Contacts of the strand formed by residues 498 - 504 (chain C) in PDB entry 5AO3
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 PHE 498 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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457C VAL* 5.5 15.7 - - + -
477C PRO* 3.7 26.7 - - + +
480C VAL* 4.0 26.7 - - + -
481C ALA* 4.1 28.0 - - + -
493C LEU* 3.5 43.1 - - + -
494C LYS 3.8 11.7 - - - -
495C ALA* 3.1 14.6 + - - +
496C GLU 3.4 2.2 - - - +
497C ASP* 1.3 84.7 - - - +
499C ILE* 1.3 73.1 + - - +
500C VAL* 5.1 2.7 - - + -
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Residues in contact with ILE 499 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220C ARG* 3.9 22.4 - - - +
384C THR* 3.7 33.9 - - + +
388C ASP* 4.4 18.6 - - - +
454C PHE* 4.1 28.5 - - + -
477C PRO* 5.1 0.9 - - + -
497C ASP 4.1 2.2 + - - +
498C PHE* 1.3 82.6 - - - +
500C VAL* 1.3 67.6 + - - +
501C ASP* 4.0 3.2 + - + +
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Residues in contact with VAL 500 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220C ARG* 2.6 26.4 + - - +
468C ILE* 6.0 1.1 - - + -
473C TYR* 5.4 2.8 - - - +
476C LEU* 3.7 47.8 - - + +
477C PRO* 4.0 12.5 - - + +
480C VAL* 3.8 29.2 - - + -
498C PHE* 4.1 3.5 + - + -
499C ILE* 1.3 77.0 - - - +
501C ASP* 1.3 63.5 + - - +
502C VAL* 3.7 6.2 + - + +
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Residues in contact with ASP 501 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220C ARG* 4.0 9.6 + - - +
380C ASN* 3.4 36.5 - - - +
381C ILE* 5.3 0.2 - - - -
384C THR* 3.9 22.3 - - + +
499C ILE* 4.0 3.9 + - + -
500C VAL* 1.3 74.7 - - - +
502C VAL* 1.3 71.5 + - - +
503C ILE* 3.6 21.9 + - + +
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Residues in contact with VAL 502 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220C ARG* 5.0 2.0 - - - +
468C ILE* 4.8 16.8 - - + +
473C TYR* 3.0 52.1 + - + +
476C LEU* 3.6 23.8 - - + -
500C VAL* 3.7 6.1 + - + +
501C ASP* 1.3 81.1 + - - +
503C ILE* 1.3 62.9 + - - +
504C ASN* 3.7 20.0 + - - +
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Residues in contact with ILE 503 (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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374C TYR 5.5 1.1 - - - +
375C GLN* 4.2 36.1 - - + +
380C ASN* 3.9 27.4 - - + +
459C GLU* 6.1 1.8 - - - +
501C ASP* 3.6 31.6 + - + +
502C VAL* 1.3 77.7 - - - +
504C ASN* 1.3 69.1 + - - +
505C MET 4.4 0.2 + - - -
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Residues in contact with ASN 504 (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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370C HIS* 5.4 2.8 + - - -
375C GLN* 5.0 3.5 + - - +
467C LYS* 5.5 6.8 - - - +
468C ILE 5.5 1.6 - - - +
470C ARG* 5.8 4.9 - - - +
473C TYR* 3.3 25.1 + - - -
502C VAL* 3.7 16.8 + - - +
503C ILE* 1.3 83.7 - - - +
505C MET* 1.3 60.7 + - - +
506C ASP* 3.4 16.3 - - - +
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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
------------------------------------------------------------
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