Contacts of the helix formed by residues 550 - 574 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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549A TYR* 1.3 73.3 - - - +
551A ARG* 1.3 62.8 + - - +
552A ARG* 3.2 3.6 - - - -
553A GLN* 3.2 21.1 + - - +
554A GLY* 3.4 3.6 + - - -
600A VAL* 3.4 34.9 - - - +
603A GLU* 4.1 17.6 + - - -
604A LEU* 5.1 5.7 - - - +
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Residues in contact with ARG 551 (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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445A PHE* 3.1 69.7 + - + +
448A GLN* 2.6 31.2 + - - -
449A ARG* 3.0 42.1 - - - +
549A TYR* 3.5 30.4 - - + +
550A GLY* 1.3 74.4 - - - +
552A ARG* 1.3 80.8 + - - +
554A GLY* 3.1 3.5 + - - -
555A ASP* 3.0 32.1 + - - +
604A LEU* 5.6 1.7 - - + +
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Residues in contact with ARG 552 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549A TYR* 5.2 7.0 - - - +
550A GLY* 3.2 1.1 - - - -
551A ARG* 1.3 98.0 - - - +
553A GLN* 1.3 59.4 + - + +
555A ASP* 2.8 38.2 + - - +
556A LEU* 2.9 24.1 + - - +
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Residues in contact with GLN 553 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
550A GLY* 3.2 15.9 + - - +
552A ARG* 1.3 76.2 - - + +
554A GLY* 1.3 60.8 + - - +
556A LEU* 3.2 14.9 + - + +
557A MET* 2.9 35.0 + - - +
596A SER* 4.4 9.3 - - - +
599A ARG* 4.0 33.8 + - - +
600A VAL* 3.3 23.4 - - + +
603A GLU* 5.1 7.5 + - - +
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Residues in contact with GLY 554 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441A TYR* 2.9 43.5 + - - -
445A PHE* 5.1 1.6 - - - -
550A GLY 3.4 6.4 + - - -
551A ARG* 3.1 10.2 + - - -
553A GLN* 1.3 77.2 - - - +
555A ASP* 1.3 60.3 + - - +
557A MET* 3.7 6.1 - - - +
558A GLU* 2.9 21.2 + - - +
600A VAL* 5.0 0.4 - - - +
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Residues in contact with ASP 555 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551A ARG* 3.0 9.8 + - - +
552A ARG* 2.8 47.3 + - - +
554A GLY* 1.3 77.1 - - - +
556A LEU* 1.3 59.9 + - - +
558A GLU* 3.3 21.6 - - - +
559A SER* 2.9 27.2 + - - -
562A GLN* 5.7 0.2 + - - -
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Residues in contact with LEU 556 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552A ARG 2.9 13.5 + - - +
553A GLN* 3.2 17.7 + - + +
555A ASP* 1.3 74.6 - - - +
557A MET* 1.3 60.1 + - + +
559A SER* 2.6 27.5 + - - +
560A LEU* 2.8 33.7 + - + +
592A HIS* 6.4 1.1 - - + -
596A SER* 5.2 9.6 - - - +
599A ARG* 5.8 2.5 - - - +
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Residues in contact with MET 557 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434A VAL* 4.7 5.3 - - + +
441A TYR* 3.6 40.8 - - + +
553A GLN 2.9 23.5 + - - +
554A GLY* 3.7 4.7 - - - +
556A LEU* 1.3 74.6 - - + +
558A GLU* 1.3 60.6 + - - +
560A LEU* 3.2 15.8 + - + +
561A GLU* 2.9 27.8 + - - +
592A HIS 4.3 1.1 - - - +
593A THR* 3.4 50.4 + - + +
596A SER* 3.6 28.9 - - - +
597A GLN* 3.8 9.2 - - - +
600A VAL* 4.8 6.5 - - + -
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Residues in contact with GLU 558 (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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438A LYS* 4.3 26.1 + - + +
441A TYR* 4.1 2.4 + - - -
554A GLY 2.9 18.3 + - - +
555A ASP* 3.3 29.1 - - - +
556A LEU 3.2 0.2 - - - -
557A MET* 1.3 76.4 - - - +
559A SER* 1.3 57.1 + - - +
561A GLU* 3.2 14.1 + - - +
562A GLN* 2.9 48.0 + - + +
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Residues in contact with SER 559 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555A ASP 2.9 12.8 + - - -
556A LEU* 2.6 34.7 + - - +
558A GLU* 1.3 74.5 - - - +
560A LEU* 1.3 59.9 + - - +
562A GLN* 3.2 23.1 + - - +
563A ARG* 2.9 40.2 + - - +
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Residues in contact with LEU 560 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
556A LEU* 2.8 28.0 + - + +
557A MET* 3.3 27.4 - - + +
559A SER* 1.3 76.3 - - - +
561A GLU* 1.3 59.9 + - - +
563A ARG* 3.1 8.3 + - + +
564A ALA 2.9 24.1 + - - -
588A LYS* 6.3 1.8 - - + -
589A ILE* 3.3 46.1 - - + +
592A HIS* 3.9 30.5 - - + -
593A THR* 4.2 9.4 - - - +
596A SER* 5.9 0.4 - - - +
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Residues in contact with GLU 561 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431A VAL* 4.9 10.0 - - + +
434A VAL* 4.1 19.6 - - + +
435A SER* 2.5 39.4 + - - +
438A LYS* 3.2 48.0 + - - +
557A MET 2.9 11.3 + - - +
558A GLU* 3.3 10.6 - - - +
560A LEU* 1.3 75.7 - - - +
562A GLN* 1.3 59.3 + - + +
564A ALA* 3.4 6.4 + - - +
565A ILE* 2.9 33.4 + - + +
589A ILE* 4.4 1.2 - - - +
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Residues in contact with GLN 562 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
558A GLU* 2.9 39.5 + - + +
559A SER* 3.2 25.8 + - - +
561A GLU* 1.3 77.3 - - + +
563A ARG* 1.3 72.5 + - - +
565A ILE* 3.3 10.6 - - + +
566A ASP* 2.9 35.8 + - - +
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Residues in contact with ARG 563 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
559A SER* 2.9 37.7 + - - +
560A LEU* 3.1 13.0 + - + +
562A GLN* 1.3 93.5 + - - +
564A ALA* 1.3 60.2 + - - +
566A ASP* 2.6 31.4 + - - +
567A LEU* 2.9 34.5 + - + +
589A ILE* 3.9 12.1 - - + -
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Residues in contact with ALA 564 (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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430A ALA 6.4 0.2 - - - -
431A VAL* 4.5 11.2 - - + +
434A VAL* 6.4 1.8 - - + -
560A LEU 2.9 15.9 + - - +
561A GLU* 3.8 6.1 - - - +
563A ARG* 1.3 75.2 - - - +
565A ILE* 1.3 57.9 + - - +
567A LEU* 3.2 16.6 + - - +
568A TYR* 3.0 24.8 + - - +
586A MET* 3.6 32.7 - - + +
589A ILE* 3.7 12.5 - - + +
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Residues in contact with ILE 565 (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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110A PRO* 3.3 36.6 - - + +
111A GLU* 4.4 15.7 - - + +
113A CYS* 4.8 0.7 - - - -
431A VAL* 3.7 32.1 - - + +
561A GLU* 2.9 20.4 + - + +
562A GLN* 3.3 20.4 - - + +
564A ALA* 1.3 73.9 - - - +
566A ASP* 1.3 63.5 + - - +
568A TYR* 3.6 24.9 - - + +
569A LYS* 2.8 36.7 + - + +
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Residues in contact with ASP 566 (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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562A GLN* 2.9 20.9 + - - +
563A ARG* 2.6 43.6 + - - +
565A ILE* 1.3 78.9 - - - +
567A LEU* 1.3 57.1 + - + +
569A LYS* 3.3 25.4 + - - +
570A GLN* 2.9 34.6 + - + +
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Residues in contact with LEU 567 (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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427A TRP* 3.2 24.7 - - + -
563A ARG* 2.9 22.3 + - + +
564A ALA* 3.2 15.2 + - - +
566A ASP* 1.3 73.9 - - + +
568A TYR* 1.3 59.4 + - - +
570A GLN* 2.8 26.3 + - + +
571A LEU* 3.0 9.5 + - - +
585A GLU* 3.7 40.8 - - + +
586A MET* 4.2 13.2 - - + +
589A ILE* 4.8 6.5 - - + -
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Residues in contact with TYR 568 (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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110A PRO* 3.9 13.7 - - + -
113A CYS* 4.0 27.2 - - + +
424A ARG* 3.1 50.1 + - + +
427A TRP* 3.5 27.5 - - + -
428A ALA* 4.2 7.1 - - + +
431A VAL* 4.9 2.0 - - + -
564A ALA 3.0 15.9 + - - +
565A ILE* 3.6 27.6 - - + -
567A LEU* 1.3 75.2 - - - +
569A LYS* 1.3 57.7 + - - +
571A LEU* 2.9 21.0 + - + +
572A LYS* 2.9 49.6 + - + +
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Residues in contact with LYS 569 (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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110A PRO* 3.8 36.6 - - + -
111A GLU* 4.2 16.4 + - - -
565A ILE* 2.8 23.4 + - - +
566A ASP* 3.3 27.0 + - - +
568A TYR* 1.3 76.1 - - - +
570A GLN* 1.3 58.1 + - - +
572A LYS* 2.8 10.8 + - + +
573A HIS* 2.8 48.7 + - + +
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Residues in contact with GLN 570 (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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566A ASP* 2.9 21.6 + - - +
567A LEU* 2.8 16.5 + - + +
569A LYS* 1.3 76.9 - - - +
571A LEU* 1.3 64.5 + - + +
573A HIS* 3.2 33.2 + - - +
574A ARG* 3.7 43.4 + - - +
577A ASP* 5.2 0.7 - - - +
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Residues in contact with LEU 571 (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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420A ILE* 3.7 18.6 - - + -
423A LEU* 3.6 43.1 - - + -
424A ARG* 3.7 21.5 - - + +
427A TRP* 3.5 42.0 - - + -
567A LEU 3.0 4.9 + - - -
568A TYR* 2.9 11.1 + - + +
570A GLN* 1.3 83.3 - - + +
572A LYS* 1.3 57.8 + - - +
573A HIS 3.5 0.2 - - - -
574A ARG 3.3 3.9 - - - +
575A PRO* 3.1 30.1 - - - +
579A SER* 6.0 2.5 - - - -
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Residues in contact with LYS 572 (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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108A ASN 5.6 3.8 - - - -
110A PRO* 4.7 14.6 - - + -
424A ARG* 4.1 17.9 - - - +
568A TYR* 2.9 55.4 + - + +
569A LYS* 2.8 12.8 + - - +
571A LEU* 1.3 78.7 - - - +
573A HIS* 1.3 64.8 + - + +
574A ARG 3.3 0.4 - - - -
575A PRO* 3.3 12.1 - - + +
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Residues in contact with HIS 573 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
569A LYS* 2.8 37.6 + - + +
570A GLN* 3.2 37.9 + - - +
572A LYS* 1.3 78.7 - - + +
574A ARG* 1.3 75.2 + - - +
575A PRO* 3.6 3.0 - - - +
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Residues in contact with ARG 574 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420A ILE* 4.1 6.2 - - - +
570A GLN* 3.7 37.6 + - - +
571A LEU* 3.3 10.7 - - - +
573A HIS* 1.3 90.1 - - + +
575A PRO* 1.3 59.8 - - - +
576A SER* 3.1 16.3 + - - +
577A ASP* 3.0 43.4 + - - +
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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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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