Contacts of the helix formed by residues 672 - 689 (chain B) in PDB entry 5FWP
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 672 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492A GLU 5.7 2.5 - - - -
493A GLN* 6.1 1.6 - - - -
496A ASN* 5.0 14.3 + - - +
670B LEU* 4.1 5.1 - - - +
671B GLU* 1.3 85.1 - - + +
673B PRO* 1.3 55.4 - - - +
674B GLN* 2.9 23.3 + - - +
675B THR* 2.7 29.9 + - - -
676B HIS* 2.9 32.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 673 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493A GLN* 4.7 24.5 - - + +
664A LEU* 3.3 30.7 - - + +
665A SER* 3.8 13.9 + - - +
670B LEU* 3.5 39.9 - - + +
671B GLU 3.8 2.0 - - - +
672B ASP* 1.3 86.2 - - - +
674B GLN* 1.3 59.7 + - - +
676B HIS* 3.8 2.1 - - + +
677B SER* 3.0 30.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 674 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496A ASN* 3.5 23.5 - - + +
497A SER* 4.5 1.7 - - - -
498A ALA* 3.6 29.3 + - - +
501A GLU* 5.2 1.6 - - - +
586A SER* 4.2 15.1 + - - +
587A SER* 4.3 15.2 - - - +
665A SER* 4.4 15.9 - - - +
672B ASP* 2.9 12.1 + - - +
673B PRO* 1.3 78.5 - - - +
675B THR* 1.3 52.0 + - - +
677B SER* 2.7 25.5 + - - -
678B ASN* 2.7 55.3 + - - +
681B TYR* 4.4 1.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 675 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
660B GLU* 5.6 1.3 - - - +
672B ASP* 2.7 31.6 + - - -
674B GLN* 1.3 75.8 - - - +
676B HIS* 1.3 66.7 + - - +
678B ASN* 3.4 13.6 + - + +
679B ARG* 2.9 37.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 676 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
664A LEU* 4.5 9.1 - - + +
680A ILE* 4.6 7.0 - - + +
657B LEU* 4.7 5.6 - - + -
660B GLU* 2.7 57.6 + - + +
661B THR* 4.2 11.2 - - - -
664B LEU* 4.0 16.5 - - + +
670B LEU* 3.9 25.7 - - + +
672B ASP 2.9 16.8 + - - +
673B PRO* 3.8 6.1 - - + +
675B THR* 1.3 79.4 - - - +
677B SER* 1.3 61.8 + - - +
679B ARG* 3.3 14.5 + - - +
680B ILE* 3.2 41.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 677 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
661A THR* 4.0 21.5 - - - -
664A LEU* 6.0 0.7 - - - -
665A SER* 4.4 3.4 - - - -
673B PRO 3.0 16.2 + - - -
674B GLN* 2.7 24.4 + - - -
676B HIS* 1.3 75.5 - - - +
678B ASN* 1.3 54.0 + - - +
680B ILE* 3.1 12.1 + - - +
681B TYR* 2.7 67.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 678 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
586A SER* 4.9 8.8 + - - +
674B GLN* 2.7 57.6 + - - +
675B THR* 3.1 16.5 + - + +
677B SER* 1.3 71.1 + - - +
679B ARG* 1.3 59.4 + - - +
681B TYR* 3.1 18.7 + - - +
682B ARG* 2.8 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 679 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
653B ASP* 4.9 6.6 + - - +
656B VAL* 3.7 19.1 - - - +
657B LEU* 3.9 33.6 - - - +
660B GLU* 2.7 44.1 + - - -
675B THR* 2.9 23.8 + - + +
676B HIS* 3.4 17.4 + - - +
677B SER 3.3 0.2 - - - -
678B ASN* 1.3 75.0 - - - +
680B ILE* 1.3 64.5 + - + +
682B ARG* 3.1 35.4 + - - +
683B MET* 2.9 33.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 680 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
657A LEU* 4.1 13.2 - - + -
661A THR* 3.6 33.2 - - + -
676A HIS* 4.5 8.1 - - + +
680A ILE* 4.8 10.1 - - + -
683A MET* 5.5 3.4 - - + -
657B LEU* 5.1 4.3 - - + -
676B HIS* 3.2 39.2 + - + +
677B SER* 3.1 10.0 + - - +
679B ARG* 1.3 78.4 - - + +
681B TYR* 1.3 58.8 + - + +
683B MET* 3.1 23.0 + - + +
684B ILE* 2.8 51.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 681 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
586A SER 4.8 4.7 - - - -
587A SER* 3.6 15.7 + - - -
588A PRO* 3.5 32.2 - - + +
589A CYS* 4.8 4.7 + - - -
632A HIS* 4.9 2.2 - - + +
634A ILE* 3.7 12.8 - - + +
658A LEU* 3.6 32.8 - - + -
661A THR* 3.7 22.0 + - - -
662A ALA* 4.7 3.5 + - - -
665A SER* 4.9 3.6 + - - -
674B GLN* 4.4 3.9 + - - -
677B SER* 2.7 44.6 + - - -
678B ASN* 3.1 24.4 + - - +
680B ILE* 1.3 74.4 - - + +
682B ARG* 1.3 57.5 + - - +
684B ILE* 3.2 4.9 + - + +
685B LYS* 2.8 41.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 682 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
653B ASP* 4.5 20.9 + - - +
678B ASN 2.8 12.8 + - - +
679B ARG* 3.3 39.2 + - - +
681B TYR* 1.3 76.3 - - - +
683B MET* 1.3 61.6 + - - +
685B LYS* 3.2 12.8 + - + +
686B LEU* 2.9 44.8 + - + +
691B ASP 5.6 4.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 683 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
680A ILE* 5.9 2.2 - - + -
683A MET* 6.0 8.1 - - + -
684A ILE* 6.1 0.9 - - - -
657B LEU* 3.7 44.2 - - + -
679B ARG* 2.9 21.5 + - + +
680B ILE* 3.5 31.9 - - + +
682B ARG* 1.3 77.7 - - + +
684B ILE* 1.3 60.5 + - + +
686B LEU* 3.2 18.1 + - + +
687B GLY* 3.0 23.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 684 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
634A ILE* 3.8 12.8 - - + -
654A LEU* 3.6 29.8 - - + -
657A LEU* 3.9 12.6 - - + -
658A LEU* 3.3 31.9 - - + -
683A MET* 5.9 1.8 - - - -
680B ILE* 2.8 35.8 + - + +
681B TYR* 3.4 9.9 - - - +
683B MET* 1.3 74.8 - - + +
685B LYS* 1.3 53.8 + - - +
687B GLY* 3.0 3.6 + - - -
688B LEU* 2.8 55.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 685 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
632A HIS* 3.5 34.2 + - - -
633A PRO* 4.2 19.2 - - - +
634A ILE* 3.8 6.1 - - + -
681B TYR* 2.8 22.5 + - - +
682B ARG* 3.5 11.7 - - + +
684B ILE* 1.3 74.7 - - - +
686B LEU* 1.3 53.6 + - - +
688B LEU 3.5 0.2 - - - -
689B GLY* 2.7 30.8 + - - -
690B ILE* 2.8 47.6 + - + -
691B ASP* 3.9 17.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 686 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
682B ARG* 2.9 33.8 + - + +
683B MET* 3.4 20.0 - - + +
685B LYS* 1.3 77.0 - - - +
687B GLY* 1.3 60.9 + - - +
689B GLY* 3.4 10.7 + - - -
691B ASP 4.1 23.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 687 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
683B MET 3.0 13.4 + - - -
684B ILE* 3.0 4.0 + - - -
686B LEU* 1.3 77.2 - - - +
688B LEU* 1.3 62.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 688 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
634A ILE* 4.0 13.5 - - + +
637A THR* 3.9 27.4 - - + +
638A LEU* 5.4 1.1 - - + -
641A LYS* 4.4 22.9 + - + +
651A VAL* 6.3 1.3 - - + -
654A LEU* 3.8 20.6 - - + -
684B ILE* 2.8 41.1 + - + +
685B LYS 3.8 0.2 - - - +
687B GLY* 1.3 75.4 - - - +
689B GLY* 1.3 61.4 + - - +
690B ILE* 3.3 34.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 689 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
685B LYS 2.7 10.0 + - - -
686B LEU* 3.4 7.8 + - - -
687B GLY 3.3 3.8 - - - -
688B LEU* 1.3 76.4 - - - +
690B ILE* 1.3 64.9 + - - +
691B ASP* 3.5 3.3 - - - -
----------------------------------------------------------
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