Contacts of the strand formed by residues 536 - 544 (chain B) in PDB entry 1J1C
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 536 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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528B VAL* 3.3 40.0 - - + +
529B SER 3.2 7.0 - - - +
530B ARG* 4.4 3.1 - - + +
534B GLY 3.1 8.0 + - - +
535B SER* 1.3 71.6 + - - +
537B VAL* 1.3 62.3 + - - +
538B THR* 3.9 13.7 - - - +
556B TYR 4.1 0.3 - - - +
557B THR* 3.2 25.5 - - - +
558B ASP 4.7 1.2 + - - -
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Residues in contact with VAL 537 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527B LYS 3.5 2.3 - - - +
528B VAL* 3.3 3.3 - - - +
529B SER* 2.8 46.0 + - - +
531B ASP* 3.2 46.4 - - + +
535B SER* 3.9 1.8 - - - +
536B LYS* 1.3 75.4 - - - +
538B THR* 1.3 63.8 + - - +
539B THR* 4.1 7.6 - - - +
555B SER* 4.0 15.0 - - - -
556B TYR 3.6 2.7 - - - -
557B THR* 3.4 19.7 - - + -
576B CYS* 3.7 21.3 - - - -
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Residues in contact with THR 538 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526B MET* 4.0 30.9 - - + +
527B LYS 3.6 3.4 - - - +
528B VAL* 4.4 5.5 - - + +
536B LYS* 3.9 21.2 + - - +
537B VAL* 1.3 73.6 - - - +
539B THR* 1.3 63.4 + - - +
540B VAL* 4.0 6.3 - - + -
554B VAL 3.5 2.1 - - - +
555B SER* 3.1 4.0 - - - -
556B TYR* 3.0 72.1 + - + +
559B THR* 5.5 0.3 + - - -
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Residues in contact with THR 539 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526B MET* 3.5 1.2 - - - -
527B LYS* 2.8 55.0 + - + +
529B SER* 5.6 0.9 + - - -
537B VAL* 4.1 6.9 - - - +
538B THR* 1.3 73.2 - - - +
540B VAL* 1.3 68.7 + - - +
541B VAL* 6.0 0.4 - - + -
553B GLU* 3.7 33.2 - - + +
554B VAL 3.3 4.0 - - - +
555B SER* 2.5 24.7 + - - +
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Residues in contact with VAL 540 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525B SER 4.6 7.6 - - - +
526B MET* 3.7 27.6 - - + -
538B THR* 4.0 11.7 - - + -
539B THR* 1.3 80.0 - - - +
541B VAL* 1.3 66.7 + - - +
542B ALA* 4.6 0.7 - - + +
553B GLU* 3.4 5.4 - - - +
554B VAL* 2.8 54.5 + - + +
556B TYR* 4.2 6.5 - - + +
616B PHE* 4.0 44.9 - - + -
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Residues in contact with VAL 541 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525B SER 4.8 6.1 + - - +
539B THR* 6.0 0.4 - - + -
540B VAL* 1.3 77.9 - - - +
542B ALA* 1.3 59.3 + - - +
551B PRO* 3.6 29.8 - - + -
552B GLN 3.4 7.4 - - - +
553B GLU* 4.5 16.8 - - + +
616B PHE* 3.8 12.5 - - - +
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Residues in contact with ALA 542 (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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540B VAL* 3.9 1.9 - - + -
541B VAL* 1.3 74.5 - - - +
543B THR* 1.3 63.3 - - - +
551B PRO* 3.4 5.2 - - - +
552B GLN* 2.8 37.9 + - - +
554B VAL* 4.2 11.9 - - + -
614B TYR* 3.7 28.7 - - + -
615B PHE 3.5 13.2 - - - +
616B PHE* 4.0 16.4 - - + -
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Residues in contact with THR 543 (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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542B ALA* 1.3 72.5 - - - +
544B PRO* 1.3 83.4 - - + +
549B ASP* 3.5 33.3 + - - +
551B PRO* 4.8 4.0 - - - +
602B ARG* 4.6 7.2 - - - +
614B TYR* 2.8 20.5 - - - +
615B PHE* 2.9 44.1 + - + -
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Residues in contact with PRO 544 (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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542B ALA 3.8 3.1 - - - +
543B THR* 1.3 102.3 - - + +
545B GLY* 1.3 65.8 + - - +
546B GLN 4.7 0.2 - - - +
547B GLY* 4.2 20.5 - - - +
548B PRO 3.6 17.0 - - - +
550B ARG* 3.1 37.2 - - + +
552B GLN* 3.5 21.7 - - - +
602B ARG* 4.6 2.8 + - - -
613B ARG 3.8 5.8 - - - +
614B TYR* 3.9 2.9 - - + -
615B PHE* 3.9 3.8 - - - -
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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
------------------------------------------------------------
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