Contacts of the strand formed by residues 509 - 514 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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402C MET* 4.3 4.5 - - + +
458C GLN* 3.5 19.7 - - - +
483C GLU* 3.6 12.5 + - - +
484C VAL* 4.0 27.9 - - + +
489C LYS* 3.3 36.1 - - + -
499C PHE* 3.6 30.3 - - + -
501C GLY 3.5 1.3 - - - +
502C GLN* 3.6 20.0 - - + +
506C GLY 4.0 8.1 - - - +
507C GLU 3.3 24.9 + - - +
508C ARG* 1.4 84.6 - - - +
510C GLU* 1.3 62.6 + - - +
524C GLN* 3.4 18.7 - - - +
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Residues in contact with GLU 510 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402C MET* 3.7 5.1 - - - +
449C ARG* 4.0 6.9 + - - -
455C THR* 3.6 35.7 - - + +
478C HIS* 3.3 26.3 + - + -
480C HIS* 2.9 23.2 + - - -
501C GLY 2.8 9.6 + - - +
502C GLN 4.4 9.2 - - - -
503C ASP* 4.4 4.3 - - - +
508C ARG* 4.5 7.4 - - - +
509C MET* 1.3 80.0 - - - +
511C ILE* 1.3 61.7 + - - +
523C VAL* 3.2 8.1 - - - +
524C GLN* 3.1 28.6 + - - +
525C TYR* 3.4 30.1 + - + +
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Residues in contact with ILE 511 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402C MET* 4.2 2.0 - - - -
455C THR* 4.6 1.1 - - + -
457C PHE* 4.2 23.6 - - + -
464C MET* 4.6 14.6 - - + -
468C TYR* 5.2 0.4 - - + -
474C LEU* 4.4 13.2 - - + -
499C PHE* 3.5 7.3 - - - +
500C VAL* 2.8 36.5 + - + -
501C GLY* 3.1 26.4 + - - +
510C GLU* 1.3 86.5 - - + +
512C VAL* 1.4 70.3 + - - +
513C GLU* 4.3 11.4 - - + +
521C VAL* 5.7 0.7 - - + -
522C GLY 3.5 6.5 - - - +
523C VAL* 4.3 4.5 - - + -
525C TYR* 3.6 32.5 - - + +
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Residues in contact with VAL 512 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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402C MET* 3.8 24.2 - - + +
405C ALA* 6.1 3.1 - - + -
406C VAL* 5.1 5.2 - - + -
497C LEU* 3.5 37.0 - - + -
498C LYS 3.2 20.2 - - - +
499C PHE* 4.0 13.0 - - + -
500C VAL 4.4 0.2 - - - +
511C ILE* 1.4 76.2 - - - +
513C GLU* 1.4 62.7 + - - +
514C LEU 4.2 0.2 - - - -
520C PHE* 5.8 4.3 - - + +
521C VAL* 3.3 8.5 - - - +
522C GLY* 3.0 40.2 + - - +
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Residues in contact with GLU 513 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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461C ASN 5.0 0.9 - - - +
462C SER* 2.6 30.9 + - - -
463C VAL* 3.2 27.6 + - - +
464C MET* 3.0 23.5 + - + +
498C LYS* 2.8 32.9 + - - +
500C VAL* 3.8 19.1 - - + +
511C ILE* 4.3 6.7 - - + +
512C VAL* 1.4 79.9 - - - +
514C LEU* 1.3 65.2 + - - +
515C GLU* 3.5 12.6 + - - +
520C PHE 3.9 3.8 - - - -
521C VAL* 3.8 15.0 - - + -
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Residues in contact with LEU 514 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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389C ARG* 3.6 35.2 - - + +
392C LYS* 5.5 2.2 - - - +
409C PHE* 3.8 21.8 - - + -
496C GLY 3.5 17.9 - - - +
497C LEU* 3.7 22.9 - - + +
512C VAL* 4.2 0.4 - - - +
513C GLU* 1.3 73.1 - - - +
515C GLU* 1.3 70.5 + - - +
517C HIS* 4.0 26.0 + - + +
520C PHE* 3.0 45.5 + - + +
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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