Contacts of the helix formed by residues 560 - 573 (chain A) 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 A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360A SER* 4.2 0.7 - - - -
386A SER 3.8 13.5 - - - +
387A GLY* 5.4 1.1 - - - -
393A TRP* 3.5 34.3 - + - -
447A CYS* 3.8 12.1 - - - -
449A PHE* 5.9 0.7 - + - -
486A GLU* 4.0 31.6 - - + +
490A PHE* 3.4 40.4 - + - -
555A VAL* 4.3 7.4 - - + -
556A GLY* 3.3 8.6 + - - +
558A TYR 3.6 0.6 - - - -
559A HIS* 1.3 96.7 - - + +
561A THR* 1.3 68.4 + - - +
562A CYS 3.2 2.2 - - - -
563A ASN* 3.1 17.1 + - - +
564A VAL* 3.1 18.9 + - - +
600A HIS* 3.5 27.1 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 561 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482A SER* 3.4 33.7 - - - +
483A ASN 4.2 2.8 + - - +
486A GLU* 3.9 9.2 - - - +
556A GLY 2.8 18.3 + - - -
557A ASP* 3.9 14.0 + - - -
560A PHE* 1.3 73.9 - - - +
562A CYS* 1.3 56.8 + - - +
564A VAL* 3.6 2.8 + - - +
565A ASN* 3.0 35.9 + - - +
582A LEU* 5.6 1.8 - - + -
678A PRO* 4.1 27.4 - - + +
679A ARG* 4.5 14.9 - - + -
683A CYS* 5.2 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 562 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557A ASP* 3.1 39.6 + - - +
558A TYR* 5.1 2.0 - - - +
561A THR* 1.3 76.0 - - - +
563A ASN* 1.3 61.3 + - - +
565A ASN* 3.4 2.8 + - - +
566A GLU* 3.0 27.9 + - - +
682A GLN 4.1 1.8 - - - -
683A CYS* 2.0 65.9 - - + +
686A TRP* 4.4 7.2 - - + -
687A LYS* 6.4 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 563 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A SER* 2.8 28.8 + - - +
390A THR* 3.4 28.2 + - + +
391A ALA* 3.5 15.7 - - + -
392A PRO* 3.6 7.2 - - - +
558A TYR 2.8 27.8 + - - +
559A HIS 3.2 24.0 + - - -
560A PHE* 3.1 5.8 + - - +
562A CYS* 1.3 76.5 - - - +
564A VAL* 1.3 64.6 + - - +
566A GLU* 3.5 5.7 + - - +
567A PHE 3.2 17.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 564 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386A SER* 4.1 7.4 - - - -
387A GLY* 3.5 35.4 - - - +
388A SER* 4.1 6.7 - - - +
480A THR* 3.3 24.4 + - + +
481A GLY 3.9 12.1 - - - +
482A SER* 3.9 16.8 - - - +
560A PHE 3.1 14.2 + - - +
561A THR 3.6 7.9 - - - +
563A ASN* 1.3 75.3 - - - +
565A ASN* 1.3 63.7 + - - +
567A PHE* 3.4 3.5 + - - +
568A ALA* 3.0 22.2 + - - +
580A MET* 4.1 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 565 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482A SER* 4.8 0.3 + - - -
561A THR* 3.0 19.8 + - - +
562A CYS* 3.5 10.5 - - - +
563A ASN 3.3 0.2 - - - -
564A VAL* 1.3 77.2 - - - +
566A GLU* 1.3 57.6 + - - +
568A ALA* 3.3 3.3 + - - +
569A GLN* 2.9 31.7 + - - +
580A MET* 3.4 25.8 - - - +
657A HIS* 4.7 2.3 + - + +
662A ARG* 6.2 1.5 - - - +
677A GLY* 3.7 10.8 - - - -
678A PRO* 2.8 37.4 + - - +
679A ARG 4.5 1.0 + - - -
680A LEU* 5.0 6.0 - - + +
683A CYS* 3.7 18.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 566 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A THR* 3.5 31.4 + - + +
465A GLN* 5.4 4.2 - - - +
468A LEU* 4.3 9.1 - - + +
562A CYS 3.0 16.7 + - - +
563A ASN* 3.7 10.3 - - - +
564A VAL 3.4 0.2 - - - -
565A ASN* 1.3 74.9 - - - +
567A PHE* 1.3 57.6 + - - +
569A GLN* 3.2 7.3 + - - +
570A ARG* 2.9 45.4 + - + +
687A LYS* 3.7 40.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 567 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367A SER* 4.0 8.5 - - - -
370A LEU* 3.8 18.2 - - + -
371A LEU* 4.2 7.4 - - + -
384A LEU* 3.7 30.3 - - + -
388A SER* 3.8 10.1 - - - +
389A PRO* 3.5 31.9 - - + -
390A THR* 4.8 1.7 - - + +
468A LEU* 3.6 30.7 - - + -
478A ILE* 4.6 9.6 - - + -
480A THR* 5.5 4.3 - - - -
563A ASN 3.2 14.6 + - - +
564A VAL* 3.7 5.2 - - - +
566A GLU* 1.3 78.0 - - - +
568A ALA* 1.3 64.8 + - - +
570A ARG* 3.3 5.5 + - - +
571A TYR* 3.1 52.8 + + - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 568 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478A ILE* 5.4 1.3 - - - -
480A THR* 3.7 18.2 - - + -
564A VAL 3.0 17.9 + - - +
565A ASN 3.7 0.7 - - - +
567A PHE* 1.3 78.7 - - - +
569A GLN* 1.3 57.6 + - - +
571A TYR* 3.5 2.6 + - - -
572A ALA* 3.0 28.4 + - - +
578A VAL* 3.4 21.6 - - + +
580A MET* 3.6 25.1 - - + -
657A HIS* 3.8 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 569 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
565A ASN 2.9 18.2 + - - +
566A GLU* 3.5 6.7 - - - +
568A ALA* 1.3 76.9 - - - +
570A ARG* 1.3 60.7 + - - +
572A ALA* 3.1 6.2 + - - +
573A GLU* 3.0 67.9 + - - +
657A HIS* 4.4 4.4 + - - +
659A ALA* 3.2 36.8 + - - +
662A ARG* 3.5 37.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 570 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468A LEU* 2.6 56.9 + - + +
469A ALA* 3.2 20.4 + - - +
471A GLY* 4.4 1.8 - - - +
473A PHE* 3.6 4.1 - - + -
566A GLU* 2.9 32.9 + - + +
567A PHE 3.8 4.0 - - - +
569A GLN* 1.3 78.6 - - + +
571A TYR* 1.3 61.0 + - - +
573A GLU* 2.9 42.2 + - - +
574A GLU* 3.2 47.7 + - - +
687A LYS* 6.3 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 571 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370A LEU* 3.3 26.7 - - + +
468A LEU* 5.2 0.7 - - + -
473A PHE* 3.4 31.1 - + + -
474A LYS 2.8 31.3 + - - -
476A THR* 3.4 22.7 - - - -
478A ILE* 3.5 27.8 - - + -
567A PHE* 3.1 52.7 + + - +
568A ALA* 3.8 6.7 - - - +
570A ARG* 1.3 75.7 - - - +
572A ALA* 1.3 62.2 + - - +
574A GLU 3.4 5.5 + - - -
575A GLY 3.6 0.3 + - - -
576A ASN* 3.1 38.9 + - + +
578A VAL* 4.0 11.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 572 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568A ALA 3.0 18.0 + - - +
569A GLN* 3.1 8.2 + - - +
571A TYR* 1.3 77.8 - - - +
573A GLU* 1.3 55.8 + - - +
574A GLU 3.2 0.2 - - - -
575A GLY* 3.2 18.2 + - - -
576A ASN 3.7 12.5 + - - +
578A VAL* 3.7 1.3 - - + +
657A HIS* 3.4 26.2 - - + +
658A THR* 4.1 1.6 + - - -
659A ALA* 3.5 23.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 573 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
569A GLN* 3.0 44.7 + - - +
570A ARG* 2.9 40.0 + - - +
572A ALA* 1.3 73.5 - - - +
574A GLU* 1.3 63.2 + - - +
575A GLY 3.2 5.3 + - - -
659A ALA* 3.7 17.3 - - + +
----------------------------------------------------------
Back to top of page
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