Contacts of the strand formed by residues 504 - 512 (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 TYR 504 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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436B ALA* 3.6 27.8 - - + -
437B ALA* 3.7 15.0 - - - +
440B PHE* 3.3 42.0 - + + -
495B ARG 3.6 4.7 - - - -
496B LYS* 3.1 39.7 + - + -
497B PRO* 3.5 30.0 - - + +
502B ASP 5.4 0.4 - - - -
503B PRO* 1.3 73.8 - - + +
505B VAL* 1.3 59.8 + - - +
532B PHE 3.9 0.2 - - - +
533B CYS* 3.2 6.2 - - - -
534B LEU* 2.8 49.1 + - + +
536B ARG* 3.6 22.5 + - + -
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Residues in contact with VAL 505 (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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392B VAL* 4.1 24.9 - - + +
395B LEU* 3.9 27.6 - - + -
396B LYS* 4.0 28.3 - - + -
440B PHE* 3.7 0.5 - - - -
493B SER 3.8 0.2 - - - +
494B ARG* 3.1 4.9 - - - +
495B ARG* 2.9 37.6 + - + +
503B PRO* 3.7 21.1 - - + +
504B TYR* 1.3 79.2 - - - +
506B ILE* 1.3 67.7 + - - +
507B ALA* 4.0 8.5 - - + +
532B PHE 3.5 2.7 - - - +
533B CYS* 4.3 5.8 - - - -
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Residues in contact with ILE 506 (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 LEU* 3.4 2.3 - - - +
440B PHE* 3.7 26.2 - - + +
443B LEU* 3.6 22.4 - - + +
444B SER* 3.6 43.1 - - - +
446B LEU* 5.9 2.0 - - + -
492B ALA* 5.4 3.8 - - + -
493B SER 3.7 4.0 - - - +
494B ARG* 4.3 5.6 - - + +
505B VAL* 1.3 77.7 - - - +
507B ALA* 1.3 59.5 + - - +
508B LEU* 4.4 15.1 - - + +
531B GLY* 3.2 7.6 - - - -
532B PHE* 2.8 53.2 + - + +
534B LEU* 4.4 7.9 - - + -
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Residues in contact with ALA 507 (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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391B ASN* 3.1 42.9 + - - +
392B VAL* 3.8 8.5 - - - -
395B LEU* 3.7 15.0 - - + -
492B ALA* 3.3 4.2 - - - -
493B SER 2.9 38.3 + - - +
505B VAL* 4.3 2.5 - - + -
506B ILE* 1.3 73.6 - - - +
508B LEU* 1.3 60.5 + - - +
530B SER 3.6 4.0 - - - +
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Residues in contact with LEU 508 (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 3.5 25.8 - - - +
391B ASN* 3.5 3.6 - - - +
446B LEU* 3.6 20.0 - - + -
449B ARG* 3.9 14.6 - - - +
456B TYR* 3.9 6.7 - - - +
490B ILE* 3.8 12.3 - - + -
491B LEU 3.4 3.1 - - - -
492B ALA* 3.5 30.5 - - + -
506B ILE* 4.4 9.6 - - + +
507B ALA* 1.3 75.3 - - - +
509B ARG* 1.3 63.4 + - - +
527B THR* 4.4 5.4 - - + +
529B CYS* 3.5 2.6 + - - -
530B SER* 2.7 43.6 + - - +
531B GLY* 4.1 18.6 - - - +
532B PHE* 5.3 2.7 - - + -
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Residues in contact with ARG 509 (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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375B LEU 2.6 30.5 + - - -
376B SER* 3.9 2.4 - - - +
377B VAL* 3.5 34.7 - - - +
387B LEU* 5.5 3.5 + - - +
390B ASN* 4.9 13.5 + - - -
391B ASN* 3.4 31.9 - - + +
394B SER* 5.9 0.2 + - - -
490B ILE* 4.1 2.6 - - - +
491B LEU* 2.8 37.0 + - + +
508B LEU* 1.3 75.0 - - - +
510B SER* 1.3 86.5 + - - +
511B VAL* 4.0 7.0 - - - -
527B THR* 3.8 10.3 - - - -
528B LEU* 3.4 36.3 + - - +
529B CYS* 4.8 0.9 - - + -
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Residues in contact with SER 510 (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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376B SER* 3.9 18.2 - - - -
377B VAL 3.1 9.7 + - - -
488B PHE* 4.5 3.5 - - - +
489B VAL 3.3 13.2 + - - -
490B ILE* 4.3 4.5 - - - +
509B ARG* 1.3 92.6 + - - +
511B VAL* 1.3 63.4 + - - +
525B GLY 4.3 3.3 + - - -
526B GLU* 3.4 11.6 - - - -
527B THR* 2.9 44.9 + - - +
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Residues in contact with VAL 511 (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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376B SER* 4.5 1.2 - - - -
377B VAL* 3.1 18.2 - - + +
379B TRP* 4.0 25.6 - - + +
387B LEU* 5.7 1.1 - - + -
471B ILE* 4.1 17.7 - - + -
489B VAL* 3.0 41.3 + - + +
491B LEU* 3.7 33.9 - - + +
509B ARG* 3.7 11.2 + - - -
510B SER* 1.3 80.1 - - - +
512B THR* 1.3 64.2 + - - +
513B LEU* 5.0 1.1 - - + -
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Residues in contact with THR 512 (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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376B SER* 3.0 26.9 + - - +
377B VAL 3.0 5.9 + - - -
378B PRO* 3.3 23.4 - - - +
379B TRP* 3.0 27.5 + - - +
489B VAL* 5.6 0.4 - - - -
511B VAL* 1.3 75.3 - - - +
513B LEU* 1.3 62.3 + - - +
514B PRO* 4.6 1.7 - - - +
517B ARG* 6.5 0.7 - - - -
524B ARG* 6.2 2.7 - - - +
526B GLU* 5.4 1.1 - - - +
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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