Contacts of the helix formed by residues 560 - 574 (chain B) in PDB entry 5X61
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 PHE 560 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360B SER* 4.4 0.2 - - - -
386B SER 3.6 18.2 - - - +
387B GLY* 5.4 1.3 - - - -
393B TRP* 3.6 34.5 - + - -
447B CYS* 4.0 8.3 - - - -
449B PHE* 6.0 1.1 - + - -
482B SER* 4.7 0.2 - - - -
486B GLU* 4.1 31.9 - - + +
490B PHE* 3.4 42.4 - + - -
555B VAL* 5.1 1.3 - - + -
556B GLY* 3.2 16.8 + - - +
557B ASP 3.9 0.2 - - - -
558B TYR 3.5 1.4 - - - -
559B HIS* 1.3 97.9 - - + +
561B THR* 1.3 67.5 + - - +
562B CYS 3.3 2.0 - - - -
563B ASN* 3.1 7.3 + - - +
564B VAL* 3.1 27.9 + - + +
600B HIS* 3.5 22.2 - + - -
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Residues in contact with THR 561 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482B SER* 3.4 29.2 - - - +
483B ASN 4.1 3.7 + - - +
486B GLU* 4.0 9.5 - - - +
556B GLY 2.8 20.5 + - - -
557B ASP* 4.0 15.5 + - - +
560B PHE* 1.3 72.0 - - - +
562B CYS* 1.3 57.0 + - - +
564B VAL* 3.3 3.6 + - - +
565B ASN* 3.0 36.5 + - - +
582B LEU* 6.1 0.7 - - + -
678B PRO* 4.2 30.7 - - + +
679B ARG* 4.5 11.3 - - + -
683B CYS* 4.9 1.3 - - - -
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Residues in contact with CYS 562 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557B ASP* 3.0 37.3 + - - +
558B TYR* 5.0 1.6 - - - -
561B THR* 1.3 78.1 - - - +
563B ASN* 1.3 60.2 + - - +
565B ASN* 3.4 4.0 + - - +
566B GLU* 3.0 27.8 + - - +
679B ARG 4.7 0.2 - - - -
682B GLN 4.0 4.7 - - - -
683B CYS* 2.0 64.5 - - + +
686B TRP* 4.2 9.6 - - + -
687B LYS* 6.4 1.1 - - + -
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Residues in contact with ASN 563 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388B SER* 2.9 26.8 + - - +
390B THR* 3.5 23.9 + - + +
391B ALA* 3.5 14.5 - - + +
392B PRO* 3.3 11.2 - - - +
558B TYR 2.8 27.5 + - - +
559B HIS 3.3 23.6 + - - -
560B PHE* 3.1 5.0 + - - +
562B CYS* 1.3 76.5 - - - +
564B VAL* 1.3 65.0 + - - +
566B GLU* 3.4 7.4 + - - +
567B PHE 3.1 17.8 + - - -
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Residues in contact with VAL 564 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386B SER* 4.1 6.3 - - - -
387B GLY* 3.6 35.0 - - - +
388B SER* 4.0 7.0 - - - -
480B THR* 3.4 29.5 + - + +
481B GLY* 3.8 16.6 - - - +
482B SER* 3.9 17.0 - - - +
560B PHE 3.1 15.7 + - - +
561B THR 3.5 7.6 - - - +
563B ASN* 1.3 74.9 - - - +
565B ASN* 1.3 63.9 + - - +
567B PHE* 3.5 3.0 + - - +
568B ALA* 3.1 23.0 + - - +
580B MET* 4.3 5.2 - - - -
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Residues in contact with ASN 565 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482B SER* 4.9 0.9 + - - -
561B THR* 3.0 16.6 + - - +
562B CYS* 3.4 9.6 - - - +
564B VAL* 1.3 78.3 - - - +
566B GLU* 1.3 62.0 + - - +
568B ALA* 3.3 2.1 + - - +
569B GLN* 3.0 27.9 + - - +
580B MET* 3.4 24.5 - - - +
657B HIS* 4.9 2.3 + - - +
677B GLY* 3.8 7.2 - - - -
678B PRO* 2.7 42.2 + - - +
679B ARG 4.5 0.4 + - - -
680B LEU* 4.6 6.8 - - + +
683B CYS* 3.7 18.3 - - + +
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Residues in contact with GLU 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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390B THR* 3.4 30.9 + - + +
465B GLN* 3.8 9.5 - - - +
468B LEU* 4.2 11.7 - - + +
562B CYS 3.0 16.6 + - - +
563B ASN* 3.6 11.6 - - - +
564B VAL 3.3 0.2 - - - -
565B ASN* 1.3 77.9 - - - +
567B PHE* 1.3 56.9 + - - +
569B GLN* 3.5 8.8 + - - +
570B ARG* 3.0 35.4 + - + +
687B LYS* 3.7 44.0 - - + +
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Residues in contact with PHE 567 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367B SER* 4.2 10.1 - - - -
370B LEU* 3.8 17.9 - - + -
371B LEU* 4.2 5.4 - - + -
384B LEU* 3.7 28.9 - - + -
387B GLY 5.5 0.2 - - - -
388B SER* 3.8 11.2 - - - -
389B PRO* 3.6 30.5 - - + -
390B THR* 4.9 0.9 - - + +
468B LEU* 3.7 30.5 - - + +
478B ILE* 4.0 20.6 - - + -
480B THR* 5.5 4.7 - - - -
563B ASN 3.1 14.6 + - - +
564B VAL 3.8 2.9 - - - +
566B GLU* 1.3 78.4 - - - +
568B ALA* 1.3 57.8 + - - +
570B ARG* 3.4 5.0 + - - +
571B TYR* 3.0 53.5 + + - +
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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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478B ILE* 4.2 7.4 - - - -
480B THR* 3.6 15.7 - - + -
564B VAL 3.1 17.7 + - - +
565B ASN 3.7 0.9 - - - +
567B PHE* 1.3 77.6 - - - +
569B GLN* 1.3 57.6 + - - +
571B TYR 3.4 0.7 + - - -
572B ALA* 3.0 24.1 + - - +
578B VAL* 3.4 25.7 - - + +
580B MET* 3.6 24.5 - - + -
657B HIS* 4.1 5.4 - - + -
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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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565B ASN 3.0 17.7 + - - +
566B GLU* 3.9 7.9 - - - +
568B ALA* 1.3 73.8 - - - +
570B ARG* 1.3 58.4 + - - +
572B ALA* 3.0 7.1 + - - +
573B GLU* 2.7 67.6 + - + +
657B HIS* 4.3 11.4 + - - +
659B ALA* 4.5 11.5 + - - +
662B ARG* 3.9 32.3 + - + +
687B LYS* 6.0 2.6 - - - +
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Residues in contact with ARG 570 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468B LEU* 3.2 49.3 + - + +
469B ALA* 3.5 24.2 + - - +
470B SER 5.3 0.2 - - - -
471B GLY 4.8 1.6 - - - +
473B PHE* 3.6 13.5 - - + -
566B GLU* 3.0 23.3 + - + +
567B PHE* 3.7 4.7 - - + +
568B ALA 3.4 0.2 - - - -
569B GLN* 1.3 78.4 - - - +
571B TYR* 1.3 60.8 + - + +
573B GLU* 3.0 31.4 + - - +
574B GLU* 3.3 32.2 + - - -
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Residues in contact with TYR 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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370B LEU* 3.3 31.5 - - + +
473B PHE* 3.3 29.3 - + + +
474B LYS 2.8 33.5 + - - -
476B THR* 3.4 24.9 - - + -
478B ILE* 3.8 27.1 - - + -
567B PHE* 3.0 50.4 + + - +
568B ALA 3.6 4.7 - - - +
569B GLN 3.2 0.2 - - - -
570B ARG* 1.3 74.8 - - + +
572B ALA* 1.3 63.9 + - - +
574B GLU* 3.4 5.4 + - - +
576B ASN* 3.1 42.0 + - + +
578B VAL* 4.0 3.1 - - + -
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Residues in contact with ALA 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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568B ALA 3.0 14.1 + - - +
569B GLN* 3.0 10.7 + - - +
571B TYR* 1.3 75.2 - - - +
573B GLU* 1.3 59.5 + - - +
575B GLY* 2.8 22.3 + - - -
576B ASN 3.4 13.4 + - - +
578B VAL* 3.7 4.0 - - + +
657B HIS 3.3 26.2 - - - +
658B THR* 4.2 1.8 - - - -
659B ALA* 4.0 18.9 + - - +
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Residues in contact with GLU 573 (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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569B GLN* 2.7 48.3 + - + +
570B ARG* 3.0 40.6 + - - +
572B ALA* 1.3 72.2 - - - +
574B GLU* 1.3 58.8 + - - +
575B GLY* 3.1 3.9 + - - -
659B ALA* 3.8 24.1 - - + +
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Residues in contact with GLU 574 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471B GLY* 4.4 13.4 - - - +
473B PHE* 3.9 17.9 - - + -
475B LYS* 3.4 30.8 + - - +
570B ARG* 3.3 42.6 + - - +
571B TYR 3.4 6.2 + - - +
572B ALA 3.1 1.0 - - - -
573B GLU* 1.3 79.6 - - - +
575B GLY* 1.3 59.0 + - - +
576B ASN* 3.4 8.1 + - - +
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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