Contacts of the strand formed by residues 530 - 546 (chain A) in PDB entry 1DQ8
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 VAL 530 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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492A VAL* 3.8 14.7 - - + +
495A ARG* 2.9 34.9 + - - +
519A TYR* 3.6 24.2 - - + -
522A VAL* 4.2 2.9 - - + -
523A MET* 3.7 33.2 - - + +
527A CYS* 3.7 27.8 - - + +
528A GLU 4.0 1.1 - - - +
529A ASN* 1.3 70.9 - - - +
531A ILE* 1.3 61.7 + - - +
532A GLY 3.6 17.5 - - - +
537B PRO* 5.0 3.6 - - + -
538B VAL 3.4 15.9 - - - +
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Residues in contact with ILE 531 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492A VAL* 3.9 7.0 - - - -
495A ARG* 4.1 13.7 - - + -
496A ARG* 2.9 43.7 + - + +
499A LEU* 3.9 19.1 - - + -
509A LEU* 4.3 6.1 - - + -
512A LEU* 3.1 7.5 - - + +
529A ASN 3.9 8.7 - - - +
530A VAL* 1.3 77.3 - - - +
532A GLY* 1.3 57.1 + - - +
538B VAL* 2.9 38.6 + - + +
539B GLY 4.5 3.1 - - - +
540B VAL* 3.9 22.9 - - + -
554B PRO* 4.9 0.2 - - + -
820B MET* 4.0 33.0 - - + -
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Residues in contact with GLY 532 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492A VAL* 4.1 1.0 - - - +
512A LEU* 3.8 2.2 - - - -
513A PRO 3.4 12.1 - - - -
514A TYR* 3.7 3.6 - - - -
519A TYR* 3.6 19.4 + - - -
530A VAL* 3.6 13.0 - - - +
531A ILE* 1.3 82.0 - - - +
533A TYR* 1.3 63.4 + - - +
537B PRO* 3.8 1.7 - - - +
538B VAL* 3.0 23.9 + - - -
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Residues in contact with TYR 533 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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512A LEU* 3.6 6.0 - - - +
513A PRO* 3.0 45.9 + - + +
514A TYR* 3.6 25.4 - - - -
515A ARG 3.7 14.7 + - - -
516A ASP 5.2 1.8 + - - -
517A TYR* 4.0 23.6 - + + -
519A TYR* 3.8 13.7 - - - +
532A GLY* 1.3 74.1 - - - +
534A MET* 1.3 60.8 + - - +
535A PRO* 3.5 22.7 - - + +
533B TYR* 4.4 22.8 + + - -
535B PRO* 3.8 22.7 - - + -
536B ILE 3.3 18.6 - - - +
537B PRO* 4.4 2.2 - - + -
538B VAL* 3.8 6.0 - - - +
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Residues in contact with MET 534 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
512A LEU* 3.9 9.6 - - + -
533A TYR* 1.3 72.2 - - - +
535A PRO* 1.3 62.0 - - - +
536A ILE* 3.5 14.6 + - + +
534B MET 3.2 5.0 - - - +
535B PRO* 4.4 0.9 - - - -
536B ILE* 2.8 36.0 + - + +
538B VAL* 3.5 12.5 - - + +
556B ALA* 4.6 7.0 - - + -
762B ILE* 3.6 21.1 - - + +
763B ALA* 3.1 23.8 - - - +
813B PRO* 3.6 22.2 - - - +
814B GLN* 3.4 32.5 - - - +
817B CYS* 3.6 20.9 - - - -
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Residues in contact with PRO 535 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513A PRO* 4.0 11.9 - - + -
533A TYR* 3.5 26.9 - - + +
534A MET* 1.3 82.9 - - - +
536A ILE* 1.3 61.5 + - - +
537A PRO* 3.9 5.4 - - - +
517B TYR* 3.7 29.7 + - + -
533B TYR* 3.6 26.2 - - + -
534B MET 3.7 5.6 - - - +
535B PRO* 4.5 0.9 - - + -
813B PRO* 3.7 21.5 - - + -
814B GLN* 3.7 19.1 + - - +
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Residues in contact with ILE 536 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534A MET* 3.9 22.9 - - + +
535A PRO* 1.3 78.9 - - - +
537A PRO* 1.3 72.7 - - + +
538A VAL* 3.4 2.4 + - - +
556A ALA* 3.7 17.0 - - + +
557A THR* 3.6 28.7 - - - +
558A THR* 4.8 5.4 - - + -
762A ILE* 4.4 10.8 - - + -
533B TYR* 3.3 2.2 - - - -
534B MET 2.7 43.5 + - - +
536B ILE* 4.1 13.7 - - + -
762B ILE* 4.0 19.1 - - + +
814B GLN* 4.0 10.3 - - - +
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Residues in contact with PRO 537 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535A PRO 3.9 6.7 - - - +
536A ILE* 1.3 82.8 - - + +
538A VAL* 1.3 59.2 + - - +
555A MET 3.8 0.2 - - - +
556A ALA* 3.2 4.0 - - - -
557A THR 2.9 47.3 + - - +
558A THR* 3.9 12.8 - - + -
517B TYR* 4.0 10.3 - - + +
519B TYR* 6.1 0.4 - - + -
522B VAL* 3.8 31.2 - - + -
526B CYS* 5.1 1.8 - - + -
527B CYS* 3.7 19.6 - - + -
530B VAL* 5.2 3.1 - - + -
532B GLY 3.8 8.3 - - - +
533B TYR* 4.3 2.9 - - + -
811B LEU* 4.3 7.0 - - + -
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Residues in contact with VAL 538 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536A ILE 3.5 14.8 - - - +
537A PRO* 1.3 74.0 - - - +
539A GLY* 1.3 70.6 + - - +
554A PRO* 4.2 9.9 - - + -
555A MET 3.3 14.1 - - - +
556A ALA* 4.2 7.2 - - + -
763A ALA* 4.8 0.9 - - + -
817A CYS* 4.4 8.1 - - - -
512B LEU* 4.5 7.4 - - + -
527B CYS* 3.9 2.7 - - - -
530B VAL* 3.5 3.1 - - - -
531B ILE* 2.8 44.4 + - + +
532B GLY 3.0 14.7 + - - +
533B TYR 3.8 4.5 - - - +
534B MET* 3.5 29.6 - - + +
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Residues in contact with GLY 539 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538A VAL* 1.3 76.9 - - - +
540A VAL* 1.3 61.2 + - - -
554A PRO* 3.4 4.0 - - - +
555A MET 2.7 36.7 + - - -
563A VAL* 4.1 7.0 - - - -
527B CYS* 3.5 7.4 - - - -
528B GLU 3.4 14.6 - - - -
529B ASN 3.1 12.6 - - - -
531B ILE* 4.6 1.1 - - - -
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Residues in contact with VAL 540 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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539A GLY* 1.3 75.3 - - - +
541A ALA* 1.3 63.0 + - - +
542A GLY 4.1 0.8 + - - +
552A GLN* 3.9 40.8 - - + +
553A VAL 3.4 11.7 - - - +
554A PRO 4.5 0.7 - - - -
563A VAL* 3.6 8.3 - - - +
820A MET* 4.7 4.0 - - - -
495B ARG* 5.0 5.8 - - + -
499B LEU* 4.5 11.0 - - + -
529B ASN* 3.0 51.1 + - + +
531B ILE* 3.9 25.1 - - + -
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Residues in contact with ALA 541 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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540A VAL* 1.3 74.8 - - - +
542A GLY* 1.3 58.3 + - - +
553A VAL* 2.9 40.7 + - + +
555A MET* 3.2 26.9 - - + +
566A THR* 4.1 11.2 - - + +
567A ASN* 3.5 28.9 - - + +
570A CYS* 4.4 6.3 - - - -
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Residues in contact with GLY 542 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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540A VAL 4.1 1.0 + - - -
541A ALA* 1.3 74.4 - - - +
543A PRO* 1.3 76.0 - - - +
544A LEU 3.7 1.6 - - - -
551A PHE 3.9 1.1 - - - -
552A GLN* 3.8 15.4 + - - +
567A ASN* 2.8 21.5 + - - +
570A CYS* 4.5 6.0 - - - -
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Residues in contact with PRO 543 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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542A GLY* 1.3 80.7 - - - +
544A LEU* 1.3 60.9 + - - +
545A CYS* 3.7 12.4 + - - -
550A GLU* 3.6 34.5 - - + +
551A PHE 3.3 5.8 - - - +
552A GLN* 3.5 20.2 - - - +
570A CYS* 3.7 17.8 - - - +
571A ARG* 5.6 0.4 - - - -
574A GLY* 5.5 0.3 - - - -
502B LYS* 5.7 6.3 - - - +
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Residues in contact with LEU 544 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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542A GLY* 3.7 0.8 - - - -
543A PRO* 1.3 71.4 - - - +
545A CYS* 1.3 65.7 + - - +
546A LEU* 3.3 27.0 + - + -
550A GLU* 3.3 3.2 - - - -
551A PHE* 2.8 42.9 + - + +
553A VAL* 4.2 12.6 - - + -
570A CYS* 4.1 23.8 - - + -
573A ILE* 4.5 16.6 - - + -
579A ALA* 5.5 2.0 - - + -
841A ILE* 4.0 12.8 - - + +
844A GLY* 4.1 20.2 - - - +
845A THR* 3.5 32.1 - - - +
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Residues in contact with CYS 545 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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543A PRO* 3.7 14.5 + - - -
544A LEU* 1.3 73.9 - - - +
546A LEU* 1.3 54.2 + - - +
547A ASP 4.3 0.2 - - - -
548A GLU* 5.3 1.6 - - - -
549A LYS 3.4 8.1 - - - +
550A GLU* 4.2 25.1 - - + -
573A ILE* 4.0 6.1 - - + +
574A GLY* 4.0 25.3 - - - -
578A GLY* 3.5 17.9 - - - +
579A ALA* 2.8 36.0 + - - +
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Residues in contact with LEU 546 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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544A LEU* 3.3 15.3 + - + -
545A CYS* 1.3 73.6 - - - +
547A ASP* 1.3 93.0 + - - +
548A GLU 3.2 1.6 - - - -
549A LYS* 3.0 26.3 + - - +
551A PHE* 3.9 24.1 - - + -
579A ALA* 3.4 13.2 - - + +
581A SER* 3.7 17.0 - - - +
708A CYS* 4.0 17.3 - - - -
837A GLN* 4.6 2.5 - - - +
840A ARG* 3.5 33.7 - - + +
841A ILE* 3.8 11.0 - - + -
844A GLY* 4.7 3.4 - - - -
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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