Contacts of the strand formed by residues 504 - 512 (chain A) 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 TYR 504 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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436A ALA* 3.6 29.2 - - + -
437A ALA* 3.5 14.6 - - + +
440A PHE* 3.3 49.1 - + + -
495A ARG 3.4 5.6 - - - -
496A LYS* 4.0 16.5 - - + +
497A PRO* 3.7 26.1 - - + +
502A ASP 5.4 0.7 - - - -
503A PRO* 1.3 73.1 - - + +
505A VAL* 1.3 60.1 + - - +
532A PHE 3.9 0.5 - - - +
533A CYS* 3.3 5.7 - - - -
534A LEU* 2.7 54.1 + - + +
536A ARG* 2.5 40.6 + - + -
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Residues in contact with VAL 505 (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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392A VAL* 4.2 26.0 - - + +
395A LEU* 3.8 27.1 - - + -
396A LYS* 4.3 25.4 - - + -
440A PHE* 3.8 0.9 - - - -
493A SER 3.6 0.5 - - - +
494A ARG* 3.2 3.8 - - - -
495A ARG* 2.8 45.3 + - + +
503A PRO* 3.8 23.8 - - + +
504A TYR* 1.3 77.7 - - - +
506A ILE* 1.3 67.1 + - - +
507A ALA* 3.9 8.7 - - + +
532A PHE 3.6 2.5 - - - +
533A CYS* 4.3 5.8 - - - -
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Residues in contact with ILE 506 (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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395A LEU* 3.4 2.2 - - - +
440A PHE* 3.6 28.9 - - + +
443A LEU* 3.6 21.1 - - + +
444A SER* 3.4 43.5 - - - +
446A LEU* 6.4 1.1 - - + -
492A ALA* 5.2 5.6 - - + -
493A SER 3.6 5.2 - - - +
494A ARG* 4.3 3.1 - - + -
504A TYR 5.4 0.2 - - - -
505A VAL* 1.3 76.8 - - - +
507A ALA* 1.3 59.1 + - - +
508A LEU* 4.5 15.7 - - + +
531A GLY* 3.2 6.9 - - - -
532A PHE* 2.9 50.2 + - + +
534A LEU* 4.2 11.2 - - + -
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Residues in contact with ALA 507 (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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391A ASN* 3.1 44.1 + - - +
392A VAL* 3.7 11.7 - - + +
395A LEU* 3.7 12.3 - - + -
492A ALA* 3.2 5.2 - - - -
493A SER 2.8 41.5 + - - +
505A VAL* 3.9 1.5 - - + -
506A ILE* 1.3 74.0 - - - +
508A LEU* 1.3 62.5 + - - +
530A SER 3.7 4.0 - - - +
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Residues in contact with LEU 508 (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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2A 1PE 3.6 30.7 - - - +
391A ASN* 3.4 4.0 - - - +
446A LEU* 4.2 12.3 - - + -
449A ARG* 3.8 12.1 - - - +
456A TYR* 4.2 4.3 - - - +
490A ILE* 3.8 15.9 - - + -
491A LEU 3.3 2.5 - - - -
492A ALA* 3.3 32.8 - - + -
506A ILE* 4.5 11.2 - - + +
507A ALA* 1.3 77.6 - - - +
509A ARG* 1.3 63.1 + - - +
527A THR* 4.4 4.7 - - + +
529A CYS* 3.6 3.1 + - - -
530A SER* 2.7 43.7 + - - +
531A GLY* 4.1 17.0 - - - +
532A PHE* 5.4 4.3 - - + -
546A TYR* 5.1 0.2 - - + -
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Residues in contact with ARG 509 (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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374A PRO* 2.9 29.7 + - - +
375A LEU 3.1 21.8 + - - -
376A SER* 3.6 2.2 - - - +
377A VAL* 3.5 30.9 - - - +
387A LEU* 5.5 2.9 - - - -
391A ASN* 3.3 32.6 - - + +
490A ILE* 3.6 3.9 - - - +
491A LEU* 2.9 37.4 + - + +
508A LEU* 1.3 77.7 - - - +
510A SER* 1.3 100.0 + - - +
511A VAL* 3.9 6.7 - - - -
527A THR* 3.6 9.4 - - - -
528A LEU* 3.5 28.0 + - - +
529A CYS* 4.8 0.4 - - - -
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Residues in contact with SER 510 (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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375A LEU 3.4 11.0 - - - -
376A SER* 3.9 10.1 - - - -
377A VAL 3.2 9.7 + - - -
488A PHE* 4.5 2.6 - - - +
489A VAL 3.2 12.5 + - - -
490A ILE* 4.3 5.0 - - - +
509A ARG* 1.3 96.8 + - - +
511A VAL* 1.3 61.6 + - - +
525A GLY 4.4 2.5 + - - -
526A GLU* 3.3 11.4 - - - -
527A THR* 2.8 42.9 + - - +
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Residues in contact with VAL 511 (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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376A SER* 4.8 0.5 - - - -
377A VAL* 3.1 18.4 - - + +
379A TRP* 4.5 19.1 - - + +
387A LEU* 5.8 0.7 - - + -
471A ILE* 4.1 18.6 - - + -
489A VAL* 2.9 48.1 + - + +
491A LEU* 3.8 38.6 - - + +
509A ARG* 3.9 11.4 - - - -
510A SER* 1.3 81.9 - - - +
512A THR* 1.3 67.2 + - - +
513A LEU* 5.0 1.1 - - + -
524A ARG* 5.2 1.0 + - - -
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Residues in contact with THR 512 (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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376A SER* 3.5 25.1 - - - +
377A VAL 3.0 5.4 + - - -
378A PRO* 3.4 22.5 - - - +
379A TRP* 2.9 28.8 + - - +
489A VAL* 5.0 0.7 - - - -
511A VAL* 1.3 79.7 - - - +
513A LEU* 1.3 62.3 + - - +
524A ARG* 5.4 9.6 - - - +
526A GLU* 5.9 1.6 - - - +
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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