138A HIS* 3.7 45.4 - - - +
139A LEU* 5.3 3.1 - - - +
232A ILE 5.1 6.4 + - - -
233A LEU* 3.6 10.9 + - - +
234A MET 3.3 0.6 - - - -
235A GLY* 1.3 74.9 - - - +
237A THR* 1.3 60.6 + - - +
239A ARG* 4.0 21.7 + - - +
240A LYS* 3.3 25.3 + - - +
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Residues in contact with THR 237 (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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135A LEU* 2.9 34.3 - - + +
204A ILE* 4.3 12.3 - - + -
229A TYR* 3.8 20.9 + - - +
233A LEU 3.1 14.0 + - - -
234A MET 2.7 11.0 + - - +
236A SER* 1.3 72.7 + - - +
238A LEU* 1.3 71.5 + - - +
239A ARG 3.2 1.1 - - - -
240A LYS* 3.3 5.3 + - - +
241A ARG* 3.2 45.0 + - - +
267A ASP* 4.7 4.8 + - - +
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Residues in contact with LEU 238 (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 ILE* 3.3 38.6 - - + -
205A TYR* 3.4 20.0 - - + +
234A MET* 2.6 51.4 + - + +
235A GLY* 4.1 4.3 - - - +
237A THR* 1.3 74.7 - - + +
239A ARG* 1.3 63.1 + - + +
241A ARG* 3.3 9.3 + - - +
242A LYS* 3.0 24.5 + - - +
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Residues in contact with ARG 239 (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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138A HIS* 6.2 1.4 - - - +
235A GLY* 3.0 26.1 + - - +
236A SER* 4.0 25.9 + - - +
238A LEU* 1.3 76.9 - - + +
240A LYS* 1.3 63.9 + - - +
242A LYS* 3.1 8.9 + - - +
243A MET* 3.0 23.8 + - - +
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Residues in contact with LYS 240 (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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134A VAL* 4.3 1.0 - - - +
138A HIS* 3.8 27.6 - - + +
236A SER 3.3 18.6 + - - +
237A THR* 3.3 6.3 + - - +
239A ARG* 1.3 77.9 - - - +
241A ARG* 1.3 63.4 + - + +
243A MET* 3.1 16.2 + - + +
244A TYR* 3.1 45.6 - - + -
266A ALA 3.1 32.8 + - - +
267A ASP* 3.2 15.7 + - - +
269A LEU* 2.6 35.6 + - - +
271A PRO* 5.0 6.0 - - + +
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Residues in contact with ARG 241 (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 GLU* 2.7 38.5 + - - +
201A LEU* 3.8 15.0 - - - +
204A ILE* 5.0 3.0 - - - +
205A TYR* 5.4 5.9 + - - -
237A THR* 3.2 29.0 + - - +
238A LEU* 3.7 9.6 - - - +
239A ARG 3.2 0.4 - - - -
240A LYS* 1.3 71.0 - - + +
242A LYS* 1.3 57.0 + - - +
243A MET 2.8 7.7 + - - -
244A TYR 2.8 0.5 + - - -
245A GLU* 2.6 39.1 + - - +
260A TRP* 4.8 3.8 - - - +
263A LEU* 3.7 49.1 - - + +
264A THR* 5.1 0.6 - - - +
266A ALA* 4.2 11.9 - - + -
267A ASP* 2.9 41.0 + - - +
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Residues in contact with LYS 242 (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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238A LEU 3.0 17.4 + - - +
239A ARG* 3.1 9.4 + - - +
241A ARG* 1.3 74.8 - - - +
243A MET* 1.3 56.8 + - - +
244A TYR 3.4 0.6 + - - -
245A GLU* 4.5 8.6 + - + +
246A GLU 5.7 0.3 + - - -
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Residues in contact with MET 243 (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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239A ARG 3.0 10.6 + - - +
240A LYS* 3.3 15.0 - - + +
241A ARG 2.8 1.0 - - - -
242A LYS* 1.3 80.5 - - - +
244A TYR* 1.3 105.0 + - + +
247A PHE* 5.0 3.3 - - - +
271A PRO* 5.1 4.9 - - + -
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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