Contacts of the strand formed by residues 509 - 514 (chain B) in PDB entry 5U03
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 MET 509 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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402B MET* 4.3 5.0 - - + +
458B GLN* 3.5 20.0 - - - +
483B GLU* 3.6 12.9 + - - +
484B VAL* 4.0 28.1 - - + +
489B LYS* 3.3 36.6 - - + -
499B PHE* 3.6 29.2 - - + -
501B GLY 3.5 2.0 - - - +
502B GLN* 3.6 20.2 - - + +
506B GLY 4.0 7.4 - - - +
507B GLU 3.3 25.4 - - - +
508B ARG* 1.4 85.5 - - - +
510B GLU* 1.3 62.6 + - - +
524B GLN* 3.4 18.5 - - - +
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Residues in contact with GLU 510 (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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402B MET* 3.7 5.0 - - - +
449B ARG* 4.0 6.6 + - - -
455B THR* 3.6 35.4 - - + +
478B HIS* 3.3 26.8 + - + -
480B HIS* 2.9 22.9 + - - -
501B GLY 2.8 9.3 + - - +
502B GLN 4.4 8.7 - - - -
503B ASP* 4.4 4.7 - - - +
508B ARG* 4.5 7.4 - - - +
509B MET* 1.3 79.2 - - - +
511B ILE* 1.3 60.2 + - - +
523B VAL* 3.2 8.1 - - - +
524B GLN* 3.1 28.4 + - - +
525B TYR* 3.4 30.2 + - + +
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Residues in contact with ILE 511 (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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402B MET* 4.2 2.0 - - - -
455B THR* 4.6 1.3 - - + -
457B PHE* 4.2 23.3 - - + -
464B MET* 4.6 13.9 - - + -
468B TYR* 5.2 0.2 - - + -
474B LEU* 4.4 13.0 - - + -
499B PHE* 3.5 6.9 - - - +
500B VAL* 2.8 37.3 + - + -
501B GLY* 3.1 25.8 + - - +
509B MET 4.0 0.2 - - - -
510B GLU* 1.3 84.7 - - + +
512B VAL* 1.4 71.2 + - - +
513B GLU* 4.3 11.4 - - + +
521B VAL* 5.7 0.7 - - + -
522B GLY 3.5 6.5 - - - +
523B VAL* 4.3 5.2 - - + -
525B TYR* 3.6 31.6 - - + +
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Residues in contact with VAL 512 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402B MET* 3.8 24.2 - - + +
405B ALA* 6.1 3.4 - - + -
406B VAL* 5.1 5.4 - - + -
497B LEU* 3.5 38.4 - - + -
498B LYS 3.2 18.4 - - - +
499B PHE* 4.0 13.0 - - + -
500B VAL 4.4 0.2 - - - +
511B ILE* 1.4 76.2 - - - +
513B GLU* 1.3 62.8 + - - +
514B LEU 4.2 0.2 - - - -
520B PHE* 6.1 3.8 - - + -
521B VAL* 3.3 8.5 - - - +
522B GLY* 3.0 40.0 + - - +
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Residues in contact with GLU 513 (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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461B ASN 5.0 0.9 - - - +
462B SER* 2.6 30.8 + - - -
463B VAL* 3.2 28.4 + - - +
464B MET* 3.0 22.8 + - + +
498B LYS* 2.8 33.2 + - - +
500B VAL* 3.8 19.6 - - + +
511B ILE* 4.3 7.1 - - + +
512B VAL* 1.3 79.1 - - - +
514B LEU* 1.3 65.5 + - - +
515B GLU* 3.5 13.1 + - - +
520B PHE 3.9 4.0 - - - -
521B VAL* 3.8 15.0 - - + -
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Residues in contact with LEU 514 (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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389B ARG* 3.6 34.8 - - + -
392B LYS* 5.5 2.5 - - - +
409B PHE* 3.8 21.5 - - + -
496B GLY 3.5 17.3 - - - +
497B LEU* 3.7 23.1 - - + +
512B VAL 4.2 0.4 - - - -
513B GLU* 1.3 74.0 - - - +
515B GLU* 1.3 70.6 + - - +
516B ASP 3.9 0.7 + - - -
517B HIS* 4.0 25.8 + - + +
520B PHE* 3.0 45.0 + - + +
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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