Contacts of the strand formed by residues 552 - 558 (chain B) in PDB entry 3J0A
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 ILE 552 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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529B ARG 3.2 4.6 + - - +
530B GLY* 3.2 36.8 - - - -
531B LEU 3.3 0.6 + - - +
550B LEU* 3.2 13.2 - - - +
551B GLU* 1.3 87.6 - - + +
553B LEU* 1.3 60.9 + - - +
554B ASP* 5.2 4.7 - - + +
571B LEU* 4.1 3.8 - - - -
572B SER* 5.9 0.2 - - - -
573B VAL* 3.7 32.5 - - + +
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Residues in contact with LEU 553 (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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522B PHE* 5.9 1.3 - - + -
531B LEU* 3.2 35.0 - - + +
533B LEU* 4.5 18.4 - - + -
541B LEU* 5.8 0.4 - - + -
543B HIS* 4.5 11.7 - - + +
550B LEU* 4.4 6.1 - - + -
552B ILE* 1.3 78.2 - - - +
554B ASP* 1.3 61.2 + - - +
555B ILE* 3.3 28.6 + - + +
568B PHE* 4.4 24.0 - - + -
571B LEU* 4.1 6.0 - - + +
573B VAL 3.6 7.0 + - - -
574B LEU* 3.5 29.6 - - + +
575B ASP 3.6 9.3 + - - -
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Residues in contact with ASP 554 (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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531B LEU 3.1 6.1 + - - +
532B SER* 4.1 16.2 - - - -
533B LEU* 2.8 31.0 + - - +
534B ASN* 3.2 28.8 - - - +
552B ILE* 4.3 4.6 - - + +
553B LEU* 1.3 71.2 - - - +
555B ILE* 1.3 64.3 + - - +
556B SER* 3.3 8.6 + - - -
575B ASP* 2.8 28.4 - - + +
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Residues in contact with ILE 555 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533B LEU* 3.3 11.9 - - + +
541B LEU* 3.9 28.7 - - + -
543B HIS* 4.7 1.6 - - + -
553B LEU* 3.6 38.6 - - + +
554B ASP* 1.3 80.6 + - - +
556B SER* 1.3 62.3 + - - +
558B ASN* 3.3 17.9 - - - +
560B LEU* 3.5 21.8 - - + -
574B LEU* 4.3 13.2 - - + -
575B ASP 2.7 29.6 + - - +
576B ILE* 3.0 27.7 + - + -
577B THR 3.6 0.2 + - - -
579B ASN* 4.1 1.4 + - - +
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Residues in contact with SER 556 (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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533B LEU 3.7 2.4 + - - -
534B ASN* 3.3 5.7 - - - +
535B SER 3.0 17.3 + - - -
554B ASP* 3.3 14.5 + - - -
555B ILE* 1.3 76.3 - - - +
557B ARG* 1.3 88.4 + - - +
558B ASN* 2.9 16.7 + - - +
575B ASP* 3.7 15.6 + - - -
577B THR* 3.4 18.6 - - - -
578B HIS* 5.4 0.4 - - - -
579B ASN* 3.6 2.7 - - - -
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Residues in contact with ARG 557 (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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534B ASN* 5.3 4.3 + - - +
535B SER* 3.6 28.4 - - - +
536B ASN 3.1 18.2 - - - +
556B SER* 1.3 94.2 + - - +
558B ASN* 1.3 60.3 + - - +
577B THR 3.6 0.2 + - - -
578B HIS* 3.1 39.4 + - + +
579B ASN* 3.2 0.2 + - - -
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Residues in contact with ASN 558 (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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533B LEU 3.5 7.0 + - - +
535B SER 4.1 0.5 + - - -
536B ASN* 3.1 45.0 + - - +
538B LEU* 4.8 7.0 - - - +
555B ILE* 3.3 18.8 - - - +
556B SER* 2.9 34.3 + - - +
557B ARG* 1.3 74.9 - - - +
559B GLN* 1.3 68.3 + - - +
560B LEU* 3.6 20.4 - - + +
578B HIS 3.8 0.4 + - - +
579B ASN* 2.9 13.2 + - - +
580B LYS* 3.2 21.0 + - - +
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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