Contacts of the strand formed by residues 509 - 514 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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402A MET* 4.3 4.7 - - + +
458A GLN* 3.5 18.6 - - - +
483A GLU* 3.6 12.3 + - - +
484A VAL* 4.0 27.6 - - + +
489A LYS* 3.3 35.9 - - + -
499A PHE* 3.6 31.2 - - + -
501A GLY 3.5 2.2 - - - +
502A GLN* 3.6 20.4 - - + +
506A GLY 4.0 8.5 - - - +
507A GLU 3.3 24.0 - - - +
508A ARG* 1.4 84.1 - - - +
510A GLU* 1.3 62.0 + - - +
511A ILE 5.1 0.2 - - - +
524A GLN* 3.4 18.7 - - - +
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Residues in contact with GLU 510 (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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402A MET* 3.7 4.5 - - - +
449A ARG* 4.0 6.8 + - - -
455A THR* 3.6 35.4 - - + +
478A HIS* 3.3 26.8 + - + -
480A HIS* 2.9 22.7 + - - -
501A GLY 2.8 8.5 + - - -
502A GLN 4.4 9.4 - - - -
503A ASP* 4.4 4.9 - - - +
508A ARG* 4.5 8.1 - - - +
509A MET* 1.3 78.6 - - - +
511A ILE* 1.3 60.7 + - + +
523A VAL* 3.2 8.7 - - - +
524A GLN* 3.1 28.4 + - - +
525A TYR* 3.4 29.4 + - + +
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Residues in contact with ILE 511 (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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402A MET* 4.2 2.2 - - - -
455A THR* 4.6 0.9 - - + -
457A PHE* 4.2 24.2 - - + -
464A MET* 4.6 14.8 - - + -
468A TYR* 5.2 0.2 - - + -
474A LEU* 4.4 12.8 - - + -
499A PHE* 3.5 7.1 - - - +
500A VAL* 2.8 36.8 + - + -
501A GLY* 3.1 26.8 + - - +
510A GLU* 1.3 85.7 - - + +
512A VAL* 1.4 69.1 + - - +
513A GLU* 4.3 10.8 - - + +
521A VAL* 5.7 0.4 - - + -
522A GLY 3.5 7.2 - - - +
523A VAL* 4.3 4.7 - - + -
525A TYR* 3.6 32.8 - - + +
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Residues in contact with VAL 512 (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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402A MET* 3.8 24.7 - - + +
405A ALA* 6.1 3.1 - - + -
406A VAL* 5.1 5.2 - - + -
497A LEU* 3.5 36.6 - - + -
498A LYS 3.2 20.0 - - - +
499A PHE* 4.0 13.0 - - + -
511A ILE* 1.4 75.6 - - - +
513A GLU* 1.4 64.3 + - - +
514A LEU 4.2 0.7 - - - +
520A PHE* 5.8 4.0 - - + +
521A VAL* 3.3 8.5 - - - +
522A GLY* 3.0 40.4 + - - +
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Residues in contact with GLU 513 (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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461A ASN 5.0 0.7 - - - +
462A SER* 2.6 31.4 + - - -
463A VAL* 3.2 29.2 + - - +
464A MET* 3.0 22.5 + - + +
498A LYS* 2.8 32.2 + - - +
500A VAL* 3.8 19.3 - - + +
511A ILE* 4.3 5.7 - - + +
512A VAL* 1.4 79.1 - - - +
514A LEU* 1.3 65.9 + - - +
515A GLU* 3.5 12.6 + - - +
520A PHE 3.9 3.6 - - - -
521A VAL* 3.8 15.0 - - + -
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Residues in contact with LEU 514 (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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389A ARG* 3.6 34.3 - - + -
392A LYS* 5.5 3.1 - - - +
409A PHE* 3.8 21.5 - - + -
496A GLY 3.5 17.0 - - - +
497A LEU* 3.7 22.9 - - + +
512A VAL* 4.2 0.8 - - - +
513A GLU* 1.3 72.0 - - - +
515A GLU* 1.3 72.4 + - - +
516A ASP 3.9 0.2 + - - -
517A HIS* 4.0 25.5 + - + +
520A PHE* 3.0 45.1 + - + +
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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