Contacts of the strand formed by residues 455 - 459 (chain A) in PDB entry 5IYB
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 ILE 455 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453A GLY 4.3 7.6 - - - +
454A ASP* 1.3 73.1 - - - +
456A VAL* 1.3 70.1 + - - +
472A HIS 3.2 13.9 - - - +
473A ARG* 4.5 7.2 - - + -
505A LEU* 3.9 3.7 - - - +
506A PRO* 3.4 20.3 - - + +
512A ARG* 4.1 24.7 + - + +
515A ILE* 3.7 31.4 - - + -
516A GLN* 3.3 34.1 - - + +
520A MET* 3.5 29.8 - - + -
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Residues in contact with VAL 456 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A VAL* 4.1 10.3 - - + -
450A MET* 4.5 3.1 - - - -
454A ASP 4.6 0.7 - - - +
455A ILE* 1.3 81.5 - - - +
457A ILE* 1.3 65.7 + - - +
458A PHE* 3.5 2.4 + - + +
471A GLY* 3.2 4.7 - - - -
472A HIS* 2.9 33.9 + - + +
474A VAL* 3.7 32.1 - - + -
503A LEU* 3.8 35.0 - - + -
504A HIS 3.6 9.2 - - - +
505A LEU* 3.6 22.2 - - + -
506A PRO* 4.1 1.6 - - - -
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Residues in contact with ILE 457 (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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456A VAL* 1.3 74.4 - - - +
458A PHE* 1.3 60.6 + - - +
469A MET* 3.7 39.0 - - + +
470A MET* 3.8 23.3 - - - -
471A GLY* 3.9 4.7 - - - +
502A ASN 4.1 0.2 - - - +
503A LEU* 3.4 2.8 - - - +
504A HIS* 2.6 53.1 + - + +
506A PRO* 4.2 1.2 - - - +
515A ILE* 3.6 17.9 - - + -
519A ALA* 4.1 16.8 - - + -
1094B GLN* 4.3 13.5 - - - +
1102B PHE* 3.6 25.1 - - + -
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Residues in contact with PHE 458 (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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378A VAL* 4.0 16.2 - - + -
456A VAL* 4.5 2.7 - - + +
457A ILE* 1.3 73.6 - - - +
459A ASN* 1.3 64.2 + - - +
469A MET* 3.5 1.7 - - - +
470A MET 3.1 28.8 + - - -
472A HIS* 3.7 27.8 - + + -
482A PHE* 3.4 44.0 - + + -
484A LEU* 3.8 20.9 - - + -
492A TYR* 3.4 20.5 + + - +
501A MET* 3.5 37.0 - - + -
502A ASN 3.5 3.4 - - - -
503A LEU* 3.7 26.9 - - + -
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Residues in contact with ASN 459 (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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458A PHE* 1.3 81.0 - - - +
460A ARG* 1.3 79.0 + - - +
461A GLN* 4.1 1.2 + - - -
463A THR* 3.5 24.5 + - - +
468A SER 3.7 4.8 - - - +
469A MET* 4.0 24.9 - - + +
492A TYR* 5.2 0.7 - - - -
501A MET* 3.6 6.6 - - - -
502A ASN* 2.7 63.4 + - + +
504A HIS* 4.3 9.4 + - + -
1090B GLU* 3.4 28.1 + - - +
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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