Contacts of the helix formed by residues 238 - 250 (chain A) in PDB entry 6XYU
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 238 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149A GLY* 4.3 4.5 - - - -
150A GLY 4.5 0.2 - - - -
237A GLU* 1.4 79.1 + - - +
239A ALA* 1.3 61.3 + - - -
241A SER* 3.1 4.0 + - - -
242A SER 3.0 18.4 + - - -
263A GLN 2.9 11.5 + - - -
264A SER 3.5 14.6 - - - -
265A GLY* 3.6 0.7 - - - -
271A TRP* 3.3 12.8 - - - -
480A HIS* 3.3 13.0 - - - -
601A I40 4.8 0.7 - - - -
602A IOD 2.1 45.5 - - - -
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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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148A TYR 4.2 0.4 - - - -
149A GLY* 3.9 2.2 - - - -
150A GLY 4.1 3.8 - - - +
151A GLY* 3.6 12.1 - - - +
152A PHE* 3.4 51.7 - - + +
180A TYR* 4.4 3.6 - - - +
237A GLU 3.1 0.2 + - - -
238A SER* 1.3 79.1 - - - +
240A GLY* 1.3 52.8 + - - +
242A SER* 3.2 2.0 + - - -
243A SER* 2.7 38.0 + - - -
271A TRP* 3.6 10.5 - - + -
602A IOD 3.5 1.8 - - - +
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Residues in contact with GLY 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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147A ILE* 3.2 24.8 - - - +
148A TYR 3.1 25.7 + - - -
149A GLY* 3.4 0.2 - - - -
236A GLY* 3.9 1.6 - - - -
237A GLU 2.7 16.2 + - - -
239A ALA* 1.3 71.6 - - - +
241A SER* 1.3 49.0 + - - -
243A SER* 2.9 3.0 + - - -
244A VAL* 2.7 37.1 + - - +
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Residues in contact with SER 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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236A GLY* 3.4 9.9 - - - -
237A GLU* 3.1 8.1 - - - +
238A SER 3.1 9.8 + - - -
240A GLY* 1.3 73.5 - - - +
242A SER* 1.3 63.9 + - - +
244A VAL* 3.1 9.4 + - - +
245A ASN* 2.9 18.4 + - - +
262A MET* 2.9 25.3 - - - +
263A GLN 3.0 30.7 + - - -
265A GLY* 2.3 27.3 + - - -
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Residues in contact with SER 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A PHE* 4.0 9.4 - - - -
238A SER 3.0 5.1 + - - -
239A ALA 3.7 6.3 - - - -
241A SER* 1.3 76.7 - - - +
243A SER* 1.3 58.5 + - - +
245A ASN* 3.0 9.0 - - - +
246A ALA* 2.8 24.1 + - - +
265A GLY 3.3 6.2 + - - -
266A THR 3.3 13.8 + - - +
267A MET* 3.6 8.6 - - - +
271A TRP* 3.1 23.9 - - - -
272A SER* 3.1 29.4 + - - -
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Residues in contact with SER 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A ILE* 3.9 9.9 - - - -
152A PHE* 3.4 16.2 - - - -
180A TYR* 4.4 1.0 + - - -
208A LEU* 4.1 2.8 - - - +
211A GLN* 3.3 39.0 + - - -
239A ALA 2.7 27.3 + - - -
240A GLY* 2.9 8.2 + - - -
242A SER* 1.3 70.8 - - - +
244A VAL* 1.3 67.3 + - - +
246A ALA* 3.0 7.7 + - - +
247A GLN* 2.8 28.8 + - - +
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Residues in contact with VAL 244 (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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147A ILE* 3.8 12.7 - - + +
234A LEU* 3.7 29.5 - - + +
235A PHE 3.5 39.7 - - - +
236A GLY* 3.6 3.1 - - - +
240A GLY 2.7 18.1 + - - +
241A SER* 3.3 7.9 - - - +
243A SER* 1.3 71.2 - - - +
245A ASN* 1.3 63.3 + - - +
247A GLN* 3.3 1.7 + - - +
248A LEU* 2.9 40.2 + - + +
260A GLY* 4.1 4.7 - - - -
261A MET 4.1 1.3 - - - +
262A MET* 3.7 18.6 - - + -
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Residues in contact with ASN 245 (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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241A SER 2.9 7.2 + - - +
242A SER* 3.0 16.2 - - - +
244A VAL* 1.3 77.9 - - - +
246A ALA* 1.3 60.1 + - - +
248A LEU* 3.2 5.0 + - - +
249A MET* 3.1 29.2 + - - +
262A MET* 3.4 27.3 - - + +
267A MET* 2.9 36.0 + - + +
447A TYR* 2.7 41.3 + - - -
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Residues in contact with ALA 246 (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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208A LEU* 4.5 15.0 - - + -
242A SER 2.8 15.6 + - - +
243A SER* 3.0 10.7 + - - +
245A ASN* 1.3 72.9 - - - +
247A GLN* 1.3 57.2 + - - +
249A MET* 5.0 1.8 - - - -
250A SER* 2.8 38.0 + - - +
267A MET* 4.0 26.5 - - + -
334A PRO* 5.5 0.2 - - + -
340A PHE* 4.2 16.4 - - + -
341A LEU* 6.5 0.4 - - + -
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Residues in contact with GLN 247 (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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147A ILE* 4.4 2.7 - - + -
208A LEU* 3.0 23.8 + - - +
211A GLN* 2.9 26.8 + - - +
212A ALA* 3.4 25.0 - - - -
215A ILE* 3.9 16.8 - - + +
234A LEU* 3.6 22.4 - - + -
243A SER 2.8 23.1 + - - +
246A ALA* 1.3 73.0 - - - +
248A LEU* 1.3 61.7 + - - +
253A THR* 2.6 35.9 + - - +
254A ARG* 4.4 0.3 - - - -
257A VAL* 5.0 5.7 + - + +
340A PHE* 3.4 20.4 - - - -
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Residues in contact with LEU 248 (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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234A LEU* 4.6 4.7 - - + -
244A VAL* 2.9 35.3 + - + +
245A ASN* 3.2 8.5 + - - +
247A GLN* 1.3 77.0 - - - +
249A MET* 1.3 75.0 + - + +
254A ARG* 3.5 11.8 - - - +
257A VAL* 3.4 34.5 - - + +
258A LYS* 4.1 3.4 - - - -
259A ARG 3.8 27.4 - - - +
260A GLY* 4.3 10.5 - - - +
262A MET* 4.5 10.1 - - - -
357A TYR* 3.5 31.9 + - + -
359A ILE* 4.8 11.0 - - + -
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Residues in contact with MET 249 (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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245A ASN* 3.1 20.6 + - - +
246A ALA* 4.4 1.6 - - - +
248A LEU* 1.3 100.1 - - + +
250A SER* 1.3 67.7 + - - +
251A PRO* 3.4 6.2 - - - +
254A ARG* 3.9 25.8 + - - +
267A MET* 6.5 0.4 - - + -
348A LEU* 4.4 22.2 - - + +
349A MET* 4.0 21.5 - - + -
354A LEU* 3.8 16.2 - - + -
357A TYR* 4.2 10.1 - - + -
359A ILE* 4.9 1.8 - - + -
447A TYR* 3.5 18.2 - - + +
451A LEU* 3.8 28.5 - - + -
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Residues in contact with SER 250 (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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246A ALA 2.8 19.5 + - - -
248A LEU 3.7 0.4 - - - -
249A MET* 1.3 76.0 - - - +
251A PRO* 1.3 58.3 - - - +
252A VAL* 3.3 11.6 + - - +
253A THR* 3.6 8.9 + - - -
254A ARG* 2.7 35.7 + - - +
340A PHE* 2.5 50.9 + - - -
348A LEU* 5.6 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