Contacts of the strand formed by residues 541 - 548 (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 LEU 541 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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431B VAL* 3.8 19.5 - - + -
432B VAL 3.4 8.3 - - - +
433B HIS* 3.6 45.3 - - + +
434B VAL 3.4 1.6 + - - -
435B ASP* 4.8 0.4 - - - +
436B ALA 5.0 1.2 + - - -
536B ARG* 3.9 2.4 - - - +
537B GLU* 3.0 37.5 + - + +
538B GLY* 3.4 17.1 + - - +
539B ASP 3.2 8.6 - - - +
540B GLN* 1.3 77.8 - - - +
542B THR* 1.3 64.1 + - - +
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Residues in contact with THR 542 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431B VAL* 3.3 4.4 - - - -
432B VAL 2.8 38.5 + - - -
434B VAL* 2.7 26.5 + - - -
435B ASP 3.4 0.5 - - - -
436B ALA* 2.9 28.5 + - + +
439B ALA* 4.7 2.2 - - + -
534B LEU* 3.8 21.1 - - + -
535B TRP 3.4 9.9 - - - +
537B GLU* 4.1 2.9 - - - -
541B LEU* 1.3 74.4 + - - +
543B LYS* 1.3 78.0 + - - +
544B VAL* 3.7 13.3 + - + +
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Residues in contact with LYS 543 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483A THR* 4.5 16.0 + - - +
414B ARG* 5.6 2.4 - - - +
429B GLU* 3.0 41.6 + - + -
430B MET 3.4 11.9 - - - +
431B VAL* 4.4 7.9 - - + +
533B CYS 3.6 1.6 - - - +
534B LEU* 3.1 7.6 - - - -
535B TRP* 2.9 56.4 + - + +
537B GLU* 3.5 34.2 - - + +
542B THR* 1.3 70.0 - - - +
544B VAL* 1.3 61.1 + - - +
545B SER* 4.4 6.3 - - - +
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Residues in contact with VAL 544 (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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429B GLU* 3.5 2.1 - - - -
430B MET* 2.9 54.9 + - + +
432B VAL* 3.9 22.7 - - + -
434B VAL* 5.3 0.2 - - + -
439B ALA* 5.0 1.3 - - + -
443B LEU* 4.3 13.2 - - + -
532B PHE* 4.5 8.1 - - + -
533B CYS 3.8 2.2 - - - -
534B LEU* 3.6 24.5 - - + -
542B THR* 3.9 13.5 - - + +
543B LYS* 1.3 75.8 - - - +
545B SER* 1.3 64.0 + - - +
573B PHE* 3.5 11.2 - - + -
576B CYS* 5.0 1.3 - - - -
580B LEU* 4.1 12.6 - - + -
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Residues in contact with SER 545 (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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427B HIS* 4.2 1.8 - - - -
428B MET 3.1 8.5 - - - -
429B GLU* 3.5 26.3 - - - +
531B GLY 3.8 0.2 - - - +
532B PHE* 3.1 10.8 - - - +
533B CYS 3.0 36.2 + - - +
535B TRP* 3.6 17.8 - - - -
543B LYS* 4.1 2.5 - - - -
544B VAL* 1.3 75.2 + - - +
546B TYR* 1.3 60.3 + - - +
547B TYR* 3.6 23.9 + - - -
573B PHE* 4.3 1.6 - - - -
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Residues in contact with TYR 546 (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 2.9 61.3 - - - +
426B PHE* 4.0 14.6 - + - -
427B HIS* 3.0 5.9 - - - +
428B MET* 2.9 33.2 + - + +
449B ARG* 3.7 26.6 + - - -
531B GLY* 3.3 20.6 - - - -
532B PHE* 3.8 22.9 - + + -
545B SER* 1.3 73.9 - - - +
547B TYR* 1.3 76.9 + - - +
548B ASN* 3.1 22.9 + - + -
573B PHE* 3.7 23.1 - - + -
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Residues in contact with TYR 547 (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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483A THR* 4.4 6.1 - - - +
395B LEU* 3.7 26.7 - - + -
398B LEU* 3.8 13.7 - - + -
399B VAL* 3.6 44.3 + - + +
404B TRP* 3.7 22.9 - + - -
426B PHE 3.6 2.5 - - - -
427B HIS* 3.3 43.7 + + + -
429B GLU* 4.8 0.7 + - - -
530B SER* 3.2 5.0 - - - -
531B GLY 2.7 38.1 + - - +
533B CYS* 4.5 7.6 - - + -
535B TRP* 4.2 7.0 - + - -
545B SER* 3.6 25.1 + - - -
546B TYR* 1.3 83.7 - - - +
548B ASN* 1.3 62.2 + - - +
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Residues in contact with ASN 548 (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 3.7 16.4 + - - -
398B LEU* 4.8 1.1 - - - -
424B LEU 4.5 0.5 - - - +
425B SER* 3.4 1.5 - - - -
426B PHE* 2.9 64.8 + - + -
529B CYS 3.9 0.2 - - - -
530B SER* 3.2 14.5 + - - -
546B TYR* 3.1 19.9 + - - +
547B TYR* 1.3 74.0 - - - +
549B GLN* 1.3 61.5 + - - +
550B ALA* 3.5 10.0 + - - -
551B THR* 2.7 35.4 + - - +
554B VAL* 5.9 1.0 - - - +
558B VAL* 6.2 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