Contacts of the helix formed by residues 594 - 601 (chain A) in PDB entry 1MVW
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 594 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
547A ASP* 2.9 13.8 + - - -
593A SER* 1.3 73.3 - - - +
595A TRP* 1.3 59.6 + - - +
596A LEU 3.2 2.5 - - - -
597A GLU* 3.1 13.0 + - - +
598A MLY 2.7 47.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 595 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473A ASN 4.5 1.8 - - - -
474A SER* 2.8 20.7 + - - -
475A PHE* 3.0 42.7 - + + +
478A LEU* 4.0 28.3 - - + -
532A ILE* 5.3 1.6 - - + -
536A LEU* 3.9 26.5 - - + -
547A ASP* 4.0 0.6 + - - +
550A PHE* 4.1 21.1 - + + -
579A PHE* 4.4 16.2 - + - -
590A TYR* 4.3 15.9 - - + -
591A ASN 2.8 32.6 + - - -
592A ILE* 3.5 9.6 - - + -
593A SER 3.1 16.4 - - - +
594A GLY* 1.3 81.7 - - - +
596A LEU* 1.3 56.6 + - - +
598A MLY 3.6 7.2 - - - +
599A ASN* 2.6 41.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 596 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536A LEU* 3.8 18.8 - - + -
539A GLU* 4.6 11.7 - - + +
540A CYS* 3.8 13.3 - - - -
545A ALA* 3.8 27.8 - - + +
546A THR 3.5 30.3 - - - +
547A ASP* 3.4 13.7 + - - +
550A PHE* 3.8 28.0 - - + -
594A GLY 3.2 0.2 - - - -
595A TRP* 1.3 80.5 - - - +
597A GLU* 1.3 62.6 + - + +
599A ASN* 3.4 3.7 + - - +
600A MLY 3.2 41.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 597 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
547A ASP* 4.9 0.2 + - - -
594A GLY* 3.1 13.8 + - - +
596A LEU* 1.3 76.4 - - - +
598A MLY 1.3 60.3 + - - +
599A ASN 2.9 1.3 - - - -
600A MLY 2.5 33.2 + - - -
601A ASP 3.2 9.5 + - - -
602A PRO* 3.3 30.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MLY 598 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A MLY 4.8 9.9 - - - -
431A MLY 6.4 2.0 - - - -
472A PHE* 5.8 3.4 - - - -
474A SER* 4.2 16.7 + - - -
475A PHE* 3.9 23.3 - - + +
476A GLU* 2.7 42.5 + - + +
593A SER 3.6 24.0 - - - -
594A GLY* 2.7 31.2 + - - +
595A TRP* 3.6 5.8 - - - +
597A GLU* 1.3 75.5 - - - +
599A ASN* 1.3 61.0 + - - +
600A MLY 3.4 0.2 + - - -
601A ASP* 3.7 6.4 + - - +
602A PRO* 5.5 0.2 - - - -
649A VAL* 3.2 17.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 599 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475A PHE* 3.6 8.1 - - + -
536A LEU* 3.6 25.9 + - + +
537A GLU* 4.4 1.0 - - - +
540A CYS* 4.0 10.5 - - - -
595A TRP 2.6 19.8 + - - +
596A LEU 3.6 5.2 - - - +
598A MLY 1.3 77.0 + - - +
600A MLY 1.3 59.0 + - - +
601A ASP 3.5 0.2 - - - -
647A GLN 4.6 0.3 - - - +
648A THR* 2.8 18.9 + - - -
649A VAL* 2.0 82.5 + - + +
650A SER* 2.7 23.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MLY 600 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539A GLU 3.8 3.8 - - - -
540A CYS* 3.3 44.9 - - + +
541A MET 4.7 0.2 - - - -
542A PHE 2.8 33.7 - - - -
543A PRO* 4.1 13.5 - - - -
545A ALA* 4.7 14.6 - - - -
596A LEU* 3.2 28.9 - - - +
597A GLU* 2.5 23.7 + - - +
599A ASN* 1.3 75.9 + - - +
601A ASP* 1.3 68.6 + - - +
602A PRO* 3.9 11.4 - - + -
640A LYS* 3.2 30.2 + - - +
646A PHE 5.3 1.4 - - - +
647A GLN 5.4 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 601 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A MLY 3.5 40.1 + - - -
428A ALA* 6.0 0.2 - - - +
432A ALA* 5.5 0.3 - - - +
436A MLY 3.6 19.4 - - - -
597A GLU 3.2 2.2 + - - -
598A MLY 3.7 3.5 + - - +
599A ASN 3.5 1.4 - - - -
600A MLY 1.3 80.2 + - - +
602A PRO* 1.3 71.9 - - - +
603A LEU* 3.4 24.7 + - - +
640A LYS* 5.0 1.4 + - - -
646A PHE* 6.6 0.4 - - + -
649A VAL* 4.0 16.6 - - + -
----------------------------------------------------------
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