Contacts of the strand formed by residues 559 - 578 (chain B) in PDB entry 4QDQ
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 ASP 559 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401B PRO 5.7 1.4 - - - +
403B LEU* 4.6 1.3 - - - -
501B VAL 4.0 0.2 - - - +
502B ILE* 3.4 5.4 - - - -
503B ILE* 2.9 37.7 + - + +
551B GLY 3.7 7.8 - - - +
552B ASN* 2.9 30.4 + - - +
553B MET* 4.4 13.9 + - - +
557B THR* 3.8 6.2 - - - +
558B PRO* 1.3 79.8 - - - +
560B ILE* 1.3 61.0 + - - +
561B ARG* 3.5 36.6 + - - +
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Residues in contact with ILE 560 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338B MET* 4.1 28.7 - - + -
403B LEU* 4.0 13.2 - - + +
429B VAL* 4.0 12.3 - - + -
501B VAL 3.5 3.4 - - - -
502B ILE* 4.1 4.3 - - + -
559B ASP* 1.3 73.5 - - - +
561B ARG* 1.3 79.2 + - - +
562B ARG* 3.2 47.9 + - + +
590B LEU* 3.3 31.0 - - + -
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Residues in contact with ARG 561 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500B GLY* 3.2 2.1 - - - -
501B VAL* 2.8 49.0 + - + +
503B ILE* 5.2 1.3 - - + -
524B PHE* 4.0 13.5 - - + -
549B PHE* 3.9 24.2 - - + -
550B GLU* 2.7 47.0 + - - +
551B GLY 3.1 23.8 + - - -
553B MET* 6.3 0.6 - - - +
559B ASP* 3.5 31.0 + - - +
560B ILE* 1.3 81.8 + - - +
562B ARG* 1.3 63.4 + - - +
563B PHE* 4.0 2.7 - - - -
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Residues in contact with ARG 562 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338B MET* 6.1 2.8 - - - +
428B ARG 5.3 0.6 + - - -
429B VAL* 3.1 26.3 + - - +
432B ALA* 3.5 18.7 - - - +
433B PRO 5.3 0.6 + - - -
435B SER* 2.7 28.7 + - - -
499B LYS* 3.4 20.6 + - + +
500B GLY* 3.9 2.0 - - - -
549B PHE* 4.3 7.8 - - - -
560B ILE* 3.2 36.9 + - + +
561B ARG* 1.3 78.3 - - - +
563B PHE* 1.3 65.2 + - - +
590B LEU* 4.7 2.8 - - + +
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Residues in contact with PHE 563 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498B VAL* 3.7 34.3 - - + -
499B LYS* 3.0 23.2 + - - +
500B GLY* 3.6 30.1 - - - -
501B VAL* 4.2 12.1 - - + -
526B VAL* 4.7 8.7 - - + -
538B ILE* 3.6 43.1 - - + -
547B LYS* 6.2 0.4 - - + -
549B PHE* 3.8 24.5 - + + -
561B ARG 4.0 3.6 - - - -
562B ARG* 1.3 79.5 - - - +
564B ASP* 1.3 84.8 + - - +
565B PRO* 3.4 2.4 - - - +
566B ILE* 4.0 7.0 - - + -
571B VAL* 6.0 0.2 - - + -
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Residues in contact with ASP 564 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538B ILE* 5.8 0.3 - - - +
563B PHE* 1.3 89.0 - - - +
565B PRO* 1.3 78.7 - - + +
566B ILE* 3.4 7.8 + - + +
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Residues in contact with PRO 565 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497B THR* 3.7 22.7 - - + -
498B VAL 3.3 9.4 - - - +
499B LYS* 4.0 28.7 - - + -
563B PHE 3.4 4.0 - - - +
564B ASP* 1.3 90.3 - - + +
566B ILE* 1.3 64.6 + - - +
567B PRO* 4.7 0.7 - - - +
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Residues in contact with ILE 566 (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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496B LYS 3.8 0.2 - - - +
497B THR* 4.6 3.6 - - - -
498B VAL* 2.9 44.2 + - + +
528B TYR* 3.5 63.7 - - + +
538B ILE* 4.8 4.9 - - + -
563B PHE* 4.0 17.0 - - + -
564B ASP* 3.7 12.6 - - + +
565B PRO* 1.3 80.3 - - - +
567B PRO* 1.3 71.7 - - + +
568B ALA* 3.6 2.0 + - + -
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Residues in contact with PRO 567 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496B LYS 3.4 7.4 - - - +
497B THR* 4.8 1.8 - - - +
528B TYR* 3.8 14.8 - - + -
530B LEU* 4.0 26.0 + - + +
565B PRO 4.7 1.3 - - - +
566B ILE* 1.3 87.7 - - + +
568B ALA* 1.3 63.8 + - - +
594B TRP* 4.0 22.9 - - + +
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Residues in contact with ALA 568 (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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492B LEU* 3.8 8.8 - - - +
495B PRO* 4.2 2.7 - - - -
496B LYS* 2.8 32.7 + - - +
498B VAL* 4.1 17.3 - - + -
528B TYR* 3.9 26.5 - - + -
529B SER 3.6 12.1 - - - +
530B LEU* 4.0 5.5 - - - +
566B ILE* 3.6 3.1 + - + +
567B PRO* 1.3 77.0 - - - +
569B GLN* 1.3 59.9 + - - +
570B TYR 3.9 5.8 - - - +
571B VAL* 4.5 1.3 - - + -
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Residues in contact with GLN 569 (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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491B ASP* 3.1 24.6 + - - +
492B LEU* 2.7 39.7 + - - +
493B GLY* 3.3 17.2 + - - -
494B THR* 3.6 23.8 - - - +
495B PRO* 3.4 22.2 - - + +
529B SER 2.9 5.3 + - - -
530B LEU* 3.6 18.8 - - - +
568B ALA* 1.3 74.6 - - - +
570B TYR* 1.3 82.9 + - + +
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Residues in contact with TYR 570 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489B GLN* 3.9 19.5 - - - -
490B VAL 3.3 4.5 - - - +
491B ASP* 3.4 36.6 + - + -
528B TYR* 3.3 5.4 - - - +
529B SER* 3.0 39.2 + - - +
530B LEU 4.4 0.4 - - - -
531B ASN 4.2 4.0 + - - -
532B GLY* 3.6 33.2 - - - -
535B TRP* 3.6 24.5 - + + -
568B ALA* 3.9 0.9 - - - +
569B GLN* 1.3 106.0 + - + +
571B VAL* 1.3 65.9 + - - +
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Residues in contact with VAL 571 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488B LEU 3.8 0.5 - - - +
489B GLN* 3.3 3.3 - - - +
490B VAL* 2.8 40.8 + - + +
492B LEU* 4.6 7.0 - - + -
498B VAL* 4.0 31.6 - - + -
501B VAL* 4.7 15.9 - - + -
526B VAL* 4.1 18.6 - - + -
527B SER 3.5 9.0 - - - +
528B TYR* 4.6 4.5 - - + -
568B ALA* 4.5 6.7 - - + -
570B TYR* 1.3 79.7 - - - +
572B ARG* 1.3 69.1 + - - +
573B VAL* 5.2 3.1 - - + -
587B LEU* 5.9 1.9 - - + +
589B VAL* 4.3 22.2 - - + -
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Residues in contact with ARG 572 (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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487B TRP* 3.4 49.6 - - + +
488B LEU 3.1 4.9 - - - +
489B GLN* 2.8 37.4 + - + +
525B LYS 3.9 0.2 - - - +
526B VAL* 3.4 9.9 - - - +
527B SER* 2.8 41.3 + - - +
535B TRP* 3.6 29.4 - - + -
571B VAL* 1.3 75.6 - - - +
573B VAL* 1.3 63.5 + - - +
574B TYR* 2.9 36.9 + - + -
587B LEU* 6.4 0.2 - - - -
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Residues in contact with VAL 573 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474B TRP* 4.7 0.2 - - - -
487B TRP* 3.3 3.8 - - - -
488B LEU* 2.9 31.7 + - + +
501B VAL* 4.7 12.8 - - + -
503B ILE* 4.6 1.8 - - + -
524B PHE* 3.6 37.2 - - + -
525B LYS 3.6 2.2 - - - -
526B VAL* 4.7 2.7 - - + -
571B VAL* 5.2 2.2 - - + -
572B ARG* 1.3 77.4 - - - +
574B TYR* 1.3 64.0 + - - +
575B PRO* 3.4 6.4 - - - +
585B MET* 3.8 29.4 - - + -
587B LEU* 3.8 34.3 - - + -
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Residues in contact with TYR 574 (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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484B GLY* 3.2 33.4 - - - -
485B GLU 4.4 1.8 - - - -
486B GLU 3.5 13.7 - - - +
487B TRP* 3.7 22.3 - + + -
524B PHE* 3.2 2.1 - - - -
525B LYS* 2.8 48.7 + - + +
527B SER* 3.2 26.3 + - - -
535B TRP* 5.8 0.3 - - - -
537B TYR* 3.6 30.8 + + - +
572B ARG* 2.9 37.9 + - + -
573B VAL* 1.3 75.6 - - - +
575B PRO* 1.3 68.2 - - - +
576B GLU* 3.4 0.7 + - - -
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Residues in contact with PRO 575 (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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474B TRP* 3.9 21.1 - - + -
484B GLY* 3.1 21.5 + - - -
485B GLU 4.7 0.5 + - - -
486B GLU* 3.2 21.5 + - + +
521B VAL* 3.9 19.5 - - + -
523B LYS 3.7 5.6 - - - +
524B PHE* 4.0 4.0 - - + -
573B VAL* 3.4 10.8 - - + +
574B TYR* 1.3 82.5 - - - +
576B GLU* 1.3 59.5 + - - +
578B TRP* 3.5 23.1 - - + -
583B ILE* 4.0 19.2 - - + +
585B MET* 4.4 4.9 - - - -
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Residues in contact with GLU 576 (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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483B PRO* 3.5 26.3 - - + +
484B GLY* 3.5 20.0 + - - +
523B LYS* 2.7 19.3 + - + +
524B PHE* 4.3 3.4 - - - +
525B LYS* 3.6 30.0 + - + +
548B LEU* 3.4 32.7 - - + +
574B TYR 3.4 1.3 + - - +
575B PRO* 1.3 73.4 - - - +
577B ARG* 1.3 75.0 + - + +
578B TRP* 3.2 16.1 - - - -
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Residues in contact with ARG 577 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521B VAL* 3.5 3.1 - - - +
522B ARG* 2.6 35.8 + - + +
523B LYS* 2.9 47.1 + - + +
548B LEU* 5.0 9.1 - - - +
576B GLU* 1.3 91.3 + - + +
578B TRP* 1.3 63.5 + - - +
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Residues in contact with TRP 578 (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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479B PRO 3.3 12.4 + - - -
480B GLN* 3.7 11.5 + - - +
481B ALA 2.8 35.4 - - - -
482B GLN 4.0 2.5 - - - -
483B PRO* 3.7 20.0 - - + -
520B PHE 3.4 13.0 - - - +
521B VAL* 4.2 5.2 - - - -
522B ARG* 3.7 14.8 - - - +
575B PRO* 3.5 19.7 - - + -
576B GLU* 3.2 22.0 - - - -
577B ARG* 1.3 92.8 - - - +
579B SER* 1.3 85.7 + - - +
580B PRO* 4.6 0.3 - - - +
582B GLY* 3.5 24.2 - - - +
583B ILE* 3.4 29.8 - - + -
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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
------------------------------------------------------------
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