Contacts of the helix formed by residues 375 - 380 (chain A) in PDB entry 4IYM
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 MSE 375 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338A GLY 4.8 0.4 - - - +
341A GLN* 3.3 44.2 - - + +
342A GLY 3.7 4.5 - - - +
343A ALA* 3.5 35.7 - - - +
370A ASP 3.7 14.4 - - - +
371A VAL* 3.9 5.6 - - - -
372A THR* 3.1 42.7 + - + +
374A ASP* 1.3 83.3 - - - +
376A ASP* 1.3 65.2 + - - +
377A ILE* 4.2 13.9 - - + -
378A TYR* 3.1 13.7 + - + +
379A LYS* 3.1 14.5 + - - +
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Residues in contact with ASP 376 (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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334A LEU* 4.4 9.0 - - + -
337A SER* 3.9 19.4 + - - +
341A GLN* 3.0 31.1 + - - +
374A ASP 3.9 0.6 + - - +
375A MSE 1.3 66.5 - - - +
377A ILE* 1.3 57.8 + - - +
378A TYR 3.0 5.2 - - - -
379A LYS* 3.6 23.4 + - - +
380A THR* 2.9 44.9 + - - +
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Residues in contact with ILE 377 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A LYS* 2.6 32.7 + - - -
334A LEU* 3.1 34.8 - - + +
337A SER* 4.1 0.9 + - - +
338A GLY* 3.9 17.9 - - - +
341A GLN* 4.9 0.2 + - - -
343A ALA* 3.9 13.2 - - + -
368A PHE* 3.6 38.8 - - + -
371A VAL* 3.9 22.9 - - + -
375A MSE 4.2 12.8 - - + -
376A ASP* 1.3 77.7 - - - +
378A TYR* 1.3 53.9 + - - +
380A THR 3.8 1.0 - - - +
382A ILE* 3.9 22.7 - - + +
388A SER* 4.0 9.4 + - - +
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Residues in contact with TYR 378 (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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249A LYS* 3.3 14.6 - - - +
251A HIS* 3.1 32.4 + + - -
284A VAL* 4.1 13.5 - - + -
371A VAL* 3.9 10.5 - - + -
372A THR 3.6 13.0 - - - +
373A PRO* 3.4 35.4 - - + -
375A MSE 3.1 8.4 + - - +
376A ASP 3.0 0.4 - - - -
377A ILE* 1.3 81.9 - - - +
379A LYS* 1.3 65.2 + - + +
380A THR 3.4 0.4 - - - -
388A SER* 5.3 0.9 - - - -
390A VAL* 3.9 28.7 - - + -
401A LEU* 3.4 34.7 + - + +
405A HIS* 3.1 38.1 + + + -
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Residues in contact with LYS 379 (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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373A PRO 3.5 23.3 - - - +
374A ASP* 3.4 23.4 + - - +
375A MSE 3.1 7.2 + - - +
376A ASP* 3.2 25.2 + - - +
378A TYR* 1.3 78.9 - - + +
380A THR* 1.3 62.5 + - - +
381A GLU 4.0 1.0 + - - -
405A HIS* 3.6 23.1 - - - -
406A GLU* 5.9 1.2 - - - +
407A TYR* 4.3 5.9 - - - -
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Residues in contact with THR 380 (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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249A LYS* 3.0 25.0 + - - -
330A ARG* 3.5 26.0 - - - +
334A LEU* 4.1 21.3 - - + +
376A ASP* 2.9 26.2 + - - +
377A ILE 3.8 0.9 - - - +
379A LYS* 1.3 81.3 - - - +
381A GLU* 1.3 66.9 + - - +
382A ILE* 3.1 5.2 + - - +
407A TYR* 5.3 0.2 - - - -
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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