Contacts of the strand formed by residues 562 - 567 (chain B) in PDB entry 1JZ3
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 562 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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350B LEU* 4.5 0.2 - - - +
520B ILE* 3.8 41.5 - - + +
521B LYS* 4.1 7.2 - - + -
524B LEU* 3.6 22.2 - - + +
533B LEU* 3.8 16.2 - - + -
555B ALA* 3.5 34.8 - - + +
556B PHE* 3.4 20.2 - - + +
559B TYR* 3.0 27.5 + - + +
561B ARG* 1.4 73.4 - - - +
563B GLN* 1.3 57.6 + - - +
564B GLY 3.4 3.7 + - - -
3102B NA 2.3 29.4 - - - -
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Residues in contact with GLN 563 (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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341B LEU* 3.5 12.7 - - - +
342B LEU* 2.8 53.6 + - - +
348B PRO* 3.7 8.0 - - + +
349B LEU* 2.9 31.1 + - - +
350B LEU* 3.8 7.6 - - - -
351B ILE* 2.9 28.9 + - + +
532B PRO* 3.4 16.8 - - - +
533B LEU 3.0 10.1 + - - +
534B ILE* 3.8 18.6 - - + -
560B PRO 3.4 17.7 - - - +
561B ARG 3.3 4.0 + - - +
562B LEU* 1.3 70.4 - - - +
564B GLY* 1.3 58.0 + - - +
3102B NA 4.4 1.3 - - - -
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Residues in contact with GLY 564 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350B LEU* 3.9 4.7 - - - +
351B ILE 3.4 11.4 - - - -
533B LEU* 4.2 1.2 + - - +
534B ILE* 3.4 7.2 - - - -
535B LEU* 3.1 18.5 + - - +
556B PHE* 3.7 39.2 - - - -
562B LEU 3.4 5.3 + - - -
563B GLN* 1.3 79.4 - - - +
565B GLY* 1.3 58.9 + - - -
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Residues in contact with GLY 565 (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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351B ILE* 3.2 8.5 + - - +
353B GLY* 2.9 27.7 + - - +
534B ILE* 3.8 6.0 - - - +
535B LEU* 3.2 15.9 - - - -
538B TYR* 3.4 20.8 + - - -
556B PHE* 4.3 2.0 - - - -
564B GLY* 1.3 75.5 - - - -
566B PHE* 1.3 63.5 + - - -
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Residues in contact with PHE 566 (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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351B ILE* 3.7 22.7 - - + -
353B GLY* 3.4 4.7 - - - -
354B VAL 3.6 15.3 - - - -
355B ASN* 3.2 24.7 + - - +
386B ALA* 3.8 18.4 - - + -
387B VAL 3.5 22.2 - - - -
388B ARG* 3.5 23.1 - - + -
408B TYR 5.5 0.7 - - - -
410B VAL* 3.6 26.0 - - + -
455B ILE* 5.7 3.8 - - + -
485B GLN* 5.4 6.7 - - - -
534B ILE* 4.0 13.0 - - + -
535B LEU 3.0 17.1 + - - -
536B CYS* 3.3 12.3 - - - +
537B GLU* 3.2 16.5 - - - -
538B TYR* 3.2 4.2 + - - -
565B GLY* 1.3 74.3 - - - -
567B VAL* 1.3 66.6 + - - +
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Residues in contact with VAL 567 (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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353B GLY 3.0 16.3 + - - +
354B VAL* 3.5 7.3 - - + +
355B ASN* 2.9 31.4 + - - -
384B PHE* 4.5 9.2 - - + -
538B TYR* 3.1 20.2 - - + +
539B ALA* 3.6 16.4 - - + +
541B ALA* 4.6 2.5 - - + -
546B LEU* 4.7 1.3 - - + -
549B PHE* 3.7 33.7 - - + -
566B PHE* 1.3 70.8 - - - +
568B TRP* 1.4 69.3 + - - +
569B ASP* 3.5 6.5 - - - +
606B LEU* 4.1 25.4 - - + -
620B ALA* 5.7 0.7 - - + -
624B GLN* 4.6 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