Contacts of the strand formed by residues 530 - 546 (chain B) in PDB entry 1DQA
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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537A PRO* 5.1 2.0 - - + -
538A VAL 3.5 13.0 - - - +
482B GLU* 5.0 2.4 + - - +
492B VAL* 3.7 15.1 - - + +
495B ARG* 3.0 30.7 + - - +
519B TYR* 3.6 33.9 - - + -
522B VAL* 4.2 10.5 - - + -
523B MET* 6.3 0.7 - - + -
527B CYS* 3.9 42.6 - - + +
528B GLU* 4.0 2.0 - - - +
529B ASN* 1.3 75.1 - - - +
531B ILE* 1.3 62.9 + - - +
532B GLY 3.6 9.6 - - - +
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Residues in contact with ILE 531 (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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538A VAL* 2.9 30.1 + - + +
539A GLY 4.5 2.2 - - - +
540A VAL* 3.9 31.6 - - + -
554A PRO* 4.9 0.7 - - + -
820A MET* 3.7 20.0 - - + -
492B VAL* 3.6 10.5 - - - -
495B ARG* 4.0 15.5 - - + -
496B ARG* 2.9 42.5 + - + +
499B LEU* 4.0 24.2 - - + -
509B LEU* 4.4 1.6 - - + -
512B LEU* 3.6 23.6 - - + +
529B ASN 4.0 0.2 - - - +
530B VAL* 1.3 78.4 - - - +
532B GLY* 1.3 57.8 + - - +
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Residues in contact with GLY 532 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537A PRO* 3.8 1.9 - - - +
538A VAL* 3.0 24.6 + - - +
492B VAL* 3.9 0.4 - - - +
512B LEU* 4.7 2.7 - - - -
513B PRO 3.3 13.0 - - - -
514B TYR* 3.7 2.5 - - - -
519B TYR* 3.5 19.6 + - - -
530B VAL* 3.6 12.8 - - - +
531B ILE* 1.3 81.7 - - - +
533B TYR* 1.3 63.1 + - - +
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Residues in contact with TYR 533 (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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533A TYR* 4.5 18.9 + + - -
535A PRO* 3.6 29.8 - - + -
536A ILE 3.2 17.7 - - - +
537A PRO* 4.3 2.7 - - + -
538A VAL* 3.8 6.0 - - - +
512B LEU* 3.6 5.5 - - - +
513B PRO* 3.1 49.6 + - + +
514B TYR* 3.8 23.7 + - - -
515B ARG 3.6 15.6 + - - -
516B ASP 5.3 0.9 + - - -
517B TYR* 3.8 25.6 - + + -
519B TYR* 3.7 13.9 - - - +
532B GLY* 1.3 74.8 - - - +
534B MET* 1.3 59.6 + - - +
535B PRO* 4.1 11.7 - - + -
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Residues in contact with MET 534 (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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534A MET 3.1 5.0 - - - +
535A PRO* 4.2 1.3 - - - -
536A ILE* 2.7 39.7 + - + +
538A VAL* 3.6 12.7 - - + +
556A ALA* 4.4 7.6 - - + -
762A ILE* 3.5 21.3 - - + +
763A ALA* 3.2 23.6 - - - +
813A PRO* 3.6 27.6 - - - +
814A GLN* 3.3 33.2 - - - +
817A CYS* 3.6 14.1 - - - -
512B LEU* 3.8 10.5 - - + -
533B TYR* 1.3 72.9 - - - +
535B PRO* 1.3 63.6 - - - +
536B ILE* 3.5 12.9 + - + -
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Residues in contact with PRO 535 (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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517A TYR* 3.6 35.5 + - + -
533A TYR* 3.7 22.7 - - + -
534A MET 3.6 5.6 - - - +
535A PRO* 4.4 1.3 - - + -
813A PRO* 3.8 22.2 - - + -
814A GLN* 3.7 12.6 + - - +
513B PRO* 3.7 20.4 - - + -
533B TYR* 3.6 16.8 - - + +
534B MET* 1.3 82.2 - - - +
536B ILE* 1.3 66.5 + - - +
537B PRO* 4.1 3.7 - - - +
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Residues in contact with ILE 536 (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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533A TYR* 4.1 2.2 - - - -
534A MET* 2.7 43.6 + - + +
536A ILE* 4.0 14.4 - - + -
762A ILE* 4.0 16.8 - - + +
814A GLN* 4.0 10.3 - - - +
534B MET* 3.8 23.1 - - + +
535B PRO* 1.3 80.9 - - - +
537B PRO* 1.3 73.1 - - + +
538B VAL* 3.4 2.3 + - - +
556B ALA* 3.7 16.4 - - + +
557B THR* 3.5 30.7 - - - +
558B THR* 4.6 6.1 - - + -
762B ILE* 4.2 13.0 - - + -
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Residues in contact with PRO 537 (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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517A TYR* 4.0 11.4 - - + +
519A TYR* 6.1 1.1 - - + -
522A VAL* 3.9 31.6 - - + -
526A CYS* 5.0 1.1 - - + -
527A CYS* 3.8 18.1 - - + -
530A VAL* 5.1 4.3 - - + -
532A GLY 3.8 7.6 - - - +
533A TYR* 4.3 3.5 - - + -
811A LEU* 4.3 6.5 - - + -
535B PRO 4.1 4.7 - - - +
536B ILE* 1.3 83.1 - - + +
538B VAL* 1.3 60.7 + - - +
555B MET 3.7 0.5 - - - +
556B ALA* 3.1 4.3 - - - -
557B THR 3.0 49.0 + - - +
558B THR* 3.8 12.1 - - + -
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Residues in contact with VAL 538 (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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512A LEU* 4.6 4.7 - - + -
527A CYS* 4.1 2.7 - - - -
530A VAL* 3.3 6.4 - - - +
531A ILE* 2.8 49.6 + - + -
532A GLY 2.9 14.9 + - - +
533A TYR 3.9 3.1 - - - -
534A MET* 3.6 32.8 - - + +
536B ILE 3.6 14.8 - - - +
537B PRO* 1.3 74.4 - - - +
539B GLY* 1.3 65.5 + - - +
554B PRO* 4.3 9.4 - - + -
555B MET 3.3 13.7 - - - +
556B ALA* 4.0 8.3 - - + -
763B ALA* 5.0 1.8 - - + -
817B CYS* 4.6 6.5 - - - -
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Residues in contact with GLY 539 (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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527A CYS* 3.7 7.6 - - - -
528A GLU 3.5 14.8 - - - -
529A ASN 3.2 12.8 - - - -
531A ILE* 4.4 2.0 - - - +
538B VAL* 1.3 78.2 - - - +
540B VAL* 1.3 59.9 + - - -
554B PRO* 3.6 4.3 - - - +
555B MET* 2.8 34.4 + - - -
563B VAL* 4.2 7.2 - - - -
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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
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495A ARG* 4.6 4.3 - - + -
499A LEU* 4.4 15.0 - - + -
529A ASN* 2.9 55.7 + - - +
531A ILE* 3.9 25.6 - - + -
539B GLY* 1.3 75.0 - - - +
541B ALA* 1.3 62.9 + - - +
552B GLN* 3.9 36.1 - - + +
553B VAL 3.4 13.2 - - - +
555B MET* 4.4 0.2 - - - -
563B VAL* 3.6 7.9 - - - +
567B ASN* 4.3 0.7 - - - +
820B MET* 5.1 2.5 - - - -
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Residues in contact with ALA 541 (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* 1.3 76.4 - - - +
542B GLY* 1.3 58.4 + - - +
552B GLN 3.9 0.3 - - - -
553B VAL* 2.9 40.8 + - + +
555B MET* 3.2 28.0 - - + +
563B VAL 4.2 0.9 - - - +
566B THR* 3.8 21.1 - - + +
567B ASN* 3.6 18.6 - - - +
570B CYS* 4.5 4.5 - - - -
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Residues in contact with GLY 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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541B ALA* 1.3 77.1 - - - +
543B PRO* 1.3 77.6 - - - +
544B LEU 3.7 1.8 - - - -
551B PHE 4.0 0.2 - - - -
552B GLN* 3.7 11.8 - - - +
567B ASN* 3.0 19.3 + - - +
570B CYS* 4.1 11.3 - - - -
571B ARG 6.1 0.2 - - - -
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Residues in contact with PRO 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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502A LYS* 6.1 2.5 - - + +
542B GLY* 1.3 82.6 - - - +
544B LEU* 1.3 61.0 + - - +
545B CYS* 3.7 12.0 + - - -
550B GLU* 4.0 36.3 - - + +
551B PHE 3.3 6.5 - - - +
552B GLN* 3.6 21.5 - - - +
570B CYS* 3.6 17.0 - - - +
571B ARG* 5.6 0.2 - - - -
574B GLY* 5.5 0.2 - - - -
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Residues in contact with LEU 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 GLY* 3.7 0.8 - - - -
543B PRO* 1.3 71.6 - - - +
545B CYS* 1.3 65.1 + - - +
546B LEU* 3.3 29.8 + - + -
549B LYS 3.6 0.2 - - - +
550B GLU* 3.4 2.6 - - - -
551B PHE* 2.8 40.4 + - + +
553B VAL* 4.3 11.0 - - + -
570B CYS* 4.1 25.1 - - + +
573B ILE* 4.4 18.2 - - + -
579B ALA* 5.4 2.7 - - + -
841B ILE* 3.9 13.9 - - + +
844B GLY* 4.0 17.7 - - - +
845B THR* 3.4 29.4 - - - +
848B ALA* 4.8 0.2 - - + -
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Residues in contact with CYS 545 (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 PRO* 3.7 13.6 + - - -
544B LEU* 1.3 72.4 - - - +
546B LEU* 1.3 54.2 + - - +
548B GLU* 5.3 1.3 - - - -
549B LYS 3.4 8.7 - - - +
550B GLU* 4.0 27.8 - - + -
570B CYS 5.5 0.6 + - - -
573B ILE* 3.9 5.5 - - - +
574B GLY* 4.0 23.6 - - - +
578B GLY* 3.5 17.6 - - - +
579B ALA* 2.7 34.8 + - - +
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Residues in contact with LEU 546 (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 LEU* 3.3 17.2 + - + -
545B CYS* 1.3 73.8 - - - +
547B ASP* 1.3 92.0 + - - +
548B GLU 3.2 1.3 - - - -
549B LYS* 2.9 27.5 + - - +
551B PHE* 3.9 22.8 - - + -
579B ALA* 3.5 23.1 - - + +
580B SER 4.4 0.2 - - - -
581B SER* 3.8 17.3 - - - +
708B CYS* 5.0 0.7 - - + -
837B GLN* 4.5 1.8 - - - +
840B ARG* 3.5 33.4 - - + +
841B ILE* 3.9 11.2 - - + +
844B GLY* 4.8 9.2 - - - -
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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