Contacts of the strand formed by residues 552 - 563 (chain B) in PDB entry 1JQI
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 SER 552 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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548B GLU* 3.5 4.0 - - - +
549B GLU* 2.6 40.2 + - - +
550B GLY 3.2 3.2 + - - -
551B ASP* 1.3 96.3 + - - +
553B TRP* 1.3 67.4 + - - +
623B ARG* 4.6 23.7 - - - +
624B ILE 3.4 15.1 + - - -
625B PRO* 4.6 1.4 - - - +
626B LYS* 4.1 1.8 - - - +
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Residues in contact with TRP 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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546B ALA* 4.4 4.7 - - + -
547B ARG 3.4 8.5 - - - -
548B GLU* 3.7 55.9 - - + -
552B SER* 1.3 76.0 - - - +
554B VAL* 1.3 61.5 + - - +
555B LEU* 4.1 10.1 - - + -
577B THR* 4.4 18.2 - - + -
587B SER* 5.8 0.2 - - - -
589B PHE* 3.5 35.7 - + + -
622B CYS 3.6 0.7 - - - +
623B ARG* 3.3 5.2 - - - +
624B ILE* 2.9 42.3 + - + -
625B PRO 3.7 6.5 - - - -
626B LYS* 3.0 44.1 + - + +
629B LEU* 4.1 28.0 - - + +
633B PRO* 5.1 11.0 - - + -
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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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545B THR 3.6 1.6 - - - +
546B ALA* 3.2 3.6 - - - -
547B ARG* 2.9 62.0 + - + +
549B GLU* 3.2 32.1 - - + -
552B SER 5.1 0.2 - - - -
553B TRP* 1.3 76.6 - - - +
555B LEU* 1.3 63.7 + - - +
556B ASN* 4.1 1.5 + - - +
621B ASP* 3.6 33.0 - - + +
622B CYS 3.3 2.9 - - - +
623B ARG* 3.7 29.2 - - + +
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Residues in contact with LEU 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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544B THR* 5.1 2.9 - - + -
545B THR 3.2 7.6 - - - +
546B ALA* 3.7 20.0 - - + -
553B TRP* 4.1 12.3 - - + -
554B VAL* 1.3 87.1 - - - +
556B ASN* 1.3 61.3 + - - +
573B VAL* 3.7 32.5 - - + -
575B ALA* 4.7 5.2 - - + -
589B PHE* 4.5 6.3 - - + -
591B VAL* 4.0 15.0 - - + -
619B PHE* 3.7 29.2 - - + +
621B ASP 3.2 7.4 + - - -
622B CYS* 2.8 36.6 + - + +
624B ILE* 4.2 13.9 - - + -
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Residues in contact with ASN 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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543B SER 4.4 0.9 - - - +
544B THR* 3.3 5.5 - - - +
545B THR* 2.8 48.8 + - - +
547B ARG* 3.5 19.8 - - - +
554B VAL* 4.1 0.8 - - - +
555B LEU* 1.3 74.5 + - - +
557B GLY* 1.3 58.8 + - - +
619B PHE* 3.3 3.7 - - - +
620B GLU* 3.4 7.8 - - - -
621B ASP* 2.9 50.1 + - - +
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Residues in contact with GLY 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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543B SER 5.3 1.3 - - - -
544B THR* 3.7 13.7 - - - -
556B ASN* 1.3 75.6 - - - +
558B THR* 1.3 64.9 + - - -
559B LYS 4.3 0.2 - - - -
618B ILE* 3.8 1.0 - - - +
619B PHE* 2.8 39.0 + - - +
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Residues in contact with THR 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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532B GLU* 3.5 20.6 - - - +
533B PRO* 3.6 28.9 - - + +
544B THR* 3.5 3.8 + - - -
557B GLY* 1.3 78.4 + - - -
559B LYS* 1.3 76.4 + - - +
616B ASN* 4.0 15.5 - - + +
617B LEU 3.4 7.4 - - - +
618B ILE* 4.2 18.1 - - + +
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Residues in contact with LYS 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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529B ALA* 3.2 36.5 + - + -
530B LEU* 2.9 25.6 + - - +
531B SER 3.3 9.0 - - - +
532B GLU* 3.0 17.1 + - - -
542B ALA* 4.5 1.8 - - - +
544B THR* 3.3 22.2 + - + +
558B THR* 1.3 75.7 - - - +
560B ALA* 1.3 60.5 + - - +
562B ILE* 4.1 5.4 - - + -
573B VAL* 3.9 13.0 - - + -
574B PHE* 2.9 24.9 + - - +
616B ASN* 3.2 7.8 - - - +
617B LEU* 2.9 35.5 + - + +
619B PHE* 3.7 26.2 - - + -
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Residues in contact with ALA 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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531B SER* 2.8 19.1 + - - +
532B GLU* 3.5 5.4 - - - +
533B PRO* 3.4 34.3 - - + -
559B LYS* 1.3 74.4 - - - +
561B TRP* 1.3 88.3 + - + +
562B ILE* 3.3 12.3 - - - +
616B ASN* 3.3 15.3 - - - +
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Residues in contact with TRP 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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273A ARG* 6.1 0.2 - - - +
345A GLY* 3.5 33.0 - - - -
346A MET* 3.3 38.6 - - + -
349A VAL* 3.6 28.9 - - + -
531B SER* 4.2 6.7 - - - -
532B GLU 4.6 6.3 + - - -
533B PRO* 5.2 4.2 + - - +
560B ALA* 1.3 95.2 - - + +
562B ILE* 1.3 54.4 + - - +
604B GLU* 4.2 17.7 - - + -
614B THR* 3.7 22.2 - - + -
615B ALA* 4.0 2.6 + - - +
616B ASN* 3.5 10.9 - - - +
799B FAD 2.5 96.6 + + + +
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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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527B CYS* 3.9 31.4 - - + -
528B PHE 3.7 17.0 - - - +
529B ALA* 3.5 27.8 - - + -
530B LEU 4.4 0.4 - - - +
559B LYS* 4.1 11.4 - - + -
560B ALA 3.3 20.6 - - - +
561B TRP* 1.3 71.1 - - - +
563B THR* 1.3 60.2 + - - +
565B SER* 2.9 34.8 + - - -
614B THR* 3.4 2.7 - - - -
615B ALA 2.9 28.3 + - - +
617B LEU* 3.8 22.4 - - + -
799B FAD 3.8 7.0 - - + +
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Residues in contact with THR 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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490B VAL* 4.5 13.5 - - + +
494B VAL* 4.0 19.9 - - + +
527B CYS* 3.2 20.3 - - - +
528B PHE 4.8 0.2 + - - -
561B TRP 3.4 0.6 + - - -
562B ILE* 1.3 66.9 - - - +
564B ASN* 1.3 81.3 + - - +
565B SER 3.1 4.7 - - - -
609B ILE* 5.8 1.5 - - + +
612B SER* 4.5 14.2 + - - +
613B SER 3.1 12.3 + - - +
614B THR* 4.6 1.7 + - - +
767B TYR* 5.0 1.7 - - - -
799B FAD 3.0 44.3 + - - +
800B CAA 3.8 10.0 - - - +
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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