Contacts of the strand formed by residues 614 - 625 (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 THR 614 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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561B TRP* 3.7 37.9 - - + -
562B ILE 3.4 4.5 - - - +
563B THR* 4.6 1.4 + - - +
603B LYS* 3.6 2.5 - - - +
604B GLU* 2.8 47.4 + - + +
606B LYS* 3.1 29.1 - - + +
612B SER* 4.0 2.0 + - - -
613B SER* 1.3 79.1 + - - +
615B ALA* 1.3 63.2 - - - +
799B FAD 3.8 26.3 - - + +
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Residues in contact with ALA 615 (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 TRP 4.3 0.7 - - - +
562B ILE* 2.9 35.9 + - - +
565B SER* 3.6 13.8 + - - +
566B TRP* 3.7 11.2 - - + +
600B LEU* 5.5 0.4 - - + -
601B GLY 3.3 24.5 - - - +
602B LYS 3.5 11.2 - - - +
604B GLU* 4.6 4.7 - - - -
614B THR* 1.3 79.4 - - - +
616B ASN* 1.3 71.8 + - - +
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Residues in contact with ASN 616 (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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533B PRO* 4.4 7.1 - - - +
558B THR* 4.0 17.2 - - + +
559B LYS 3.2 12.3 - - - +
560B ALA* 3.3 25.9 - - - +
561B TRP* 3.5 6.3 - - - +
600B LEU* 3.6 3.8 - - - -
601B GLY* 2.8 35.0 + - - +
602B LYS 5.0 0.6 + - - -
604B GLU* 4.8 10.7 + - - +
615B ALA* 1.3 79.1 - - - +
617B LEU* 1.3 63.8 + - - +
618B ILE* 4.6 6.1 - - + -
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Residues in contact with LEU 617 (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* 4.6 0.2 - - - -
529B ALA* 4.2 8.5 - - + -
557B GLY 4.0 0.2 - - - +
558B THR* 3.4 4.7 - - - -
559B LYS* 2.9 35.6 + - + +
562B ILE* 3.8 25.8 - - + -
565B SER* 4.1 10.8 - - - -
571B THR* 4.1 27.6 - - + +
593B MET* 3.8 18.6 - - + -
598B LEU* 4.1 7.6 - - + -
599B THR 3.8 1.6 - - - -
600B LEU* 3.3 33.0 - - + -
616B ASN* 1.3 76.2 - - - +
618B ILE* 1.3 60.7 + - - +
619B PHE* 4.0 20.5 + - + -
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Residues in contact with ILE 618 (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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557B GLY 3.8 2.9 - - - +
558B THR* 4.2 22.2 - - + +
597B GLY 3.3 1.7 - - - +
598B LEU* 3.3 7.6 - - - +
599B THR* 2.8 51.2 + - - +
600B LEU 5.1 1.3 - - - +
601B GLY* 4.9 13.9 - - - -
616B ASN* 4.6 8.3 - - + +
617B LEU* 1.3 78.2 - - - +
619B PHE* 1.3 62.1 + - - +
620B GLU* 3.9 27.3 + - + +
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Residues in contact with PHE 619 (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* 4.7 6.3 - - + -
555B LEU* 3.7 32.5 - - + +
556B ASN* 3.3 5.0 - - - +
557B GLY* 2.8 48.0 + - - +
559B LYS* 3.7 27.4 - - + -
571B THR* 4.7 6.3 - - + -
573B VAL* 4.1 22.4 - - + -
591B VAL* 4.2 17.3 - - + -
597B GLY 3.4 1.8 - - - -
598B LEU* 3.8 25.1 - - + -
617B LEU* 4.0 22.0 - - + -
618B ILE* 1.3 74.3 - - - +
620B GLU* 1.3 64.3 + - - +
622B CYS* 3.7 21.3 - - + -
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Residues in contact with GLU 620 (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 ASN* 3.4 5.6 - - - +
597B GLY* 2.9 24.6 + - - +
599B THR* 4.9 8.6 + - - +
618B ILE* 3.9 21.0 - - + +
619B PHE* 1.3 76.3 - - - +
621B ASP* 1.3 75.3 - - - +
622B CYS 3.2 0.8 + - - -
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Residues in contact with ASP 621 (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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547B ARG* 3.3 19.9 + - - -
554B VAL* 3.6 13.6 - - + +
555B LEU 3.2 5.6 + - - -
556B ASN* 2.9 33.1 + - - +
596B PRO 4.9 0.5 - - - +
597B GLY* 4.6 2.4 - - - -
620B GLU* 1.3 75.8 - - - +
622B CYS* 1.3 62.9 + - - +
623B ARG* 3.5 17.2 + - - +
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Residues in contact with CYS 622 (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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553B TRP 3.6 1.6 - - - +
554B VAL* 3.3 2.3 - - - -
555B LEU* 2.8 37.4 + - + +
591B VAL* 4.3 7.9 - - - -
595B THR* 3.8 21.3 - - - -
596B PRO 3.6 20.4 - - - +
597B GLY 3.6 17.7 - - - +
619B PHE* 3.7 29.8 - - + -
620B GLU 3.2 1.5 - - - -
621B ASP* 1.3 75.1 - - - +
623B ARG* 1.3 62.6 + - - +
624B ILE* 4.0 9.3 + - - +
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Residues in contact with ARG 623 (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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547B ARG* 5.3 3.6 - - - +
549B GLU* 3.3 29.5 + - - +
552B SER* 4.6 18.9 - - - +
553B TRP 3.3 3.1 - - - +
554B VAL* 3.7 29.2 - - + +
595B THR* 4.8 6.6 + - - -
596B PRO 4.4 4.6 + - - +
621B ASP* 3.5 18.1 + - - +
622B CYS* 1.3 75.8 - - - +
624B ILE* 1.3 65.4 - - - +
625B PRO* 4.7 0.9 - - - +
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Residues in contact with ILE 624 (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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552B SER* 3.4 6.5 - - - -
553B TRP* 2.9 37.5 + - + +
555B LEU* 4.2 11.9 - - + -
589B PHE* 3.7 41.1 - - + -
590B LEU 4.0 3.1 - - - +
591B VAL* 4.1 32.3 - - + -
592B PRO* 4.4 6.3 - - + -
595B THR* 5.6 1.1 - - - +
622B CYS* 4.4 8.7 - - - +
623B ARG* 1.3 80.6 - - - +
625B PRO* 1.3 78.8 - - + +
628B ASN* 4.0 21.8 - - + +
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Residues in contact with PRO 625 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551B ASP 3.9 6.7 - - - +
552B SER* 4.6 2.2 - - - +
553B TRP* 3.7 4.3 - - - -
592B PRO* 6.0 2.0 - - + -
623B ARG 4.7 1.1 - - - +
624B ILE* 1.3 90.9 - - + +
626B LYS* 1.3 65.7 + - - +
627B GLU* 3.2 20.0 - - + +
628B ASN* 3.1 37.7 + - - +
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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