Contacts of the strand formed by residues 462 - 466 (chain B) in PDB entry 1F89
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 GLY 462 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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306B ILE 3.5 13.5 - - - -
459B THR* 3.0 35.8 + - - +
461B TYR* 1.3 81.5 - - - +
463B LYS* 1.3 65.2 + - - -
487B PHE* 3.4 8.2 - - - -
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Residues in contact with LYS 463 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305B LYS 5.9 0.6 + - - -
306B ILE 4.2 1.6 + - - -
456B THR* 4.1 17.0 - - + +
457B ILE 3.3 12.3 - - - +
458B ASP* 4.4 23.3 - - - +
462B GLY* 1.3 78.7 - - - -
464B PHE* 1.3 62.1 + - - +
484B LYS* 3.7 29.6 + - + +
485B GLY* 4.2 13.1 + - - -
486B ALA* 3.0 7.6 - - - +
487B PHE* 2.9 33.3 + - - -
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Residues in contact with PHE 464 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348B LEU* 4.3 15.3 - - + -
393B ILE* 4.2 19.5 - - + -
395B VAL* 4.1 19.1 - - + -
415B ILE* 4.4 4.9 - - + -
456B THR* 4.2 2.5 - - - -
457B ILE* 3.0 46.6 + - + +
459B THR* 3.8 26.0 - - + -
463B LYS* 1.3 77.7 - - - +
465B GLY* 1.3 67.0 + - - +
466B VAL* 3.8 20.2 - - + -
486B ALA* 3.8 4.3 - - - -
487B PHE* 4.1 25.6 - + + -
488B ALA* 3.2 20.0 - - + +
490B ILE* 4.1 13.7 - - + -
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Residues in contact with GLY 465 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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455B THR 3.4 11.2 - - - -
456B THR* 4.3 0.2 - - - -
464B PHE* 1.3 74.6 - - - +
466B VAL* 1.3 61.3 + - - +
481B SER* 3.7 8.9 - - - -
486B ALA* 4.0 5.1 - - - +
488B ALA 2.8 10.2 + - - +
489B MET* 3.5 21.5 - - - -
490B ILE* 2.7 31.0 + - - +
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Residues in contact with VAL 466 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395B VAL* 4.7 5.6 - - + -
413B SER* 3.8 30.1 - - - +
415B ILE* 4.3 10.8 - - + -
426B HIS* 3.5 32.0 + - + -
455B THR* 3.1 13.8 + - - +
457B ILE* 3.6 26.5 - - + -
464B PHE* 3.8 16.2 - - + -
465B GLY* 1.3 79.1 - - - +
467B GLY* 1.3 66.5 + - - +
489B MET* 3.9 5.8 - - - +
490B ILE* 3.1 13.9 - - + +
492B PRO* 4.4 4.7 - - + -
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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