Contacts of the helix formed by residues 250 - 264 (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 SER 250 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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203A LYS* 4.7 0.9 - - - +
249A PHE* 1.3 80.0 - - - +
251A THR* 1.3 63.3 + - - +
252A ALA* 3.5 9.4 + - - +
253A GLN* 3.4 42.5 + - - +
254A GLY 3.1 17.2 + - - -
340A VAL* 5.4 1.0 - - - +
343A TRP* 4.0 1.9 - - - +
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Residues in contact with THR 251 (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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8A ALA 5.8 0.4 - - - -
11A LEU* 4.0 15.3 - - + -
12A ASP* 2.5 33.9 + - - +
15A ILE* 4.0 9.7 - - + +
203A LYS* 3.3 20.2 + - - +
206A SER* 5.9 0.5 - - - -
207A LEU* 3.8 12.0 + - + +
210A LEU* 3.9 25.1 - - + -
249A PHE* 3.5 13.2 + - - -
250A SER* 1.3 71.2 + - - +
252A ALA* 1.3 58.4 + - - +
254A GLY* 3.2 2.1 + - - -
255A PHE* 2.9 27.5 + - - +
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Residues in contact with ALA 252 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A ALA* 3.5 35.6 + - + +
11A LEU* 3.6 18.5 - - + +
250A SER* 3.2 9.3 + - - +
251A THR* 1.3 80.4 - - - +
253A GLN* 1.3 57.1 + - - +
255A PHE* 3.5 2.3 + - - +
256A GLN* 3.0 29.1 + - - +
331A CYS 3.9 4.0 - - - +
332A CYS* 4.2 3.1 - - - -
340A VAL* 3.7 14.3 - - + +
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Residues in contact with GLN 253 (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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250A SER* 3.2 27.3 + - - +
252A ALA* 1.3 75.0 - - - +
254A GLY* 1.3 56.3 + - - +
256A GLN* 3.6 1.8 + - - +
257A THR* 2.5 38.7 + - - -
340A VAL* 3.4 26.8 + - + -
341A GLY* 3.1 27.0 + - - +
342A ALA* 4.1 5.9 + - - -
343A TRP* 3.6 25.6 + - + +
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Residues in contact with GLY 254 (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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207A LEU* 3.9 14.0 - - - +
250A SER 3.1 11.2 + - - -
251A THR 3.2 2.9 + - - -
253A GLN* 1.3 74.7 - - - +
255A PHE* 1.3 63.3 + - - +
257A THR* 3.3 3.5 + - - -
258A VAL* 3.1 28.1 + - - +
343A TRP* 3.5 32.9 - - - -
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Residues in contact with PHE 255 (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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3A LEU* 4.8 7.4 - - + -
11A LEU* 4.7 4.3 - - + -
207A LEU* 3.7 5.5 - - + +
210A LEU* 3.9 28.9 - - + -
211A VAL* 4.3 18.8 - - + -
214A TRP* 4.0 42.4 - + + -
251A THR 2.9 16.8 + - - +
252A ALA* 3.7 5.6 - - - +
254A GLY* 1.3 73.4 - - - +
256A GLN* 1.3 64.2 + - - +
258A VAL* 3.3 5.0 + - + +
259A LEU* 3.1 51.1 + - + +
326A TRP* 4.4 5.8 - + - -
331A CYS* 3.8 29.8 - - + -
332A CYS* 3.8 17.3 - - - -
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Residues in contact with GLN 256 (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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252A ALA 3.0 17.1 + - - +
253A GLN* 4.0 3.8 - - - +
255A PHE* 1.3 77.1 - - - +
257A THR* 1.3 62.7 + - - +
259A LEU* 3.3 4.6 + - - +
260A GLU* 2.9 45.2 + - - +
327A LEU* 3.7 17.4 - - + +
332A CYS* 3.6 21.4 - - + +
339A LEU* 3.8 20.9 - - - +
340A VAL* 3.3 14.3 + - + +
341A GLY* 2.9 25.7 + - - +
342A ALA* 3.5 19.0 - - - +
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Residues in contact with THR 257 (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* 3.8 15.5 - - + -
253A GLN 2.5 23.6 + - - -
254A GLY 3.4 6.7 - - - -
255A PHE 3.2 0.2 - - - -
256A GLN* 1.3 76.9 - - - +
258A VAL* 1.3 57.4 + - - +
260A GLU* 3.3 3.1 + - - +
261A LEU* 3.0 32.8 + - + +
342A ALA* 3.7 10.5 - - + +
343A TRP* 2.7 35.9 + - + +
345A MET* 3.7 31.0 - - + -
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Residues in contact with VAL 258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A LEU* 5.0 0.9 - - + -
211A VAL* 4.2 25.4 - - + -
214A TRP* 5.4 3.1 - - + -
232A LEU* 4.5 8.3 - - + -
235A LEU* 4.4 16.8 - - + +
236A THR* 3.8 42.2 - - + +
239A ALA* 4.1 10.5 - - + -
254A GLY 3.1 15.7 + - - +
255A PHE* 3.7 7.0 - - + +
256A GLN 3.3 0.2 - - - -
257A THR* 1.3 72.6 - - - +
259A LEU* 1.3 68.1 + - + +
261A LEU* 3.1 8.6 + - - +
262A VAL* 3.0 24.5 + - + +
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Residues in contact with LEU 259 (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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214A TRP* 3.5 46.4 - - + +
255A PHE* 3.1 46.1 + - + +
256A GLN* 3.6 6.7 - - - +
258A VAL* 1.3 78.2 - - + +
260A GLU* 1.3 60.5 + - - +
262A VAL* 3.4 6.6 + - - +
263A LEU* 3.3 24.5 + - - +
323A ALA* 3.5 14.0 - - + +
326A TRP* 4.3 13.2 - - + -
327A LEU* 3.8 32.3 - - + -
332A CYS* 3.9 10.1 - - - -
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Residues in contact with GLU 260 (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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256A GLN* 2.9 45.5 + - + +
257A THR* 3.8 6.1 - - - +
259A LEU* 1.3 75.0 - - - +
261A LEU* 1.3 65.6 + - + +
263A LEU* 3.3 13.1 + - + +
264A LYS* 3.2 43.8 + - - +
327A LEU* 4.4 14.1 - - + +
339A LEU* 5.4 1.6 - - - +
342A ALA* 3.4 21.6 - - + +
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Residues in contact with LEU 261 (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* 3.8 30.5 - - + +
238A TYR* 4.1 10.3 - - + -
239A ALA* 3.6 35.0 - - + -
257A THR* 3.0 22.8 + - + +
258A VAL* 3.1 8.7 + - - +
260A GLU* 1.3 75.6 - - - +
262A VAL* 1.3 63.6 + - - +
264A LYS* 3.1 24.7 + - + +
265A HIS 3.4 8.3 + - - -
268A LEU* 3.6 27.3 - - + +
345A MET* 4.2 20.0 - - + -
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Residues in contact with VAL 262 (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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214A TRP* 4.4 8.5 - - + -
232A LEU* 3.9 20.0 - - + -
235A LEU* 3.9 18.4 - - + -
258A VAL* 3.0 20.8 + - + +
259A LEU 3.5 7.6 - - - +
261A LEU* 1.3 76.5 - - - +
263A LEU* 1.3 58.0 + - - +
265A HIS* 2.9 30.5 + - - +
316A TRP* 4.4 11.2 - - + -
319A LEU* 3.9 20.6 - - + -
320A ALA* 3.8 28.8 - - - +
323A ALA* 4.0 7.2 - - + -
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Residues in contact with LEU 263 (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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259A LEU 3.3 11.6 + - - +
260A GLU* 3.3 14.1 + - + +
261A LEU 3.2 0.4 - - - -
262A VAL* 1.3 77.0 - - - +
264A LYS* 1.3 60.3 + - + +
265A HIS* 3.3 11.8 + - - -
266A GLN* 5.0 0.9 + - - +
320A ALA* 3.3 38.1 - - + +
323A ALA* 4.0 7.6 - - + -
324A ARG* 3.5 44.2 - - + +
327A LEU* 3.7 22.9 - - + -
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Residues in contact with LYS 264 (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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260A GLU* 3.2 32.4 + - - +
261A LEU* 3.1 23.2 + - + +
263A LEU* 1.3 80.4 - - + +
265A HIS* 1.3 57.7 + - - -
266A GLN* 3.1 4.9 - - - +
267A LYS* 2.9 30.6 + - + +
268A LEU* 3.4 13.2 + - + +
345A MET* 6.2 2.0 - - - +
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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