Contacts of the strand formed by residues 546 - 552 (chain B) in PDB entry 3PE3
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 546 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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539B LEU* 3.7 20.1 - - + +
544B GLY 4.0 1.0 + - - -
545B ARG* 1.3 71.8 - - - +
547B ARG* 1.3 59.5 + - - +
548B VAL* 3.4 10.3 + - + -
575B LYS 2.8 17.0 + - - +
576B PHE* 3.4 30.6 - - + +
577B GLU 3.0 20.0 + - - +
624B HIS* 3.4 33.0 - - + -
625B ILE* 3.9 25.4 - - + -
648B ILE* 6.4 0.9 - - + -
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Residues in contact with ARG 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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541B LEU* 3.9 23.4 + - - +
542B SER* 3.4 26.7 - - - +
546B LEU* 1.3 69.2 - - - +
548B VAL* 1.3 61.1 + - - +
577B GLU* 2.8 39.5 + - + +
579B PHE* 3.5 15.3 - - + -
621B ASP 3.5 24.7 + - - -
622B GLY* 3.5 22.1 + - - +
623B ILE* 3.5 7.5 - - - +
624B HIS* 2.8 45.7 + - + +
625B ILE 3.2 7.4 + - - -
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Residues in contact with VAL 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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546B LEU* 4.0 20.0 - - + +
547B ARG* 1.3 75.2 - - - +
549B GLY* 1.3 57.3 + - - +
550B TYR* 3.8 34.3 + - + +
571B HIS* 5.3 5.4 - - + +
576B PHE* 4.2 20.2 - - + -
577B GLU 3.0 9.2 + - - +
578B VAL* 3.6 8.6 - - + +
579B PHE* 2.8 32.2 + - - +
623B ILE* 4.3 2.5 - - - -
625B ILE* 3.5 20.2 - - + +
627B VAL* 4.3 12.3 - - + -
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Residues in contact with GLY 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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548B VAL* 1.3 73.2 - - - +
550B TYR* 1.3 60.0 + - - -
579B PHE* 3.2 8.1 - - - -
581B TYR* 4.0 17.5 - - - -
623B ILE* 3.6 5.9 - - - +
625B ILE 2.8 13.2 + - - +
626B LEU* 3.6 13.0 - - - +
627B VAL* 2.7 34.3 + - - +
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Residues in contact with TYR 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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548B VAL* 3.8 18.7 - - + +
549B GLY* 1.3 71.4 - - - -
551B VAL* 1.3 57.3 + - - +
555B PHE* 3.8 13.3 - - + -
564B MET* 5.3 3.4 - - + -
567B ILE* 4.3 8.6 - - + +
568B PRO* 5.1 8.5 - - + -
571B HIS* 2.9 37.5 + + - -
578B VAL* 3.9 26.2 - - + -
579B PHE 2.7 11.4 + - - +
580B CYS* 3.6 8.6 - - - -
581B TYR 2.7 32.3 + - - +
627B VAL* 3.8 25.8 - - + -
629B MET* 3.9 11.0 - - - -
652B TRP* 3.6 37.4 - + - -
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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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550B TYR* 1.3 73.7 - - - +
552B SER* 1.3 64.5 + - - +
581B TYR* 3.4 17.7 - - + +
583B LEU* 3.8 33.0 - - + -
618B ILE* 4.8 4.3 - - + -
626B LEU* 3.5 32.8 - - + -
627B VAL 2.9 11.2 + - - +
628B ASN* 4.3 0.5 - - - +
629B MET* 3.2 26.3 + - - +
630B ASN* 4.2 2.6 + - - +
640B LEU* 4.2 7.6 - - + -
641B PHE* 3.8 28.0 - - + -
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Residues in contact with SER 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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551B VAL* 1.3 77.3 - - - +
553B SER* 1.3 54.7 + - - +
554B ASP* 2.8 37.4 + - - +
555B PHE* 3.8 26.4 - - - -
560B THR* 4.2 6.4 - - - +
581B TYR 3.1 7.5 + - - -
582B ALA* 3.3 8.0 - - - +
583B LEU* 2.7 31.4 + - - -
629B MET* 3.9 16.2 - - - +
630B ASN* 3.3 7.9 + - - -
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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