Contacts of the helix formed by residues 228 - 244 (chain A) in PDB entry 4RWN
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 228 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215A TYR* 4.2 1.1 - - - +
226A LEU 4.6 0.4 - - - +
227A PRO* 1.3 89.8 - - + +
229A GLN* 1.3 66.2 + - - +
230A TYR* 4.2 5.8 - - + +
231A ALA* 3.0 21.8 + - - +
232A LEU* 3.7 5.2 - - - +
308A VAL* 3.3 27.1 - - + +
309A GLY 4.0 7.6 - - - +
310A GLY* 4.5 9.4 - - - -
401A APC 3.8 27.4 - - - +
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Residues in contact with GLN 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A LEU* 5.8 0.3 - - - +
212A LYS* 3.6 29.9 - - + +
215A TYR* 3.5 38.3 + - + -
216A GLN* 2.9 32.9 + - - +
227A PRO 3.5 2.0 + - - -
228A PRO* 1.3 73.1 - - - +
230A TYR* 1.3 57.3 + - - +
232A LEU* 2.9 21.0 + - + +
233A GLU* 3.1 10.7 + - + +
401A APC 2.8 51.8 + - + +
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Residues in contact with TYR 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A LYS* 3.6 22.0 - - - -
193A GLN* 3.8 20.4 + - - +
196A PHE* 5.5 0.9 - - - -
197A LEU* 5.2 2.2 - - + +
228A PRO* 3.1 1.3 - - + +
229A GLN* 1.3 78.5 - - - +
231A ALA* 1.3 60.8 + - - +
233A GLU* 3.3 20.2 + - - -
234A LEU* 3.0 51.9 + - + +
300A ASP* 2.9 33.3 + - - -
301A PRO* 4.1 4.7 - - - +
308A VAL* 3.5 22.0 - - + -
401A APC 3.5 62.9 + + + +
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Residues in contact with ALA 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A PRO* 3.0 17.9 + - + +
230A TYR* 1.3 80.1 - - - +
232A LEU* 1.3 55.6 + - - +
234A LEU* 3.5 5.0 + - - +
235A LEU* 2.9 27.9 + - - +
298A ILE* 4.1 13.0 - - + +
308A VAL* 3.4 34.4 - - + +
316A TRP* 4.1 25.1 - - + -
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Residues in contact with LEU 232 (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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211A VAL* 3.9 21.4 - - + +
212A LYS* 6.3 2.0 - - + -
214A TRP* 4.0 12.1 - - + -
215A TYR* 4.1 23.1 - - + -
227A PRO* 4.8 2.7 - - + -
228A PRO 3.7 14.8 - - - +
229A GLN* 2.9 10.9 + - + +
231A ALA* 1.3 77.0 - - + +
233A GLU* 1.3 63.4 + - - +
235A LEU* 3.7 13.2 - - + +
236A THR* 2.8 30.0 + - - -
258A VAL* 4.5 2.7 - - + -
262A VAL* 3.9 28.3 - - + -
316A TRP* 4.3 9.6 - - + -
319A LEU* 3.7 25.4 - - + -
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Residues in contact with GLU 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A LYS* 2.7 33.1 + - - +
67A THR* 3.6 18.9 + - - +
197A LEU* 4.1 17.6 - - + +
208A ILE* 3.6 38.0 - - + +
211A VAL* 5.9 0.4 - - - -
212A LYS* 4.5 12.1 + - + +
229A GLN* 3.1 11.0 + - + +
230A TYR* 3.3 21.2 + - + +
232A LEU* 1.3 78.2 - - - +
234A LEU* 1.3 61.5 + - - +
236A THR* 3.4 7.4 + - - -
237A VAL* 3.3 21.5 + - - +
401A APC 4.4 8.5 + - - -
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Residues in contact with LEU 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A PHE* 3.8 30.3 - - + -
197A LEU* 5.0 4.0 - - + -
230A TYR* 3.0 44.8 + - + +
231A ALA 3.8 3.6 - - - +
233A GLU* 1.3 73.7 - - - +
235A LEU* 1.3 60.8 + - - +
237A VAL* 3.3 5.8 + - + +
238A TYR* 3.0 23.9 + - - +
272A TRP* 3.5 16.7 - - + -
298A ILE* 3.9 20.0 - - + -
300A ASP* 4.4 0.7 - - - -
301A PRO* 3.9 23.3 - - + -
308A VAL* 3.7 30.1 - - + -
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Residues in contact with LEU 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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231A ALA 2.9 17.7 + - - +
232A LEU* 3.7 15.5 - - + +
233A GLU 3.3 0.2 - - - -
234A LEU* 1.3 77.7 - - - +
236A THR* 1.3 58.1 + - - +
238A TYR* 3.5 5.2 + - + +
239A ALA* 3.0 26.7 + - - +
258A VAL* 4.3 8.7 - - + +
261A LEU* 3.8 30.1 - - + -
262A VAL* 3.9 30.5 - - + +
268A LEU* 3.9 20.6 - - + -
270A ILE* 3.6 29.2 - - + -
298A ILE* 4.9 4.4 - - + +
316A TRP* 4.7 8.1 - - + -
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Residues in contact with THR 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A LEU* 4.2 3.4 - - + -
207A LEU* 3.7 36.0 - - + +
208A ILE* 3.8 23.8 - - + +
211A VAL* 3.5 22.3 - - + +
232A LEU 2.8 21.2 + - - -
233A GLU* 3.6 6.4 - - - -
234A LEU 3.2 0.2 - - - -
235A LEU* 1.3 75.1 - - - +
237A VAL* 1.3 66.0 + - - +
239A ALA* 3.3 2.6 + - - +
240A TRP* 3.1 22.3 + - - +
258A VAL* 3.8 14.0 - - + +
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Residues in contact with VAL 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A PHE* 3.9 17.5 - - + -
197A LEU* 3.7 30.7 - - + -
200A ARG* 3.8 19.7 - - - +
204A LEU* 4.7 13.5 - - + -
208A ILE* 4.3 6.1 - - + -
233A GLU 3.3 15.8 + - - +
234A LEU* 3.5 7.9 - - - +
236A THR* 1.3 77.5 - - - +
238A TYR* 1.3 57.5 + - - +
240A TRP* 3.2 3.3 + - - +
241A GLU* 2.9 53.0 + - + +
272A TRP* 4.2 1.8 - - + -
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Residues in contact with TYR 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A LEU 3.0 13.5 + - - +
235A LEU 3.5 7.6 - - - +
237A VAL* 1.3 76.9 - - - +
239A ALA* 1.3 63.5 + - - +
241A GLU* 3.8 5.1 - - - -
242A GLN* 3.0 56.6 + - + +
261A LEU* 4.1 21.8 - - + -
268A LEU* 5.0 4.4 - - + +
269A CYS 5.6 1.6 + - - -
270A ILE* 3.6 51.1 - - + +
272A TRP* 4.1 15.0 - + + -
345A MET* 4.4 15.8 - - - +
346A LEU 5.1 3.1 + - - -
348A LYS* 4.9 16.1 + - + +
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Residues in contact with ALA 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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235A LEU 3.0 17.8 + - - +
236A THR 3.3 5.6 + - - +
238A TYR* 1.3 76.9 - - - +
240A TRP* 1.3 57.3 - - - +
243A GLY 2.9 23.7 + - - -
257A THR* 3.8 15.0 - - + -
258A VAL* 4.1 13.7 - - + -
261A LEU* 3.6 22.7 - - + -
343A TRP* 3.3 16.3 - - + -
345A MET* 3.4 8.6 - - - +
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Residues in contact with TRP 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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200A ARG* 4.1 17.5 - - - -
201A PRO* 3.6 30.7 - - + -
204A LEU* 3.6 38.1 - - + -
207A LEU* 5.4 0.4 - - + -
236A THR 3.1 9.8 + - - +
237A VAL 3.7 1.6 - - - +
239A ALA* 1.3 74.3 - - - +
241A GLU* 1.3 75.4 + - + +
244A SER* 2.9 26.7 + - - -
245A ARG* 2.8 67.9 + - + -
246A LYS 2.8 25.8 + - - -
249A PHE* 3.5 25.0 - + - -
343A TRP* 3.5 15.2 - + + -
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Residues in contact with GLU 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 ARG* 2.7 32.3 + - - +
237A VAL* 2.9 23.0 + - - +
238A TYR* 3.9 6.4 - - - +
240A TRP* 1.3 93.3 - - + +
242A GLN* 1.3 70.5 + - - +
245A ARG* 3.1 55.5 + - - +
272A TRP* 2.8 35.0 + - - -
346A LEU* 6.1 0.5 - - - +
348A LYS* 5.3 2.6 + - - -
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Residues in contact with GLN 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 TYR* 3.0 41.4 + - + +
241A GLU* 1.3 90.8 + - - +
243A GLY* 1.3 57.7 + - - +
244A SER 3.9 0.2 - - - -
245A ARG* 5.0 3.6 + - - -
344A THR 3.6 0.2 - - - +
345A MET* 4.0 15.0 - - + -
346A LEU* 2.5 79.6 + - - +
347A GLN 4.1 0.4 + - - -
348A LYS* 3.4 42.0 - - - +
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Residues in contact with GLY 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 ALA 2.9 16.0 + - - -
242A GLN* 1.3 79.8 - - - +
244A SER* 1.3 61.3 + - - +
343A TRP* 3.5 25.8 - - - +
344A THR 4.0 6.8 + - - +
345A MET* 3.6 13.2 - - - +
346A LEU* 5.2 2.2 - - - -
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Residues in contact with SER 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A TRP* 2.9 27.2 + - - -
242A GLN 3.9 0.6 - - - -
243A GLY* 1.3 82.3 - - - +
245A ARG* 1.3 71.9 + - - +
246A LYS* 3.1 30.0 + - - +
249A PHE* 3.7 16.3 - - - +
343A TRP* 4.0 18.6 - - - -
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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
------------------------------------------------------------
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