Contacts of the helix formed by residues 550 - 574 (chain B) in PDB entry 5TQW
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 GLY 550 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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445B PHE* 4.6 0.2 - - - -
549B TYR* 1.3 73.9 - - - +
551B ARG* 1.3 63.6 + - - +
552B ARG* 3.2 3.4 - - - -
553B GLN* 3.2 21.2 + - - -
554B GLY 3.4 3.3 + - - -
600B VAL* 3.4 34.3 - - - +
603B GLU* 4.1 17.9 + - - -
604B LEU* 5.1 5.3 - - - +
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Residues in contact with ARG 551 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445B PHE* 3.1 69.3 + - + +
448B GLN* 2.6 30.4 + - - -
449B ARG* 3.0 42.2 - - - +
549B TYR* 3.5 30.4 - - + +
550B GLY* 1.3 75.1 - - - +
552B ARG* 1.3 80.0 + - - +
554B GLY* 3.1 3.4 + - - +
555B ASP* 3.0 32.5 + - - +
604B LEU* 5.6 1.4 - - + +
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Residues in contact with ARG 552 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549B TYR* 5.2 7.2 - - - +
550B GLY* 3.2 1.1 - - - -
551B ARG* 1.3 98.4 - - - +
553B GLN* 1.3 59.8 + - + +
555B ASP* 2.8 38.3 + - - +
556B LEU* 2.9 24.1 + - - +
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Residues in contact with GLN 553 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
550B GLY* 3.2 17.0 + - - +
552B ARG* 1.3 75.9 - - + +
554B GLY* 1.3 60.5 + - - +
556B LEU* 3.2 15.4 + - + +
557B MET* 2.9 34.2 + - - +
596B SER* 4.4 9.6 - - - +
599B ARG* 4.0 33.7 + - - +
600B VAL* 3.3 23.0 - - + +
603B GLU* 5.1 8.5 + - - +
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Residues in contact with GLY 554 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438B LYS* 5.6 0.2 - - - +
441B TYR* 2.9 43.0 + - - -
445B PHE* 5.1 1.3 - - - -
550B GLY 3.4 6.4 + - - -
551B ARG* 3.1 10.5 + - - -
553B GLN* 1.3 77.7 - - - +
555B ASP* 1.3 60.9 + - - +
557B MET* 3.7 6.3 - - - +
558B GLU* 2.9 21.0 + - - +
600B VAL* 5.0 0.4 - - - +
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Residues in contact with ASP 555 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551B ARG* 3.0 9.6 + - - +
552B ARG* 2.8 47.8 + - - +
554B GLY* 1.3 77.3 - - - +
556B LEU* 1.3 58.8 + - - +
558B GLU* 3.3 22.1 - - - +
559B SER* 2.9 27.4 + - - -
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Residues in contact with LEU 556 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552B ARG 2.9 12.2 + - - +
553B GLN* 3.2 17.5 + - + +
555B ASP* 1.3 74.7 - - - +
557B MET* 1.3 60.8 + - + +
559B SER* 2.6 28.6 + - - +
560B LEU* 2.8 33.7 + - + +
592B HIS* 6.4 1.1 - - + -
596B SER* 5.2 9.4 - - - +
599B ARG* 5.8 2.5 - - - +
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Residues in contact with MET 557 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434B VAL* 4.7 5.5 - - + +
441B TYR* 3.6 40.4 - - + +
553B GLN 2.9 23.7 + - - +
554B GLY* 3.7 4.9 - - - +
556B LEU* 1.3 74.8 - - + +
558B GLU* 1.3 60.8 + - - +
560B LEU* 3.2 16.2 + - + +
561B GLU* 2.9 28.5 + - - +
592B HIS 4.3 0.7 - - - +
593B THR* 3.4 49.8 - - + +
596B SER* 3.6 29.6 - - - +
597B GLN* 3.8 8.7 - - - +
600B VAL* 4.8 6.1 - - + -
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Residues in contact with GLU 558 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438B LYS* 4.3 27.4 + - + +
441B TYR* 4.1 1.9 + - - -
554B GLY 2.9 18.7 + - - +
555B ASP* 3.3 30.1 - - - +
557B MET* 1.3 76.7 - - - +
559B SER* 1.3 57.1 + - - +
561B GLU* 3.2 14.0 + - - +
562B GLN* 2.9 47.4 + - + +
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Residues in contact with SER 559 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555B ASP 2.9 12.2 + - - -
556B LEU* 2.6 33.8 + - - +
558B GLU* 1.3 73.9 - - - +
560B LEU* 1.3 60.5 + - - +
562B GLN* 3.2 22.6 + - - +
563B ARG* 2.9 40.6 + - - +
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Residues in contact with LEU 560 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
556B LEU* 2.8 29.3 + - + +
557B MET* 3.3 27.1 - - + +
558B GLU 3.2 0.2 - - - -
559B SER* 1.3 75.2 - - - +
561B GLU* 1.3 59.1 + - - +
563B ARG* 3.1 8.8 + - + -
564B ALA* 2.9 23.9 + - - +
588B LYS* 6.3 2.2 - - + -
589B ILE* 3.3 45.8 - - + +
592B HIS* 3.9 30.7 - - + -
593B THR* 4.2 9.4 - - - +
596B SER* 5.9 0.2 - - - +
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Residues in contact with GLU 561 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431B VAL* 4.9 10.7 - - + +
434B VAL* 4.1 18.2 - - + +
435B SER* 2.5 38.8 + - - +
438B LYS* 3.2 49.5 + - - +
557B MET 2.9 12.5 + - - +
558B GLU* 3.2 10.5 + - - +
560B LEU* 1.3 74.1 - - - +
562B GLN* 1.3 59.6 + - + +
564B ALA* 3.8 6.6 - - - +
565B ILE* 2.9 32.3 + - + +
589B ILE* 4.4 1.3 - - - +
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Residues in contact with GLN 562 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
558B GLU* 2.9 39.5 + - + +
559B SER* 3.2 26.3 + - - +
561B GLU* 1.3 77.7 - - + +
563B ARG* 1.3 71.5 + - - +
565B ILE* 3.3 11.2 - - + +
566B ASP* 2.9 35.7 + - - +
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Residues in contact with ARG 563 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
559B SER* 2.9 38.5 + - - +
560B LEU* 3.1 13.6 + - + +
562B GLN* 1.3 92.8 + - - +
564B ALA* 1.3 60.0 + - - +
566B ASP* 2.6 32.2 + - - +
567B LEU* 2.9 34.3 + - + +
589B ILE* 3.9 13.0 - - + -
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Residues in contact with ALA 564 (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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430B ALA 6.4 0.2 - - - -
431B VAL* 4.5 10.7 - - + +
434B VAL* 6.4 1.6 - - + -
560B LEU 2.9 15.7 + - - +
561B GLU* 3.4 6.9 + - - +
563B ARG* 1.3 76.4 - - - +
565B ILE* 1.3 59.0 + - - +
567B LEU* 3.2 16.1 + - - +
568B TYR* 3.0 24.8 + - - +
586B MET* 3.6 32.4 - - + +
589B ILE* 3.7 12.5 - - + +
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Residues in contact with ILE 565 (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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110B PRO* 3.3 36.6 - - + +
111B GLU* 4.4 15.7 - - + +
113B CYS* 4.8 0.4 - - - -
431B VAL* 3.7 32.5 - - + +
561B GLU* 2.9 19.2 + - + +
562B GLN* 3.3 21.3 - - + +
564B ALA* 1.3 74.1 - - - +
566B ASP* 1.3 64.2 + - - +
568B TYR* 3.6 23.6 - - + -
569B LYS* 2.8 36.8 + - + +
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Residues in contact with ASP 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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562B GLN* 2.9 21.2 + - - +
563B ARG* 2.6 43.4 + - - +
565B ILE* 1.3 77.5 - - - +
567B LEU* 1.3 58.0 + - + +
569B LYS* 3.3 25.2 + - - +
570B GLN* 2.9 34.2 + - - +
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Residues in contact with LEU 567 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427B TRP* 3.2 24.6 - - + -
563B ARG* 2.9 21.7 + - + +
564B ALA* 3.3 15.7 - - - +
566B ASP* 1.3 75.7 - - + +
568B TYR* 1.3 58.9 + - - +
570B GLN* 2.8 27.8 + - + +
571B LEU* 3.0 9.7 + - - +
585B GLU* 3.7 40.2 - - + +
586B MET* 4.2 13.0 - - + +
589B ILE* 4.8 6.1 - - + -
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Residues in contact with TYR 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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110B PRO* 3.9 13.0 - - + -
113B CYS* 4.0 28.1 - - + +
424B ARG* 3.1 48.7 + - + +
427B TRP* 3.5 28.6 - - + -
428B ALA* 4.2 6.7 - - + +
431B VAL* 4.9 2.9 - - + -
564B ALA 3.0 14.9 + - - +
565B ILE* 3.6 28.3 - - + -
566B ASP 3.4 0.2 - - - -
567B LEU* 1.3 74.6 - - - +
569B LYS* 1.3 57.3 + - - +
571B LEU* 2.9 20.4 + - + +
572B LYS* 2.9 50.0 + - + +
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Residues in contact with LYS 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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110B PRO* 3.8 36.6 - - + -
111B GLU* 4.2 16.6 + - - -
565B ILE* 2.8 23.6 + - - +
566B ASP* 3.3 27.4 + - - +
568B TYR* 1.3 77.9 - - - +
570B GLN* 1.3 58.0 + - - +
572B LYS* 2.8 9.6 + - + +
573B HIS* 2.8 49.8 + - + +
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Residues in contact with GLN 570 (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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566B ASP* 2.9 21.1 + - - +
567B LEU* 2.8 17.4 + - + +
569B LYS* 1.3 77.5 - - - +
571B LEU* 1.3 64.4 + - + +
573B HIS* 3.2 33.1 + - - +
574B ARG* 3.7 43.6 + - - +
577B ASP* 5.2 0.9 - - - +
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Residues in contact with LEU 571 (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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420B ILE* 3.7 19.5 - - + -
423B LEU* 3.6 44.4 - - + +
424B ARG* 3.7 21.0 - - + +
427B TRP* 3.5 41.3 - - + -
567B LEU 3.0 4.6 + - - -
568B TYR* 2.9 11.5 + - + +
570B GLN* 1.3 83.9 - - + +
572B LYS* 1.3 56.9 + - - +
574B ARG 3.3 4.3 - - - +
575B PRO* 3.1 30.3 - - - +
579B SER* 6.0 2.9 - - - -
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Residues in contact with LYS 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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108B ASN 5.6 3.8 - - - -
110B PRO* 4.7 13.9 - - + -
424B ARG* 4.1 17.5 - - - +
568B TYR* 2.9 56.2 + - + +
569B LYS* 2.8 12.4 + - + +
571B LEU* 1.3 78.4 - - - +
573B HIS* 1.3 67.3 + - + +
574B ARG 3.3 0.4 - - - -
575B PRO* 3.3 11.8 - - + +
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Residues in contact with HIS 573 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
569B LYS* 2.8 38.1 + - + +
570B GLN* 3.2 38.0 + - - +
571B LEU 3.5 0.2 - - - -
572B LYS* 1.3 79.0 - - + +
574B ARG* 1.3 74.2 + - + +
575B PRO* 3.6 3.2 - - - +
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Residues in contact with ARG 574 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420B ILE* 4.1 6.6 - - - +
570B GLN* 3.7 37.9 + - - +
571B LEU* 3.3 11.8 - - - +
573B HIS* 1.3 88.0 - - + +
575B PRO* 1.3 59.6 - - - +
576B SER* 3.1 13.6 + - - +
577B ASP* 3.0 43.7 + - - +
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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
------------------------------------------------------------
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