Contacts of the strand formed by residues 461 - 467 (chain B) in PDB entry 3F8I
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 461 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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423B PHE* 4.2 7.9 - - - -
456B GLY* 3.2 1.9 - - - -
457B ARG 3.0 26.5 + - - -
460B ASP* 1.3 80.3 - - - +
462B ALA* 1.3 61.1 + - - -
463B TYR* 4.0 6.4 - - - -
512B ALA* 3.1 24.0 - - - -
515B LEU* 4.1 3.8 - - - +
516B ASN* 3.4 7.2 - - - -
535B LYS* 4.9 0.2 - - - -
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Residues in contact with ALA 462 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423B PHE* 3.6 5.9 - - - -
454B ILE* 4.2 11.2 - - + -
455B HIS 3.2 11.9 - - - +
456B GLY* 3.9 1.1 - - - -
461B GLY* 1.3 73.5 - - - -
463B TYR* 1.3 62.5 + - - +
464B SER 4.7 4.5 - - - +
465B LEU* 6.2 0.4 - - + -
512B ALA 3.3 0.4 + - - -
513B LEU* 3.7 35.9 - - + +
516B ASN* 2.7 34.7 + - - +
536B PRO 3.7 2.9 - - - +
537B VAL* 4.0 4.8 - - + +
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Residues in contact with TYR 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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420B ALA 3.8 9.9 - - - -
421B ASN* 3.3 29.1 - - - +
422B HIS 3.6 18.6 - - - +
423B PHE* 3.4 35.9 - + - +
424B GLY 5.4 0.7 + - - -
455B HIS* 2.8 41.6 + + - +
456B GLY* 4.2 7.0 - - - -
457B ARG* 3.5 20.6 - - + -
460B ASP* 2.5 25.5 + - - +
461B GLY 4.0 12.8 - - - -
462B ALA* 1.3 73.7 - - - +
464B SER* 1.3 62.0 + - - +
536B PRO 4.2 4.5 - - - +
537B VAL* 3.7 3.1 - - - -
538B ARG* 2.9 49.6 + - - +
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Residues in contact with SER 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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446B VAL* 3.2 25.1 + - - -
447B HIS* 2.7 29.5 + - - -
454B ILE* 3.8 2.1 - - - +
455B HIS* 3.1 33.3 + - - +
462B ALA* 3.6 2.9 - - - +
463B TYR* 1.3 80.7 + - - +
465B LEU* 1.3 65.0 + - - +
537B VAL* 3.7 5.8 - - - +
538B ARG* 3.0 22.5 + - - -
540B VAL* 6.0 0.9 - - - -
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Residues in contact with LEU 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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447B HIS* 3.9 3.3 + - - -
453B GLY 3.0 14.6 - - - +
454B ILE* 4.6 4.9 - - + -
464B SER* 1.3 76.4 - - - +
466B VAL* 1.3 66.2 + - - +
467B LEU* 4.7 0.9 - - + +
481B PHE* 3.8 24.5 - - + -
483B TYR* 4.1 34.8 - - + +
513B LEU* 4.3 12.3 - - + -
537B VAL* 3.8 22.2 - - + -
538B ARG 3.0 5.3 + - - +
539B VAL* 3.5 13.5 - - + -
540B VAL* 3.1 22.1 + - - +
584B LEU* 4.3 23.6 - - + -
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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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438B ARG* 3.8 28.0 - - - +
447B HIS* 3.3 34.3 - - + +
453B GLY* 3.0 12.2 + - - +
465B LEU* 1.3 75.1 - - - +
467B LEU* 1.3 71.6 + - - +
468B ALA* 3.7 15.3 + - + -
483B TYR* 2.9 21.9 + - - -
540B VAL* 3.1 22.7 - - + +
542B ASN* 4.3 9.0 - - + -
407F 5CM 3.9 7.4 + - + -
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Residues in contact with LEU 467 (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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465B LEU* 4.7 1.8 - - + -
466B VAL* 1.3 70.0 - - - +
468B ALA* 1.3 61.0 + - - +
469B GLY 3.9 1.6 - - - +
474B ASP* 4.7 15.5 - - + +
475B VAL 5.6 0.7 - - - +
476B ASP* 3.9 14.4 - - + +
481B PHE* 3.8 40.2 - - + -
482B THR 5.5 0.4 - - - +
483B TYR* 3.8 16.6 - - + -
539B VAL* 4.2 10.1 - - + -
540B VAL 2.9 8.2 + - - +
541B ARG* 3.6 48.1 - - + +
542B ASN 2.9 27.0 + - - +
545B GLY* 4.8 3.2 + - - -
407F 5CM 4.4 0.2 - - - -
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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