Contacts of the strand formed by residues 490 - 495 (chain A) in PDB entry 4MSL
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 HIS 490 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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442A PRO* 3.7 8.4 - - - +
443A MET 4.6 0.2 + - - -
458A HIS* 3.1 28.9 + - - -
472A VAL* 3.8 9.7 - - + +
486A LEU* 3.5 32.7 - - + +
487A GLU 3.2 27.1 - - - -
488A GLY 2.7 21.3 + - - -
489A PRO* 1.3 77.8 + - - +
491A TYR* 1.3 66.4 + - - +
492A TYR* 3.4 8.3 - - + -
503A ALA* 4.2 6.5 - - + -
504A ILE 3.2 8.1 - - - +
505A GLU* 3.5 29.5 - - + +
506A HIS 4.1 1.3 - - - +
515A LYS* 3.1 28.9 + - - -
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Residues in contact with TYR 491 (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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442A PRO* 3.8 27.4 - - + +
443A MET* 3.9 17.7 - - + -
490A HIS* 1.3 74.5 - - - +
492A TYR* 1.3 59.8 + - - +
503A ALA* 3.2 5.4 - - - +
504A ILE* 2.8 42.7 + - + +
505A GLU 4.6 0.7 - - - -
506A HIS* 3.5 39.6 + - + -
536A PHE* 3.3 54.7 + + + -
537A THR* 5.5 2.2 - - - -
538A GLY* 5.1 5.6 - - - -
539A LEU* 4.1 13.2 - - + +
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Residues in contact with TYR 492 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443A MET* 3.2 56.7 + - + +
444A ALA 2.7 25.5 + - - -
446A LEU* 3.7 22.4 - - + +
456A ILE* 3.6 46.1 + - + -
457A ALA* 3.7 5.0 - - - -
458A HIS* 3.4 28.7 + + - -
472A VAL* 4.2 15.0 - - + -
485A MET* 4.6 10.1 - - + -
490A HIS* 3.4 12.6 - - + -
491A TYR* 1.3 74.7 - - - +
493A THR* 1.3 62.0 + - - +
501A ILE* 5.3 0.7 - - + -
502A VAL 3.3 9.6 - - - +
503A ALA* 4.7 2.2 - - + -
539A LEU* 4.2 4.0 - - - +
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Residues in contact with THR 493 (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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446A LEU* 4.1 5.8 - - - -
456A ILE* 5.7 0.2 - - - -
492A TYR* 1.3 75.7 - - - +
494A ILE* 1.3 71.8 + - - +
495A LEU* 4.6 3.7 - - + +
501A ILE* 3.7 6.3 - - - +
502A VAL* 2.9 55.3 + - + +
539A LEU* 3.8 15.3 - - + -
541A SER* 3.6 20.8 + - - -
550A ILE* 3.8 22.9 - - + +
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Residues in contact with ILE 494 (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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446A LEU* 3.7 26.3 - - + +
447A SER* 4.7 1.6 - - - -
448A GLU* 4.1 29.1 + - + +
451A ALA* 4.3 9.0 - - + -
454A ILE* 3.9 26.5 - - + -
456A ILE* 4.3 12.8 - - + -
493A THR* 1.3 85.2 + - - +
495A LEU* 1.3 66.5 + - - +
498A GLY* 3.4 33.0 - - - +
500A ILE 3.7 3.1 - - - +
501A ILE* 4.5 8.1 - - + -
541A SER* 4.9 1.9 + - - -
545A ALA* 3.4 28.7 - - + +
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Residues in contact with LEU 495 (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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493A THR* 4.6 5.2 - - + +
494A ILE* 1.3 80.8 - - - +
496A ASP* 1.3 68.0 + - + +
497A SER 3.2 2.9 - - - -
498A GLY 3.0 11.6 + - - -
500A ILE* 2.8 39.4 + - + +
502A VAL* 3.6 30.1 - - + -
541A SER* 4.3 14.1 - - - +
545A ALA* 3.7 3.1 - - - -
547A SER* 3.3 21.8 - - - +
548A MET* 4.2 7.2 - - - +
549A ASN 3.8 21.3 - - - +
550A ILE* 4.2 11.2 - - + -
571A PHE* 4.1 16.6 - - + -
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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