Contacts of the strand formed by residues 486 - 495 (chain B) in PDB entry 3FO5
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 GLN 486 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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475B THR* 3.3 5.2 - - - -
476B SER* 2.8 37.3 + - - +
477B PRO 5.2 4.2 - - - +
479B LEU* 5.0 6.1 + - - +
482B HIS* 4.6 1.7 + - - -
485B PRO* 1.3 74.9 - - - +
487B ASP* 1.3 61.3 + - - +
488B PHE* 3.3 34.4 - - + -
522B TYR* 4.0 1.7 - - - -
523B ARG* 3.0 52.1 + - + +
525B GLY* 4.7 7.2 - - - +
551B THR* 5.3 0.4 - - - +
553B GLY* 3.1 27.1 + - - +
554B VAL* 3.8 18.2 - - - +
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Residues in contact with ASP 487 (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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473B HIS* 2.7 31.7 + - - +
474B VAL 3.1 8.1 - - - +
475B THR* 4.0 4.5 - - + -
486B GLN* 1.3 75.4 - - - +
488B PHE* 1.3 65.2 + - - +
518B GLU* 5.2 1.8 - - - +
519B THR* 5.5 3.0 + - - -
522B TYR* 3.4 29.0 - - + +
523B ARG 2.9 8.7 + - - +
524B ARG* 2.8 47.2 + - - +
525B GLY 2.8 27.2 + - - -
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Residues in contact with PHE 488 (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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1B 1PE 3.6 40.2 - - - -
472B TYR 3.7 0.3 - - - +
473B HIS* 3.3 6.5 - - - -
474B VAL* 2.7 49.5 + - + +
476B SER* 3.9 10.1 - - - -
486B GLN* 3.3 41.5 - - + -
487B ASP* 1.3 73.8 - - - +
489B VAL* 1.3 63.9 + - - +
490B ILE* 3.8 22.9 - - + -
510B SER* 4.5 1.6 - - - +
524B ARG* 4.4 1.3 - - - +
525B GLY* 3.6 33.0 - - - -
526B GLU* 3.8 12.8 - - - -
527B THR* 4.3 4.3 - - - -
551B THR* 3.9 14.8 - - + -
554B VAL* 5.2 0.4 - - + -
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Residues in contact with VAL 489 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462B VAL* 5.3 1.8 - - + -
471B ILE* 3.8 23.3 - - + -
472B TYR 3.4 5.6 - - - +
473B HIS* 4.1 10.3 - - + -
488B PHE* 1.3 74.8 - - - +
490B ILE* 1.3 61.1 + - - +
510B SER* 3.3 10.3 + - - -
511B VAL* 3.0 47.0 + - + +
512B THR* 6.2 0.4 - - - -
513B LEU* 4.3 15.9 - - + +
516B HIS* 3.8 18.6 - - + +
524B ARG* 3.8 35.2 - - - +
525B GLY 5.1 0.4 + - - -
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Residues in contact with ILE 490 (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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1B 1PE 4.2 19.5 - - - +
446B LEU* 4.7 5.8 - - + -
456B TYR* 4.2 13.5 - - - +
470B ALA 3.6 1.0 - - - +
471B ILE* 3.2 6.3 - - - -
472B TYR* 2.8 43.6 + - + +
474B VAL* 4.0 20.0 - - + -
488B PHE* 3.8 25.1 - - + -
489B VAL* 1.3 78.9 - - - +
491B LEU* 1.3 75.0 + - - +
492B ALA 3.7 0.4 + - - +
508B LEU* 3.8 28.0 - - + -
509B ARG 3.6 5.6 - - - +
510B SER* 4.3 1.8 - - - +
511B VAL* 4.6 0.2 - - - -
527B THR* 4.3 14.8 - - + -
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Residues in contact with LEU 491 (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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379B TRP* 3.5 34.5 - - + -
387B LEU* 4.0 26.7 - - + +
388B SER* 4.2 2.0 - - - +
391B ASN* 2.9 35.0 + - + +
465B VAL* 4.6 2.5 - - + -
469B ASP* 4.7 4.3 - - + -
470B ALA 3.5 16.2 - - - +
471B ILE* 4.0 11.2 - - + +
490B ILE* 1.3 70.5 - - - +
492B ALA* 1.3 63.7 + - - +
493B SER* 3.9 9.9 - - - +
508B LEU* 3.4 2.1 - - - -
509B ARG* 2.8 33.7 + - + +
511B VAL* 3.7 23.5 - - + +
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Residues in contact with ALA 492 (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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444B SER 5.5 3.6 - - - +
446B LEU* 4.1 3.4 - - + -
468B ASP 3.9 0.7 - - - +
469B ASP* 3.2 5.2 - - - +
470B ALA* 2.7 34.6 + - + +
472B TYR* 3.8 29.6 - - + -
490B ILE* 3.7 0.6 + - + -
491B LEU* 1.3 74.3 - - - +
493B SER* 1.3 61.8 + - - +
494B ARG 4.3 0.2 - - - -
506B ILE* 5.4 5.4 - - + -
507B ALA 3.3 4.7 - - - -
508B LEU* 3.5 22.0 - - + -
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Residues in contact with SER 493 (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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388B SER* 3.5 15.8 + - - -
391B ASN* 3.0 20.9 + - - -
392B VAL* 3.6 23.8 - - - +
468B ASP 3.4 0.4 - - - -
469B ASP* 2.7 25.2 + - - -
491B LEU* 3.9 5.2 - - - +
492B ALA* 1.3 73.9 - - - +
494B ARG* 1.3 60.6 + - - +
495B ARG* 4.2 0.2 - - - -
505B VAL 3.8 0.3 - - - +
506B ILE* 3.7 1.6 - - - -
507B ALA* 2.9 35.8 + - - +
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Residues in contact with ARG 494 (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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440B PHE* 3.7 20.4 - - + -
441B LEU* 4.0 23.4 + - - +
444B SER* 3.0 41.2 + - - -
445B ASP* 5.4 0.6 - - - +
467B GLU* 3.3 23.3 + - - +
468B ASP* 2.7 51.5 + - - +
493B SER* 1.3 74.7 - - - +
495B ARG* 1.3 80.2 + - - +
505B VAL 3.1 9.6 - - - +
506B ILE* 4.4 6.5 - - + -
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Residues in contact with ARG 495 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358A ILE* 4.7 23.8 - - - +
385B VAL 5.1 0.4 + - - -
388B SER* 2.5 39.8 + - - -
389B TYR* 4.1 6.1 - - - +
392B VAL* 3.9 32.3 - - + +
396B LYS* 5.7 4.9 - - - +
440B PHE* 3.7 6.7 - - - -
468B ASP* 4.0 10.1 + - - +
469B ASP* 3.5 17.6 + - - -
493B SER* 4.2 1.8 - - - -
494B ARG* 1.3 93.3 + - - +
496B LYS* 1.3 68.2 + - - +
497B PRO 3.9 0.2 - - - -
503B PRO 4.5 1.0 - - - +
504B TYR* 3.6 4.3 - - - -
505B VAL* 2.9 37.7 + - + +
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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