Contacts of the strand formed by residues 500 - 505 (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 ILE 500 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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494A ILE* 3.7 2.1 - - - +
495A LEU* 2.8 50.7 + - + +
496A ASP* 4.8 3.8 - - + -
498A GLY 4.4 0.2 - - - -
499A GLY* 1.3 88.4 - - - +
501A ILE* 1.3 72.8 + - - +
502A VAL* 3.7 25.4 - - + -
516A PHE* 4.4 9.9 - - + -
517A SER 3.5 3.8 - - - +
518A THR* 4.0 17.3 - - + -
548A MET* 4.8 2.5 - - - -
571A PHE* 4.6 20.2 - - + -
574A ILE* 4.5 9.4 - - + -
575A LEU* 3.5 31.9 - - + -
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Residues in contact with ILE 501 (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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454A ILE* 4.5 13.7 - - + -
456A ILE* 4.0 22.7 - - + -
474A ILE* 4.0 16.4 - - + -
485A MET* 4.7 2.7 - - + -
492A TYR* 5.3 0.2 - - + -
493A THR 3.7 10.8 - - - +
494A ILE* 4.5 9.6 - - + -
498A GLY* 4.8 6.3 - - - +
500A ILE* 1.3 79.2 - - - +
502A VAL* 1.3 67.0 + - - +
516A PHE* 3.1 6.8 - - - +
517A SER* 2.9 37.5 + - - +
520A GLU* 3.7 36.1 - - - -
521A GLY* 4.0 1.3 - - - +
524A TRP* 3.5 25.3 - - + -
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Residues in contact with VAL 502 (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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492A TYR* 3.3 5.7 - - - +
493A THR* 2.9 51.5 + - + +
495A LEU* 3.6 29.2 - - + -
500A ILE* 3.7 10.1 - - + -
501A ILE* 1.3 81.3 - - - +
503A ALA* 1.3 64.5 + - - +
504A ILE* 5.4 1.8 - - + -
514A ILE* 3.4 36.1 - - + -
515A LYS 3.3 4.9 - - - +
516A PHE* 4.4 2.2 - - + -
524A TRP* 4.2 1.1 - - - -
539A LEU* 5.5 1.6 - - + -
550A ILE* 4.8 5.8 - - + -
571A PHE* 4.1 15.3 - - + -
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Residues in contact with ALA 503 (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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485A MET* 4.7 0.2 - - + -
486A LEU* 3.5 32.3 - - + -
490A HIS* 4.2 5.8 - - + -
491A TYR 3.2 10.3 - - - +
492A TYR* 4.7 6.3 - - + -
502A VAL* 1.3 74.7 - - - +
504A ILE* 1.3 67.1 + - - +
514A ILE* 3.8 1.1 - - - +
515A LYS* 2.8 42.3 + - + +
524A TRP* 3.8 13.2 - - + -
539A LEU* 5.7 0.4 - - - -
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Residues in contact with ILE 504 (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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490A HIS* 3.2 5.2 - - - -
491A TYR* 2.8 40.5 + - + +
503A ALA* 1.3 75.6 - - - +
505A GLU* 1.3 76.0 + - - +
511A ILE* 3.9 16.8 - - + -
513A VAL 3.4 21.5 - - - +
514A ILE* 3.6 26.5 - - + -
529A PHE* 4.3 2.2 - - + -
536A PHE* 3.5 42.8 - - + -
539A LEU* 4.1 15.5 - - + -
552A ILE* 4.2 11.0 - - + -
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Residues in contact with GLU 505 (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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489A PRO 4.8 1.6 - - - +
490A HIS* 3.5 24.9 - - + +
491A TYR* 4.6 1.9 - - - -
503A ALA 4.2 0.6 + - - -
504A ILE* 1.3 86.8 - - - +
506A HIS* 1.3 73.8 + - - +
507A SER* 3.6 19.9 + - - -
511A ILE* 4.4 22.0 - - + +
513A VAL 5.1 3.4 + - - +
515A LYS* 4.8 15.4 + - - +
536A PHE* 5.2 2.6 - - - +
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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