Contacts of the strand formed by residues 494 - 504 (chain B) in PDB entry 5M9N
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 GLU 494 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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492B GLY 3.6 8.1 + - - +
493B ASP* 1.3 81.5 - - - +
495B PHE* 1.3 65.7 + - - +
636B THR* 4.0 17.0 - - + +
637B VAL 3.3 6.3 - - - +
638B LYS* 3.8 38.5 + - + +
654B LYS* 6.0 0.7 - - - -
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Residues in contact with PHE 495 (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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489B LEU* 4.1 22.7 - - + -
493B ASP* 5.1 0.9 - - + -
494B GLU* 1.3 82.9 - - - +
496B CYS* 1.3 76.9 + - - +
497B GLY* 4.6 0.2 - - - -
510B CYS* 4.4 10.5 - - + -
511B GLN 4.5 1.6 - - - -
512B GLN* 3.6 44.4 - - + +
514B GLN* 4.2 14.1 - - - +
604B ILE* 3.6 23.3 - - + -
636B THR* 3.6 5.4 - - - +
637B VAL* 2.9 69.9 + - + +
639B VAL* 4.5 7.0 - - + -
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Residues in contact with CYS 496 (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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495B PHE* 1.3 82.1 - - - +
497B GLY* 1.3 59.8 + - - +
513B LEU* 3.0 44.5 + - + +
514B GLN* 3.6 10.4 + - - +
634B ILE* 3.8 12.3 - - + -
635B ILE 3.5 4.0 - - - -
636B THR* 4.2 17.7 - - - -
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Residues in contact with GLY 497 (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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495B PHE* 3.9 8.6 + - - -
496B CYS* 1.3 75.4 - - - +
498B VAL* 1.3 64.7 + - - -
511B GLN 3.0 15.0 - - - -
512B GLN* 4.3 0.7 - - - -
513B LEU* 4.0 6.4 - - - +
634B ILE* 3.5 7.3 - - - +
635B ILE* 2.8 36.2 + - - +
637B VAL* 4.8 4.5 - - - +
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Residues in contact with VAL 498 (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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497B GLY* 1.3 78.6 - - - +
499B VAL* 1.3 65.8 + - - +
500B ALA* 4.1 5.7 + - + +
510B CYS* 3.3 6.1 - - - +
511B GLN* 3.0 59.4 + - + +
512B GLN 6.2 0.2 - - - -
513B LEU* 4.0 18.2 - - + +
633B LYS 4.2 15.9 - - - +
634B ILE* 5.1 1.8 - - + -
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Residues in contact with VAL 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 VAL* 1.3 76.3 - - - +
500B ALA* 1.3 67.9 - - - +
502B ILE* 4.0 14.0 - - + +
508B PHE* 3.6 28.7 - - + -
509B PHE 3.5 3.6 - - - +
510B CYS* 4.0 13.9 - - - -
626B MET* 4.5 3.1 - - + -
630B VAL* 3.6 50.4 + - + +
631B GLN* 6.0 0.5 - - - -
633B LYS 4.9 2.8 + - - -
635B ILE* 4.2 15.5 - - + -
637B VAL* 5.3 0.4 - - + -
651B LEU* 4.2 13.7 - - + -
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Residues in contact with ALA 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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498B VAL* 4.1 7.6 + - + +
499B VAL* 1.3 79.2 - - - +
501B HIS* 1.3 97.8 + - + +
502B ILE* 3.1 7.7 + - - -
508B PHE* 4.1 0.9 - - - +
509B PHE* 2.8 32.2 + - - +
510B CYS* 6.0 0.4 - - - -
511B GLN* 6.0 2.7 - - + +
578B TYR 5.1 2.7 - - - +
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Residues in contact with HIS 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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566A ALA 6.1 0.4 - - - -
500B ALA* 1.3 93.6 - - + +
502B ILE* 1.3 63.8 + - - +
503B GLN* 3.3 15.9 + - - +
507B ASP 3.9 0.3 - - - +
508B PHE* 3.8 9.5 - - - -
509B PHE* 4.2 18.0 + - + +
578B TYR* 3.3 25.0 + - + -
579B GLY 3.8 5.1 - - - +
580B ASN* 3.4 32.5 + - + +
701B 2MR 3.6 27.6 - - - -
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Residues in contact with ILE 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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565A TYR* 5.9 1.9 - - - +
499B VAL* 4.0 13.5 - - + +
500B ALA* 4.2 4.3 - - - +
501B HIS* 1.3 76.0 - - - +
503B GLN* 1.3 64.5 + - - +
504B THR 3.9 15.3 - - - +
508B PHE* 3.7 20.2 - - + -
623B ILE* 4.2 16.8 - - + +
626B MET* 3.9 27.4 - - + -
627B LYS* 3.8 46.9 + - + +
630B VAL* 3.8 29.4 - - + -
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Residues in contact with GLN 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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543A ILE* 3.7 17.1 - - + +
564A ALA* 3.5 17.7 - - + +
565A TYR* 2.9 51.0 + - - +
501B HIS* 3.3 13.5 + - - +
502B ILE* 1.3 76.5 + - - +
504B THR* 1.3 73.6 - - + +
507B ASP* 2.8 39.2 + - + +
509B PHE* 6.3 2.0 - - + -
581B PHE* 4.2 7.1 - - - -
623B ILE* 3.7 19.2 - - - +
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Residues in contact with THR 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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543A ILE* 4.5 17.5 - - + -
502B ILE* 3.9 9.9 - - - +
503B GLN* 1.3 88.4 - - + +
505B PRO* 1.3 72.7 - - - +
506B GLU* 2.8 24.8 + - - +
507B ASP* 2.8 31.2 + - + +
508B PHE* 3.8 3.8 - - - -
618B TRP* 3.5 21.0 - - + -
623B ILE* 4.4 10.5 - - + -
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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