Contacts of the strand formed by residues 498 - 504 (chain A) in PDB entry 1MS4
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 498 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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494A PRO* 3.4 18.7 - - - +
496A GLY 3.2 3.5 + - - -
497A ALA* 1.3 72.7 + - - +
499A PRO* 1.3 70.8 - - - +
517A SER* 3.1 6.4 - - - -
518A TYR* 2.9 56.5 + - - -
596A THR* 4.3 8.4 - - - -
597A ASP 4.1 9.5 + - - -
598A SER* 3.5 11.9 - - - -
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Residues in contact with PRO 499 (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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497A ALA 4.7 0.2 - - - +
498A SER* 1.3 84.9 - - - +
500A LEU* 1.3 62.8 + - - +
517A SER* 3.6 12.6 - - - +
518A TYR* 3.9 3.1 - - - -
585A TYR* 4.0 19.5 - - + +
588A GLY* 3.8 14.6 + - - -
589A TYR* 3.5 42.2 - - + +
596A THR* 3.7 18.2 - - + +
598A SER* 2.6 43.1 + - - +
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Residues in contact with LEU 500 (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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488A VAL* 3.9 34.9 - - + +
490A ILE* 4.5 5.2 - - + -
499A PRO* 1.3 74.1 - - - +
501A LEU* 1.3 67.7 + - + +
516A LEU* 3.0 22.5 + - + +
518A TYR* 3.5 24.9 - - + -
524A TRP* 3.8 26.0 - - + -
585A TYR* 4.6 2.5 - - - -
586A VAL* 3.7 0.9 - - - +
587A GLY* 2.5 33.8 + - - +
588A GLY 4.6 0.7 - - - -
600A VAL* 3.7 39.9 - - + -
602A VAL* 5.0 2.2 - - + +
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Residues in contact with LEU 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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484A LEU* 4.1 23.8 - - + +
486A ALA* 4.1 26.0 - - + -
488A VAL* 5.5 5.2 - - + -
500A LEU* 1.3 84.7 - - + +
502A GLY* 1.3 60.5 + - - +
515A GLY* 3.3 1.0 - - - -
516A LEU* 2.8 36.9 + - + +
547A VAL* 4.2 19.1 - - + -
549A LEU* 3.9 22.7 - - + +
585A TYR* 3.4 24.0 + - - +
586A VAL* 3.6 29.8 - - + -
602A VAL* 5.5 0.4 - - + -
605A VAL* 5.1 1.1 - - + -
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Residues in contact with GLY 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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484A LEU* 4.2 2.8 - - - +
501A LEU* 1.3 79.8 - - - +
503A ALA* 1.3 58.0 + - - -
514A LEU 3.3 9.6 - - - -
515A GLY* 3.8 0.9 - - - -
549A LEU* 4.0 7.9 - - - -
584A PHE* 3.1 13.0 - - - +
585A TYR* 2.8 54.0 + - - +
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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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482A PHE* 4.1 16.4 - - + -
502A GLY* 1.3 72.9 - - - -
504A SER* 1.3 56.6 + - - +
512A LYS* 3.5 4.9 - - - +
513A LEU* 2.8 45.2 + - + -
514A LEU 2.7 15.7 + - - +
549A LEU* 5.1 0.4 - - - +
581A ILE* 4.4 9.9 - - + -
583A HIS 3.8 4.3 - - - -
584A PHE* 3.9 22.2 - - + -
585A TYR* 3.7 2.6 - - - -
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Residues in contact with SER 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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503A ALA* 1.3 72.0 - - - +
505A LEU* 1.3 52.1 + - - +
506A ASP* 2.3 35.3 + - - -
509A GLY* 3.1 22.8 - - - -
511A LYS 3.5 4.5 + - - -
512A LYS* 4.5 1.6 - - - +
581A ILE* 3.5 5.0 - - - -
582A SER* 2.7 31.7 + - - -
583A HIS* 2.9 34.4 + - - -
585A TYR* 4.1 8.4 - - - -
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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