Contacts of the strand formed by residues 571 - 576 (chain B) in PDB entry 1JSC
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 571 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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489B ARG* 5.3 3.1 - - - +
543B LEU* 3.8 33.9 - - + -
544B VAL 2.9 15.0 + - - +
545B ILE* 3.4 8.6 - - + +
546B ASP 2.9 26.2 + - - -
569B PRO* 3.3 16.9 + - - +
570B VAL* 1.3 69.9 - - - +
572B ILE* 1.3 63.4 + - - +
573B LEU 3.6 0.7 + - - -
632B PHE* 3.3 34.6 - - + +
633B VAL* 4.0 7.9 - - - -
635B THR 2.6 30.0 + - - -
636B LYS* 4.6 0.2 - - - +
637B GLY 2.9 22.0 + - - +
639B VAL* 3.4 21.5 - - + +
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Residues in contact with ILE 572 (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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529B LEU* 3.5 29.2 - - + -
532B ALA* 5.1 0.4 - - + -
546B ASP* 3.7 26.2 - - + +
553B PHE* 3.6 30.1 - - + -
560B LEU* 4.5 10.1 - - + -
570B VAL* 3.5 26.0 - - + +
571B LYS* 1.3 73.2 - - - +
573B LEU* 1.3 60.3 + - - +
574B ILE* 4.3 9.9 - - + -
614B LEU* 4.9 3.4 - - + -
632B PHE* 3.5 3.2 - - - -
639B VAL 2.8 17.2 + - - +
640B LEU* 3.3 11.8 - - + +
641B LEU 2.8 28.2 + - - +
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Residues in contact with LEU 573 (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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476B VAL* 4.2 12.1 - - + -
477B ILE* 5.5 2.5 - - + -
480B LEU* 3.9 22.7 - - + -
545B ILE* 4.7 3.1 - - + -
546B ASP 2.8 16.5 + - - +
547B ILE* 4.2 22.0 - - + -
548B ASP* 2.8 32.2 + - - +
571B LYS 3.6 1.4 + - - -
572B ILE* 1.3 72.7 - - - +
574B ILE* 1.3 62.3 + - - +
575B LEU* 4.1 21.1 - - + -
629B LEU* 5.2 0.9 - - + -
632B PHE* 4.0 14.1 - - + -
641B LEU* 3.5 27.6 - - + +
643B VAL* 3.8 24.5 - - + -
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Residues in contact with ILE 574 (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 ASP* 3.6 4.7 - - + -
549B GLY 4.4 0.2 - - - -
550B ASP* 4.1 25.1 - - - +
553B PHE* 3.3 50.5 - - + -
572B ILE* 4.3 6.3 - - + -
573B LEU* 1.3 78.1 - - - +
575B LEU* 1.3 59.5 + - - +
576B ASN* 3.1 14.8 + - + +
605B PHE* 3.9 26.9 - - + -
640B LEU* 3.7 21.1 - - + -
641B LEU 2.9 12.9 + - - +
642B GLU* 3.5 5.5 - - + -
643B VAL 3.0 26.7 + - - -
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Residues in contact with LEU 575 (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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473B PRO* 4.5 13.5 - - + -
476B VAL* 3.8 33.7 - - + -
477B ILE* 4.5 15.9 - - + -
500B HIS* 3.9 27.1 - - + -
503B TRP* 4.9 2.7 - - + -
547B ILE* 4.1 16.2 - - + -
548B ASP 3.0 15.0 + - - +
549B GLY* 4.2 3.8 - - - -
550B ASP* 3.8 13.3 + - - +
573B LEU* 4.1 13.7 - - + -
574B ILE* 1.3 70.1 - - - +
576B ASN* 1.3 62.2 + - - +
577B ASN* 3.4 8.0 + - - +
643B VAL* 3.9 8.7 - - + -
645B VAL* 4.3 23.1 - - + -
1700B TPP 5.2 1.8 + - - +
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Residues in contact with ASN 576 (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 ASP* 3.3 20.7 - - + -
574B ILE* 3.1 10.5 + - + -
575B LEU* 1.3 69.7 - - - +
577B ASN* 1.3 57.5 + - - +
578B GLU* 2.7 57.5 + - - +
602B ASN* 3.8 3.4 - - - +
605B PHE* 4.0 5.4 - - + -
642B GLU* 2.9 35.6 + - + +
643B VAL 3.2 5.7 + - - +
644B GLU* 3.8 8.7 - - - +
645B VAL 3.0 26.1 + - - +
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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