Contacts of the strand formed by residues 454 - 457 (chain C) in PDB entry 5W5G
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 HIS 454 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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452C ILE* 3.6 4.8 - - - +
453C ASP* 1.3 91.3 + - + +
455C VAL* 1.3 62.8 + - - +
456C TYR* 4.0 9.2 - - + -
480C LEU* 4.2 4.7 - - + -
483C ARG* 3.1 34.4 + - - +
553C CYS* 3.1 44.9 - - + +
556C LYS* 3.5 29.9 + - + +
557C GLY* 3.5 11.6 - - - -
559C ASN 3.2 5.6 + - - +
560C ILE* 3.5 6.7 - - + +
561C LEU 2.9 26.3 + - - -
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Residues in contact with VAL 455 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452C ILE* 3.8 18.4 - - + -
454C HIS* 1.3 79.7 - - - +
456C TYR* 1.3 64.3 + - - +
467C ALA* 4.4 14.4 - - + -
471C LEU* 3.9 26.7 - - + -
480C LEU* 4.0 12.0 - - + +
481C LYS 4.0 6.6 + - - +
482C ILE* 3.5 24.4 - - + -
483C ARG* 2.8 36.2 + - - +
561C LEU* 3.3 21.3 - - + +
563C VAL* 4.6 2.0 - - + -
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Residues in contact with TYR 456 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454C HIS* 4.0 11.2 - - + -
455C VAL* 1.3 80.4 - - - +
457C CYS* 1.3 63.4 + - - +
482C ILE* 4.6 0.2 - - - -
483C ARG* 2.9 44.4 + - + +
485C GLU* 4.5 3.1 - - + -
488C LEU* 3.8 17.7 - - + -
520C TYR* 3.6 21.8 - - - -
549C ILE* 3.5 37.7 - - + -
552C GLU* 2.8 21.7 + - - +
553C CYS* 2.8 37.1 - - - -
560C ILE* 4.0 10.1 - - + -
561C LEU 2.9 8.6 + - - +
562C ILE* 3.4 5.0 - - + -
563C VAL 2.9 24.1 + - - -
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Residues in contact with CYS 457 (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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456C TYR* 1.3 78.9 - - - +
458C SER* 1.3 75.8 + - - +
463C CYS 4.2 5.8 - - - +
464C VAL* 3.5 26.5 - - - -
467C ALA* 4.3 2.0 - - + -
482C ILE* 3.3 28.9 - - + -
483C ARG 3.2 5.5 + - - -
484C VAL* 4.3 7.2 - - - -
485C GLU 2.9 26.7 + - - +
488C LEU* 3.9 9.4 - - - +
563C VAL* 3.1 22.9 - - + +
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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