Contacts of the helix formed by residues 248 - 259 (chain A) in PDB entry 6PXC
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 248 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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239A TYR* 3.8 13.2 - - - -
246A PHE* 3.3 7.3 - - - +
247A SER* 1.3 79.4 - - - +
249A LEU* 1.3 63.7 + - - +
250A SER* 3.5 11.0 + - - -
251A ASP* 3.0 36.0 + - - +
252A LEU* 3.1 17.0 + - - +
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Residues in contact with LEU 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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178A THR* 6.1 0.4 - - + -
181A TRP* 3.7 33.4 - - + -
182A TYR* 5.0 7.0 - - + -
206A ILE* 4.1 29.4 - - + -
216A PHE* 5.4 6.1 - - + -
232A ILE* 4.1 17.9 - - + -
239A TYR* 3.6 50.1 - - + +
248A SER* 1.3 70.4 - - - +
250A SER* 1.3 60.2 + - - +
252A LEU* 3.2 7.2 + - + +
253A ILE* 2.9 36.1 + - - +
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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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174A THR* 4.8 3.3 + - - +
175A ALA* 3.3 35.4 + - - +
176A PRO 5.5 1.8 - - - -
181A TRP* 4.7 8.9 - - - -
248A SER* 3.2 11.1 - - - -
249A LEU* 1.3 78.0 - - - +
251A ASP* 1.3 62.1 + - - +
253A ILE* 4.8 0.7 - - - -
254A GLY* 2.9 24.9 + - - -
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Residues in contact with ASP 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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246A PHE* 3.8 13.8 - - + -
247A SER* 4.6 10.5 + - - +
248A SER* 3.0 34.1 + - - +
250A SER* 1.3 80.9 + - - +
252A LEU* 1.3 58.3 + - - +
254A GLY* 3.7 1.6 - - - +
255A TYR* 2.9 29.6 + - - +
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Residues in contact with LEU 252 (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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206A ILE* 4.9 2.2 - - + -
218A LEU* 4.2 20.2 - - + -
232A ILE* 3.8 37.9 - - + -
239A TYR* 4.4 5.4 - - + +
241A ILE* 3.6 23.6 - - + -
246A PHE* 3.7 30.7 - - + -
248A SER 3.1 12.8 + - - +
249A LEU* 3.5 13.0 - - + +
251A ASP* 1.3 73.6 - - - +
253A ILE* 1.3 75.6 + - + +
255A TYR* 3.2 4.5 + - - +
256A TYR* 3.2 33.5 + - + -
268A LEU* 5.3 0.2 - - + -
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Residues in contact with ILE 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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175A ALA* 4.0 13.7 - - + -
176A PRO* 4.3 2.9 - - + -
181A TRP* 3.3 47.6 - - + +
204A TYR* 3.4 37.0 - - + +
206A ILE* 3.9 21.1 - - + -
218A LEU* 5.4 0.4 - - + -
249A LEU 2.9 15.4 + - - +
250A SER* 3.9 3.6 - - - +
252A LEU* 1.3 78.8 - - + +
254A GLY* 1.3 60.3 + - - +
256A TYR 3.4 1.0 + - - -
257A SER* 2.6 41.0 + - - +
268A LEU* 4.0 13.0 - - + -
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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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174A THR 3.7 21.8 - - - -
175A ALA* 4.1 0.6 - - - +
250A SER 2.9 17.7 + - - -
251A ASP* 3.3 2.7 + - - -
253A ILE* 1.3 77.4 - - - +
255A TYR* 1.3 61.6 + - - +
257A SER* 3.3 1.3 + - - -
258A HIS* 3.0 34.7 + - - +
259A VAL* 4.0 2.1 + - - +
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Residues in contact with TYR 255 (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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244A ARG* 3.7 36.7 + - + -
246A PHE* 3.4 35.7 - + + -
251A ASP 2.9 9.4 + - - +
252A LEU 3.2 2.4 + - - +
254A GLY* 1.3 75.9 - - - +
256A TYR* 1.3 83.6 + + - +
259A VAL* 2.9 43.4 + - + +
260A SER* 2.9 53.1 + - - -
1110U ASP* 4.3 8.4 + - - +
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Residues in contact with TYR 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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218A LEU* 5.0 0.7 - - + -
241A ILE* 3.9 34.0 + - + +
244A ARG* 4.8 4.3 - - - +
246A PHE* 4.2 3.1 - + - -
252A LEU* 3.2 25.1 + - + +
253A ILE 3.7 0.4 - - - -
255A TYR* 1.3 100.3 - + - +
257A SER* 1.3 58.7 + - - +
260A SER* 3.5 16.6 - - - +
261A SER 3.6 3.1 - - - -
262A LEU* 3.7 24.3 + - + -
267A LYS* 3.3 10.9 - - - +
268A LEU* 2.9 43.1 + - + -
1108U PRO* 3.4 22.1 - - + +
1110U ASP* 2.6 40.6 + - - -
1111U SER* 5.6 0.2 - - - -
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Residues in contact with SER 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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176A PRO* 5.9 0.2 - - - +
204A TYR* 4.7 2.1 + - - -
253A ILE* 2.6 34.5 + - - +
254A GLY 3.8 3.1 - - - -
256A TYR* 1.3 79.2 - - - +
258A HIS* 1.3 82.0 + - - +
267A LYS* 3.3 20.0 - - - +
268A LEU* 3.4 30.2 + - - +
269A LEU* 5.7 1.0 - - - +
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Residues in contact with HIS 258 (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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174A THR* 3.6 26.4 + - - -
175A ALA* 5.6 1.1 - - - -
254A GLY* 3.0 18.7 + - - +
257A SER* 1.3 98.1 - - - +
259A VAL* 1.3 68.7 + - + +
260A SER 4.0 0.2 - - - -
267A LYS* 4.3 10.4 - - - -
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Residues in contact with VAL 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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254A GLY 4.3 3.8 - - - +
255A TYR* 2.9 46.3 + - + +
257A SER 4.0 0.2 - - - -
258A HIS* 1.3 87.4 - - + +
260A SER* 1.3 60.8 + - - +
267A LYS* 4.3 6.0 - - - -
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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