Contacts of the strand formed by residues 245 - 253 (chain A) in PDB entry 5MCO
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 TYR 245 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240A ILE* 3.8 22.5 - - + +
241A ASP 3.7 9.9 - - - -
242A HIS* 3.2 52.8 + - - +
243A SER 3.3 2.5 - - - +
244A LEU* 1.3 79.4 - - - +
246A THR* 1.3 69.7 + - - +
247A GLY 3.5 22.2 - - - -
249A LEU* 3.6 26.5 - - + +
403A TYR* 3.2 33.9 - + + -
416A ALA* 3.6 16.4 - - + -
417A VAL 3.1 15.9 - - - +
419A ALA* 3.8 3.7 - - - +
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Residues in contact with THR 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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245A TYR* 1.3 85.3 - - - +
247A GLY* 1.3 68.6 + - - +
248A SER 3.9 0.5 + - - -
416A ALA* 4.1 0.2 - - - +
417A VAL* 3.1 41.0 + - + +
418A SER 5.4 0.4 - - - -
419A ALA* 4.7 16.6 - - + -
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Residues in contact with GLY 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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245A TYR* 3.5 16.3 - - - -
246A THR* 1.3 79.3 + - - +
248A SER* 1.3 60.0 + - - -
417A VAL* 6.2 0.7 - - - -
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Residues in contact with SER 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A TYR* 4.9 0.2 - - - -
246A THR 4.6 0.2 - - - +
247A GLY* 1.3 73.9 - - - -
249A LEU* 1.3 63.3 + - - +
250A TRP* 3.9 27.5 + - - -
415A PHE 3.5 3.5 - - - +
416A ALA* 3.3 20.0 - - - +
431A VAL* 4.7 4.7 + - - +
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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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240A ILE* 4.1 18.2 - - + -
245A TYR* 3.6 34.2 - - + +
248A SER* 1.3 76.1 - - - +
250A TRP* 1.3 64.3 + - - +
251A TYR* 3.9 32.9 - - + +
403A TYR* 4.6 4.5 - - + +
405A VAL* 3.6 23.8 - - + -
414A GLY* 4.0 11.2 - - - -
415A PHE 3.4 19.5 - - - -
416A ALA* 3.9 12.6 - - + +
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Residues in contact with TRP 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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248A SER* 3.9 23.0 - - - -
249A LEU* 1.3 78.9 - - - +
251A TYR* 1.3 62.8 + - - +
355A GLN* 3.7 22.9 - - - -
357A PHE* 3.4 45.9 - + + -
413A ILE 3.7 0.9 - - - +
414A GLY* 3.1 0.9 - - - -
415A PHE 2.7 37.6 + - - -
431A VAL* 3.6 32.4 + - + -
432A GLU* 4.6 0.2 - - - +
433A GLY 3.3 24.8 - - - +
434A PRO* 3.3 32.8 - - + -
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Residues in contact with TYR 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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240A ILE* 4.0 13.9 - - - +
249A LEU* 3.9 43.0 - - + +
250A TRP* 1.3 76.2 - - - +
252A THR* 1.3 58.9 + - - +
349A MET 3.8 0.3 - - - +
350A GLY* 3.9 0.5 - - - -
351A GLU* 3.5 47.0 + - + +
355A GLN* 5.6 0.2 + - - -
357A PHE* 3.3 14.6 - - - -
405A VAL* 4.5 8.3 - - + -
407A ASP* 4.4 7.9 + - + -
412A ARG* 3.3 58.7 + - + -
413A ILE 3.1 6.1 - - - +
414A GLY* 3.3 30.1 - - - -
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Residues in contact with THR 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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251A TYR* 1.3 75.3 - - - +
253A PRO* 1.3 69.0 + - - +
262A VAL* 3.9 28.9 - - + +
263A ILE 4.4 2.9 + - - -
348A LEU* 3.7 9.8 - - + +
349A MET* 2.6 30.3 + - - +
351A GLU* 5.4 1.3 - - - -
357A PHE* 3.8 9.1 - - - -
412A ARG* 3.2 5.1 - - - +
413A ILE* 2.8 45.8 + - + +
415A PHE* 4.1 13.5 - - + -
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Residues in contact with PRO 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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251A TYR 4.8 0.2 - - - -
252A THR* 1.3 92.4 + - - +
254A ILE* 1.3 68.0 + - - +
255A ARG* 3.2 5.4 + - - +
261A GLU 3.6 6.1 - - - +
262A VAL* 4.0 13.0 - - - +
263A ILE 4.9 0.7 + - - -
349A MET* 3.3 38.9 - - + +
350A GLY 3.4 19.3 - - - +
351A GLU* 4.7 6.5 - - + +
411A LYS 3.6 8.1 - - - +
412A ARG* 4.3 2.7 - - + -
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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