Contacts of the strand formed by residues 251 - 258 (chain A) in PDB entry 9PAI
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 251 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A ASN* 4.3 3.8 - - + -
107A ASP* 3.7 34.1 - - + +
109A ILE* 3.8 17.7 - - + -
189A PHE* 3.8 28.3 - - + -
245A PRO* 3.7 2.6 - - - +
246A TYR* 3.0 28.6 + - + +
248A GLY 4.9 0.4 - - - -
249A ASP 4.5 0.9 - - - +
250A THR* 1.3 97.7 + - - +
252A SER* 1.3 63.4 + - - +
380B VAL* 4.7 2.2 - - + -
381B ARG 3.4 11.9 - - - +
382B HIS* 4.0 12.1 - - + -
383B ASN* 4.4 0.2 - - - -
389B LEU* 3.4 33.9 - - + -
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Residues in contact with SER 252 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A GLU* 2.7 33.4 + - - -
244A LEU 3.6 2.0 - - - -
245A PRO* 3.4 19.5 - - - -
246A TYR* 3.3 15.8 - - - -
251A LEU* 1.3 76.6 - - - +
253A MET* 1.3 60.3 + - - +
254A PHE* 3.2 10.9 - - - -
379B VAL 3.8 1.0 - - - +
380B VAL* 3.2 2.3 - - - +
381B ARG 2.9 30.0 + - - -
383B ASN* 3.1 10.0 + - - -
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Residues in contact with MET 253 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A TRP* 3.9 23.6 - - + -
242A LEU 3.8 0.3 - - - +
243A GLU* 3.7 0.9 - - - -
244A LEU* 3.0 34.3 + - + +
246A TYR* 3.5 24.1 - - + +
252A SER* 1.3 72.9 - - - +
254A PHE* 1.3 73.9 + - - +
255A ILE* 4.0 11.5 + - + +
293A LEU* 5.6 3.6 - - - -
296A PHE* 5.6 2.5 - - - -
344A ILE* 4.0 2.9 - - + -
346A VAL* 4.3 10.1 - - + -
351A THR* 3.8 22.2 - - + +
378B PHE* 3.5 42.0 - - + -
379B VAL 3.5 7.0 - - - +
380B VAL* 3.9 9.0 - - + +
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Residues in contact with PHE 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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241A ILE* 4.4 11.4 - - + -
242A LEU 3.3 4.5 - - - +
243A GLU* 3.1 23.6 - - + -
252A SER* 3.2 21.3 - - - -
253A MET* 1.3 78.2 - - - +
255A ILE* 1.3 62.4 + - - +
256A ALA* 5.5 0.6 - - - +
277A ILE* 4.7 6.1 - - + -
280A TRP* 4.4 25.1 - + + -
281A LYS* 3.4 36.6 - - + -
284A MET* 3.8 14.1 - - + -
377B LEU 4.3 0.2 - - - -
378B PHE* 3.0 9.4 - - - +
379B VAL* 2.7 53.8 + - + +
381B ARG* 3.9 17.9 - - + -
383B ASN* 3.6 11.7 - - - -
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Residues in contact with ILE 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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240A ASP 3.4 1.0 - - - +
241A ILE* 3.2 5.9 - - - +
242A LEU* 2.7 53.7 + - + +
244A LEU* 4.1 19.3 - - + -
253A MET* 4.4 14.1 - - + +
254A PHE* 1.3 73.9 - - - +
256A ALA* 1.3 63.7 + - - +
291A LEU* 5.6 1.8 - - + -
293A LEU* 4.3 16.8 - - + -
296A PHE* 6.3 0.2 - - + -
372B MET* 3.6 41.3 - - + -
376B PHE* 4.1 14.8 - - + -
377B LEU 3.6 3.4 - - - +
378B PHE* 3.6 27.8 - - + -
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Residues in contact with ALA 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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239A TYR* 5.1 0.4 - - + -
240A ASP 3.0 10.3 - - - +
241A ILE* 4.2 15.3 - - + -
254A PHE 4.1 0.6 + - - +
255A ILE* 1.3 75.7 - - - +
257A ALA* 1.3 59.3 + - - +
265A LEU* 3.9 0.2 - - - +
268A LEU* 3.7 24.3 - - + +
280A TRP* 4.4 15.9 - - + -
376B PHE* 3.7 1.2 - - - -
377B LEU* 2.8 48.1 + - + +
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Residues in contact with ALA 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 TYR* 3.1 7.3 - - - -
240A ASP* 2.7 35.7 + - - +
255A ILE 4.3 0.2 - - - -
256A ALA* 1.3 72.5 - - - +
258A PRO* 1.3 70.0 - - + +
265A LEU* 5.0 0.2 - - - -
372B MET* 3.1 39.5 - - + +
374B ARG* 3.8 12.1 - - - -
376B PHE* 3.7 11.0 - - + +
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Residues in contact with PRO 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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238A TYR 3.7 3.6 - - - +
239A TYR* 3.1 40.8 - - + +
240A ASP* 3.6 4.1 - - - +
257A ALA* 1.3 91.0 - - + +
259A TYR* 1.3 63.1 + - - +
260A GLU 3.3 21.8 - - - +
261A LYS* 5.1 0.2 - - - -
263A VAL* 3.7 18.4 - - + +
264A PRO 5.5 0.4 - - - -
265A LEU* 4.9 0.9 - - + -
374B ARG* 3.3 41.3 + - + -
375B PRO 4.3 7.2 - - - +
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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