Contacts of the strand formed by residues 552 - 564 (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 GLN 552 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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541B VAL* 3.4 5.0 - - - -
542B ALA 2.8 36.4 + - - +
544B PRO* 3.5 24.4 - - + +
550B ARG 3.9 5.2 - - - +
551B PRO* 1.3 75.4 - - - +
553B GLU* 1.3 65.7 + - - +
554B VAL* 3.7 5.4 + - + +
614B TYR* 3.4 37.7 - - + -
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Residues in contact with GLU 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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539B THR* 3.7 27.2 - - + +
540B VAL 3.4 6.1 - - - +
541B VAL* 4.5 15.0 - - + +
552B GLN* 1.3 77.1 - - - +
554B VAL* 1.3 62.0 + - - +
555B SER* 4.3 1.2 + - - +
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Residues in contact with VAL 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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538B THR 3.5 1.6 - - - +
539B THR* 3.3 1.3 - - - -
540B VAL* 2.8 50.3 + - + +
542B ALA* 4.2 11.2 - - + -
552B GLN* 3.9 14.8 - - + +
553B GLU* 1.3 80.1 - - - +
555B SER* 1.3 64.4 + - - +
556B TYR* 4.5 10.8 - - + -
575B LEU* 4.0 19.3 - - + -
614B TYR* 3.8 48.2 - - + +
631B VAL* 5.9 2.5 - - + -
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Residues in contact with SER 555 (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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537B VAL* 4.0 5.6 - - - +
538B THR 3.1 4.5 - - - -
539B THR* 2.5 31.5 + - - +
553B GLU* 4.3 1.1 + - - +
554B VAL* 1.3 75.1 + - - +
556B TYR* 1.3 63.2 + - - +
575B LEU* 3.7 6.6 - - - +
576B CYS* 2.9 42.2 + - - +
577B ASP* 5.9 1.3 - - - -
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Residues in contact with TYR 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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526B MET* 4.4 5.2 - - - -
536B LYS 4.1 0.2 - - - +
537B VAL* 3.6 0.3 - - - -
538B THR* 3.0 66.9 + - + +
540B VAL* 4.2 17.1 - - + +
554B VAL* 4.5 12.8 - - + -
555B SER* 1.3 77.8 - - - +
557B THR* 1.3 67.8 + - - +
559B THR* 3.6 25.6 - - + -
573B ALA* 3.9 13.7 - - + -
574B LYS 3.0 19.1 - - - +
575B LEU* 4.4 8.1 - - + -
576B CYS* 3.7 2.0 - - - -
582B VAL* 6.2 0.4 - - + -
584B ILE* 3.9 23.2 - - + +
616B PHE* 3.9 20.2 - + - -
631B VAL* 6.2 0.7 - - + -
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Residues in contact with THR 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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535B SER* 4.4 11.8 + - - +
536B LYS 3.2 24.2 - - - +
537B VAL* 3.4 22.4 - - + -
556B TYR* 1.3 79.9 - - - +
558B ASP* 1.3 80.8 + - - +
559B THR* 3.3 5.0 + - - -
573B ALA* 3.6 3.3 - - - +
574B LYS* 2.8 43.4 + - - +
576B CYS* 3.5 12.1 - - - -
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Residues in contact with ASP 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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535B SER* 5.1 4.6 + - - -
536B LYS 4.7 1.8 + - - -
557B THR* 1.3 88.0 + - - +
559B THR* 1.3 61.7 + - - +
560B LYS* 3.4 17.2 + - + +
572B GLN* 3.2 11.6 - - - +
573B ALA* 4.0 2.3 - - - -
574B LYS* 3.0 40.6 + - + -
581B LEU* 6.1 1.0 - - + +
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Residues in contact with THR 559 (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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556B TYR* 3.6 31.5 - - + -
557B THR 4.2 0.9 - - - -
558B ASP* 1.3 73.1 - - - +
560B LYS* 1.3 61.6 + - - +
571B TYR* 3.5 38.6 - - + -
572B GLN 3.2 5.8 - - - -
573B ALA* 3.9 5.0 - - + +
584B ILE* 6.1 0.9 - - + -
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Residues in contact with LYS 560 (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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558B ASP* 3.9 16.6 - - + +
559B THR* 1.3 75.1 - - - +
561B VAL* 1.3 65.4 + - - +
562B ILE* 3.4 6.1 + - + +
571B TYR* 4.2 3.4 - - - -
572B GLN* 2.7 72.7 + - + +
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Residues in contact with VAL 561 (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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560B LYS* 1.3 75.3 - - - +
562B ILE* 1.3 63.6 + - - +
563B GLY 3.0 30.3 - - - +
564B ASN* 4.6 5.2 - - + +
569B VAL* 3.5 12.8 - - + -
570B VAL 3.6 4.3 - - - -
571B TYR* 3.8 26.4 - - + +
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Residues in contact with ILE 562 (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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560B LYS* 3.5 7.9 - - + +
561B VAL* 1.3 78.1 - - - +
563B GLY* 1.3 57.8 + - - +
570B VAL* 2.8 25.0 + - + +
571B TYR 3.9 16.2 - - - +
572B GLN* 3.3 27.1 - - + -
583B ALA* 4.2 2.0 - - + -
634B TYR* 3.9 17.3 - - + +
930B ADP 3.4 54.6 + - + +
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Residues in contact with GLY 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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561B VAL* 3.0 24.3 - - - +
562B ILE* 1.3 81.3 - - - +
564B ASN* 1.3 63.4 + - - +
569B VAL* 3.4 9.5 - - - +
570B VAL* 3.2 12.4 + - - -
930B ADP 4.0 16.4 - - - -
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Residues in contact with ASN 564 (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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561B VAL* 4.6 4.7 - - + +
563B GLY* 1.3 76.2 - - - +
565B GLY* 1.3 72.1 + - - +
568B GLY 3.0 22.1 + - - -
569B VAL* 3.4 21.8 - - - +
570B VAL* 4.5 1.5 - - - +
930B ADP 4.0 14.9 + - - +
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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