Contacts of the helix formed by residues 658 - 672 (chain A) in PDB entry 2VXO
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 PRO 658 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
604A TYR* 3.5 47.6 - - + +
653A PRO* 4.8 0.7 - - - -
657A ILE* 1.3 94.9 - - + +
659A VAL* 1.3 67.4 + - - +
660A GLU* 4.3 7.9 - - + +
661A VAL* 3.2 26.1 + - + +
662A VAL* 3.3 11.6 + - - +
85B ASP* 3.0 16.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 659 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538A PRO* 6.4 0.4 - - + -
540A TRP* 4.2 23.8 - - + +
653A PRO* 3.9 13.5 - - + +
654A GLY* 3.6 20.6 - - - +
657A ILE 3.6 1.4 + - - -
658A PRO* 1.3 71.0 - - - +
660A GLU* 1.3 63.9 + - - +
662A VAL* 3.0 6.2 + - + +
663A LEU* 2.9 44.0 + - + +
85B ASP* 3.2 25.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 660 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
658A PRO* 3.2 6.8 - - + +
659A VAL* 1.3 80.2 - - - +
661A VAL* 1.3 61.3 + - + +
663A LEU* 3.3 8.6 + - - +
664A LYS* 2.8 35.1 + - + +
84B GLU* 4.9 12.3 - - - +
85B ASP* 4.4 1.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 661 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
598A ILE* 3.7 13.5 - - + +
599A LEU* 4.4 3.6 - - - -
602A SER* 3.7 35.2 - - - +
604A TYR* 4.6 1.1 - - + -
657A ILE* 4.4 10.5 - - + -
658A PRO* 3.2 35.1 + - + +
660A GLU* 1.3 80.8 - - + +
662A VAL* 1.3 64.4 + - - +
664A LYS* 3.3 9.1 + - - +
665A MET* 3.2 41.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 662 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540A TRP* 5.1 2.0 - - + -
564A PHE* 3.7 30.1 - - + -
637A ILE* 5.0 4.0 - - + -
639A THR* 5.8 0.2 - - + -
653A PRO* 4.2 14.8 - - + -
657A ILE* 4.0 27.8 - - + -
658A PRO 3.3 10.5 + - - +
659A VAL* 3.0 9.2 + - - +
661A VAL* 1.3 75.2 - - - +
663A LEU* 1.3 64.4 + - + +
665A MET* 3.0 25.5 + - + +
666A VAL* 3.2 11.7 + - + +
680A TYR* 3.9 30.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 663 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537A GLU* 6.0 1.8 - - - +
538A PRO* 6.0 4.3 - - + -
540A TRP* 5.7 2.2 - - + -
564A PHE* 3.9 31.0 - - + -
659A VAL* 2.9 42.1 + - + +
660A GLU* 3.8 7.9 - - - +
662A VAL* 1.3 74.1 - - + +
664A LYS* 1.3 57.3 + - - +
666A VAL* 3.1 9.3 + - + +
667A THR* 2.9 33.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 664 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
598A ILE* 4.1 27.5 - - + +
660A GLU* 2.8 26.3 + - + +
661A VAL* 3.5 6.7 - - - +
662A VAL 3.2 0.2 - - - -
663A LEU* 1.3 69.3 - - - +
665A MET* 1.3 66.6 + - - +
667A THR* 3.4 7.8 + - + -
668A GLU* 3.0 37.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 665 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
595A ALA* 3.7 35.9 - - + +
598A ILE* 3.8 17.9 - - + -
599A LEU* 3.9 14.6 - - + +
611A MET* 4.2 10.1 - - - +
637A ILE* 3.8 33.2 - - + -
657A ILE* 4.5 11.4 - - + -
661A VAL* 3.2 36.9 + - + +
662A VAL* 3.0 13.1 + - + +
664A LYS* 1.3 74.6 - - - +
666A VAL* 1.3 58.8 + - - +
668A GLU* 3.3 1.0 + - - +
669A ILE* 2.9 44.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 666 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
564A PHE* 3.6 57.9 - - + -
637A ILE* 4.5 4.3 - - + -
662A VAL 3.3 14.6 - - - +
663A LEU* 3.1 12.0 + - + +
665A MET* 1.3 76.0 - - - +
667A THR* 1.3 63.0 + - - +
670A LYS* 3.1 27.7 + - + +
678A ILE* 3.8 30.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 667 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
663A LEU* 2.9 20.4 + - - +
664A LYS* 3.6 10.3 - - + -
666A VAL* 1.3 79.5 - - - +
668A GLU* 1.3 76.8 + - - +
670A LYS* 3.8 8.3 + - - +
671A LYS* 3.6 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 668 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
594A GLU* 3.3 27.8 - - + +
598A ILE* 3.8 20.4 - - + -
664A LYS* 3.0 33.5 + - + +
665A MET 3.3 2.7 + - - +
667A THR* 1.3 85.1 - - - +
669A ILE* 1.3 65.7 + - - +
671A LYS* 3.2 52.7 + - - +
672A ILE 3.8 1.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 669 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
591A ALA* 4.1 14.1 - - + +
594A GLU* 3.5 18.8 - - + +
595A ALA* 4.1 25.8 - - + +
613A VAL* 5.3 0.2 - - + -
635A VAL* 3.8 36.3 - - + -
637A ILE* 4.6 8.1 - - + -
665A MET* 2.9 29.4 + - + +
668A GLU* 1.3 75.9 - - - +
670A LYS* 1.3 61.9 + - - +
672A ILE* 3.0 30.0 + - + +
675A ILE* 3.7 6.8 - - + +
678A ILE* 3.5 23.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 670 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
632A GLN* 4.9 4.6 + - - +
666A VAL* 3.1 21.3 + - + +
667A THR* 3.9 7.4 - - - +
668A GLU 3.2 0.2 - - - -
669A ILE* 1.3 77.5 - - - +
671A LYS* 1.3 61.7 + - + +
672A ILE 3.4 8.8 + - - +
675A ILE* 3.1 21.8 + - - +
676A SER* 3.0 27.8 + - - +
677A ARG* 6.1 0.9 - - - +
678A ILE* 4.0 14.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 671 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
594A GLU* 6.0 0.2 - - - +
667A THR* 3.6 22.7 - - - +
668A GLU* 3.2 42.1 + - - +
669A ILE 3.2 0.4 - - - -
670A LYS* 1.3 74.8 - - + +
672A ILE* 1.3 65.0 + - - +
673A PRO* 3.2 8.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 672 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587A THR* 4.1 20.0 - - + +
590A GLN* 4.0 17.0 - - + -
591A ALA* 3.6 34.3 - - + +
594A GLU* 3.3 30.7 - - - +
669A ILE* 3.0 23.4 + - + +
670A LYS 3.4 5.9 - - - +
671A LYS* 1.3 77.0 - - - +
673A PRO* 1.3 85.5 - - + +
675A ILE* 3.3 25.9 + - + +
----------------------------------------------------------
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