Contacts of the strand formed by residues 410 - 415 (chain A) in PDB entry 2I91
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 410 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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371A PHE* 3.2 23.6 - - - -
373A LEU* 4.2 15.9 - - - -
404A ALA* 3.5 18.6 + - - +
407A GLU* 2.6 23.9 + - - -
408A LYS 2.7 13.9 + - - +
409A ASP* 1.3 75.7 - - - +
411A HIS* 1.3 61.8 + - - +
412A MET* 4.1 4.0 + - - +
426A VAL* 5.4 8.0 - - - +
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Residues in contact with HIS 411 (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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371A PHE 3.1 7.4 + - - +
372A LEU* 3.4 18.8 - - + +
373A LEU* 3.0 22.8 + - - -
410A SER* 1.3 73.3 - - - +
412A MET* 1.3 76.8 + - - +
413A VAL* 3.4 18.2 - - + +
422A CYS* 5.9 0.9 - - + -
453A TRP* 4.1 21.9 - + + -
459A THR* 5.6 6.7 - - + -
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Residues in contact with MET 412 (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 LEU* 3.3 11.2 - - + +
375A ILE* 5.7 0.7 - - + -
400A CYS* 3.8 29.4 - - - +
401A MET* 4.5 12.6 - - - +
404A ALA* 4.0 24.7 - - + -
410A SER 4.1 3.3 + - - +
411A HIS* 1.3 81.0 + - - +
413A VAL* 1.3 71.4 + - - +
422A CYS* 3.6 21.7 - - - +
424A ILE* 3.6 29.8 - - + +
425A THR* 3.7 2.9 - - - -
426A VAL* 3.6 36.3 - - + +
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Residues in contact with VAL 413 (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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372A LEU* 3.7 14.6 - - + -
373A LEU 2.8 10.2 + - - +
374A ALA* 3.1 27.4 - - + -
375A ILE* 2.7 34.2 + - - +
411A HIS* 3.4 23.1 - - + +
412A MET* 1.3 81.2 - - - +
414A ALA* 1.3 54.5 + - - +
415A PHE* 5.5 0.4 - - + -
419A MET* 4.0 25.4 - - + -
420A LEU 5.4 1.8 - - - +
422A CYS* 4.1 9.6 - - + -
450A PRO* 5.1 2.2 - - + -
453A TRP* 4.3 17.3 - - + -
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Residues in contact with ALA 414 (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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375A ILE* 3.3 15.0 - - + +
377A VAL* 3.9 17.7 - - + -
413A VAL* 1.3 75.8 - - - +
415A PHE* 1.3 65.1 + - - +
419A MET* 4.1 6.1 - - - +
420A LEU* 3.2 33.1 + - + +
422A CYS* 4.4 3.1 - - - +
423A PRO* 4.1 14.8 - - + -
437A MET* 5.5 0.7 - - + -
440A ILE* 4.1 17.7 - - + -
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Residues in contact with PHE 415 (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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374A ALA* 3.8 15.5 - - + -
375A ILE 3.0 12.3 + - - -
376A ASP* 3.5 32.9 - - + +
377A VAL* 2.7 34.9 + - - +
378A SER 3.9 0.3 + - - -
413A VAL* 5.5 0.7 - - + -
414A ALA* 1.3 77.7 - - - +
416A SER* 1.3 70.5 + - - +
418A GLU 3.5 12.8 - - - +
419A MET* 4.2 10.8 - - - -
420A LEU* 4.3 1.1 - - - -
445A THR* 4.7 0.2 - - + -
446A ASP 3.5 24.5 - - - -
447A CYS* 3.7 21.5 - - - -
449A LEU* 4.2 8.3 - - + -
450A PRO* 3.7 26.2 - - + -
466A VAL* 3.8 22.0 - - + -
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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