Contacts of the strand formed by residues 544 - 552 (chain B) in PDB entry 3RFU
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 LYS 544 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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445B ASP* 5.3 7.7 + - - -
446B PHE* 6.1 2.2 - - - -
516B GLY* 3.8 1.0 - - - -
517B GLY* 3.8 9.2 - - - +
518B ASP 6.0 0.7 - - - +
540B ALA* 3.1 15.1 - - - +
541B VAL* 3.2 16.1 + - - +
542B ASP* 3.1 12.7 - - - +
543B GLY* 1.3 80.2 - - - +
545B THR* 1.3 68.0 + - - +
546B VAL* 3.1 29.3 + - + +
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Residues in contact with THR 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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512B MET* 3.8 28.8 - - - +
517B GLY 2.9 29.5 + - - +
518B ASP 5.3 0.7 + - - +
519B ASN* 3.1 29.2 + - + +
522B LEU* 3.8 25.1 - - + -
523B PHE* 4.2 9.2 - - + -
538B PHE* 4.8 11.0 - - + -
539B MET 4.2 5.8 - - - +
540B ALA* 3.4 9.4 - - - +
544B LYS* 1.3 72.5 - - - +
546B VAL* 1.3 62.2 + - - +
547B ALA 4.7 1.6 - - - +
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Residues in contact with VAL 546 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443B THR* 3.6 13.2 + - - -
444B ASP* 3.7 9.7 - - - +
446B PHE* 3.9 32.3 - - + +
519B ASN* 4.8 0.2 - - - +
522B LEU* 3.7 11.2 - - - +
539B MET* 2.9 27.0 + - + +
540B ALA* 3.8 0.4 - - - -
541B VAL* 3.5 48.2 - - + +
544B LYS* 3.1 29.1 + - + +
545B THR* 1.3 75.0 - - - +
547B ALA* 1.3 65.8 + - - +
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Residues in contact with ALA 547 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441B ILE* 4.4 6.7 - - + -
442B VAL 3.5 12.3 - - - +
443B THR* 4.2 4.7 - - - +
446B PHE* 4.6 0.7 - - + -
451B ALA* 3.7 15.5 - - + -
522B LEU* 3.8 8.9 - - - +
538B PHE* 3.9 2.8 - - - +
539B MET* 3.0 56.3 + - + +
545B THR* 4.8 1.0 - - - +
546B VAL* 1.3 80.9 - - - +
548B LEU* 1.3 62.3 + - - +
549B LEU* 5.1 0.2 - - + -
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Residues in contact with LEU 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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441B ILE* 3.1 9.9 - - - +
442B VAL* 3.0 58.6 + - + -
522B LEU* 3.2 33.6 - - + +
525B LYS* 4.4 6.3 - - + +
526B ALA* 3.9 16.8 - - + +
529B LEU* 5.4 1.6 - - + -
536B VAL* 3.8 17.9 - - + -
537B MET 3.6 12.6 - - - +
538B PHE* 3.3 35.7 - - + -
547B ALA* 1.3 76.8 - - - +
549B LEU* 1.3 65.6 + - - +
550B VAL* 4.1 1.1 - - + -
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Residues in contact with LEU 549 (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 LEU* 4.4 7.9 - - + -
440B ARG 4.0 0.9 - - - -
441B ILE* 3.5 35.0 - - + -
452B LEU* 5.3 2.7 - - + -
455B ALA* 3.6 30.3 - - + -
470B ILE* 4.3 22.9 - - + -
506B ILE* 3.8 23.1 - - + -
535B SER 3.8 1.6 - - - +
536B VAL* 3.7 1.7 - - - -
537B MET* 3.0 42.2 + - + +
539B MET* 4.8 14.4 - - + -
548B LEU* 1.3 84.6 - - - +
550B VAL* 1.3 62.9 + - - +
551B VAL* 4.1 3.4 + - + +
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Residues in contact with VAL 550 (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 LEU* 3.1 18.1 - - - +
439B THR* 3.2 14.8 + - - +
440B ARG* 3.0 46.4 + - + +
442B VAL* 4.8 7.6 - - + -
529B LEU* 3.6 32.1 - - + -
534B ALA* 4.7 10.5 - - + -
535B SER 3.7 4.5 - - - +
536B VAL* 3.9 17.3 - - + -
549B LEU* 1.3 77.1 - - - +
551B VAL* 1.3 64.3 + - - +
552B GLU* 5.6 1.3 - - - -
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Residues in contact with VAL 551 (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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281B ILE* 6.2 2.0 - - + -
436B PRO* 5.0 5.2 - - + -
437B LYS 3.3 13.7 - - - +
438B LEU* 4.0 18.2 - - + +
466B LEU* 3.5 43.7 - - + -
469B ALA* 4.8 2.5 - - + -
470B ILE* 4.4 6.1 - - + -
534B ALA* 3.4 4.3 - - - +
535B SER* 3.0 54.6 + - - +
537B MET* 6.1 2.9 - - + -
549B LEU* 5.0 3.6 - - + +
550B VAL* 1.3 78.9 - - - +
552B GLU* 1.3 70.4 + - - +
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Residues in contact with GLU 552 (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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436B PRO* 3.4 6.3 - - - +
437B LYS 2.8 28.7 + - - +
439B THR* 3.1 33.9 + - + +
532B LYS* 4.6 14.7 + - - +
534B ALA* 3.3 27.5 + - + +
535B SER* 5.0 0.9 - - - +
550B VAL* 5.6 1.8 - - - -
551B VAL* 1.3 81.9 - - - +
553B ASP* 1.3 62.1 + - - +
554B PRO* 3.0 18.0 - - + +
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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