Contacts of the strand formed by residues 498 - 504 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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494B PRO* 3.5 8.8 - - - +
496B GLY 3.1 13.4 + - - -
497B ALA* 1.3 71.7 + - - +
499B PRO* 1.3 72.1 - - - +
517B SER* 3.1 6.6 - - - -
518B TYR* 2.9 63.4 + - - -
596B THR* 4.3 7.5 - - - +
597B ASP 4.1 9.5 + - - -
598B SER* 3.7 5.6 - - - -
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Residues in contact with PRO 499 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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498B SER* 1.3 88.4 - - - +
500B LEU* 1.3 61.7 + - - +
516B LEU 3.9 0.7 - - - +
517B SER* 3.5 11.2 - - - +
518B TYR* 3.9 3.5 - - - -
585B TYR* 3.7 26.7 - - + +
587B GLY 4.5 0.2 - - - -
588B GLY* 4.0 12.2 + - - -
589B TYR* 3.4 41.3 - - + +
596B THR* 3.7 15.9 - - + +
598B SER* 2.8 39.7 + - - +
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Residues in contact with LEU 500 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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488B VAL* 4.1 33.8 - - + +
490B ILE* 4.3 5.2 - - + -
499B PRO* 1.3 73.4 - - - +
501B LEU* 1.3 67.7 + - + +
516B LEU* 2.8 25.3 + - + +
518B TYR* 3.5 22.2 - - + -
524B TRP* 3.5 32.8 - - + -
585B TYR* 4.6 2.0 - - - -
586B VAL* 3.6 1.6 - - - +
587B GLY* 2.6 32.1 + - - +
600B VAL* 3.5 39.7 - - + -
602B VAL* 4.9 2.5 - - + +
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Residues in contact with LEU 501 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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484B LEU* 3.8 29.8 - - + +
486B ALA* 4.3 22.9 - - + -
488B VAL* 5.6 3.6 - - + -
500B LEU* 1.3 85.7 - - + +
502B GLY* 1.3 60.5 + - - +
515B GLY* 3.3 0.7 - - - -
516B LEU* 2.7 35.8 + - + +
547B VAL* 3.9 24.2 - - + +
549B LEU* 3.8 20.1 - - + +
585B TYR* 3.3 24.0 + - - +
586B VAL* 3.9 27.6 - - + -
602B VAL* 5.7 0.2 - - + -
605B VAL* 5.1 1.3 - - + -
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Residues in contact with GLY 502 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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484B LEU* 4.4 3.6 - - - +
501B LEU* 1.3 79.9 - - - +
503B ALA* 1.3 59.2 + - - -
514B LEU 3.2 11.7 - - - -
515B GLY* 3.8 1.1 - - - -
549B LEU* 4.0 7.0 - - - -
584B PHE* 3.2 11.5 - - - +
585B TYR* 2.8 48.9 + - - +
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Residues in contact with ALA 503 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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482B PHE* 4.0 18.2 - - + -
502B GLY* 1.3 71.9 - - - -
504B SER* 1.3 61.1 + - - +
512B LYS* 3.5 4.3 - - - +
513B LEU* 2.9 38.6 + - + -
514B LEU 2.6 16.4 + - - +
549B LEU* 5.1 0.6 - - - +
581B ILE* 4.4 9.4 - - + -
583B HIS 3.8 3.8 - - - -
584B PHE* 3.8 23.3 - - + -
585B TYR* 3.9 2.2 - - - -
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Residues in contact with SER 504 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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502B GLY 4.1 1.0 - - - -
503B ALA* 1.3 73.4 - - - +
505B LEU* 1.3 56.1 + - - +
506B ASP 2.4 30.9 + - - -
509B GLY* 3.2 21.4 - - - -
511B LYS 3.5 5.1 + - - -
512B LYS* 4.4 1.1 - - - +
581B ILE* 3.4 7.2 - - - +
582B SER* 2.6 30.8 + - - -
583B HIS* 2.9 30.7 + - - -
585B TYR* 4.1 8.7 - - - -
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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