Contacts of the helix formed by residues 289 - 295 (chain 3) 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 ILE 289 (chain 3).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1663 TYR* 3.7 40.4 - - + -
1713 LEU* 3.6 32.8 - - + -
2853 CYS* 4.0 7.6 - - + -
2863 ASP* 3.1 42.2 + - + +
2873 ILE 3.2 0.8 - - - -
2883 ASP* 1.4 76.9 - - + +
2903 ARG* 1.3 65.8 + - - +
2913 LYS* 3.3 5.6 - - - +
2923 ASP* 3.0 16.8 + - - +
2933 LEU* 3.3 30.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 290 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2823 ILE* 3.4 36.5 + - + +
2833 MET* 3.9 47.6 + - - +
2853 CYS* 2.4 33.2 + - + -
2863 ASP 3.3 9.1 + - - +
2873 ILE* 3.8 10.7 - - - +
2883 ASP 3.4 1.2 - - - -
2893 ILE* 1.3 78.7 - - - +
2913 LYS* 1.4 61.9 + - - +
2923 ASP 3.3 0.5 + - - -
2933 LEU* 4.1 7.7 - - - +
2943 TYR* 3.1 32.7 + - + -
3253 MET* 4.7 5.2 - - + -
2015 VAL* 5.0 7.1 - - - +
2025 THR* 1.7 43.8 + - - +
2055 GLU* 5.8 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 291 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2873 ILE 4.7 2.3 + - - +
2883 ASP* 3.0 29.4 + - - +
2893 ILE* 3.2 1.6 + - - +
2903 ARG* 1.4 75.4 - - - +
2923 ASP* 1.4 97.2 + - - +
2943 TYR* 3.4 2.9 + - - +
2953 ALA* 3.2 23.6 + - - +
3253 MET* 3.7 25.3 - - + +
3263 LYS* 4.5 2.1 - - - +
2045 ALA* 6.3 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 292 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1493 THR* 3.9 22.6 - - + +
1663 TYR* 4.0 20.1 + - - -
2893 ILE* 3.0 9.7 + - - +
2913 LYS* 1.4 105.5 + - - +
2933 LEU* 1.3 67.8 + - - +
2953 ALA* 3.1 6.0 + - - -
2963 ASN* 2.9 31.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 293 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1493 THR* 3.8 22.7 - - + -
1503 GLY* 3.8 20.9 - - - +
1513 ILE* 3.4 31.1 - - + +
1643 PRO* 4.4 7.2 - - + -
1653 ILE 4.3 4.9 - - - +
2823 ILE* 4.5 17.5 - - + -
2853 CYS* 4.0 21.5 - - + -
2893 ILE* 3.3 42.3 + - + +
2903 ARG* 4.1 7.4 - - - +
2923 ASP* 1.3 77.9 - - - +
2943 TYR* 1.3 62.9 + - - +
2963 ASN 3.0 21.3 + - - -
2973 ASN* 3.7 1.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 294 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2793 TYR* 3.4 20.0 - + - -
2823 ILE* 3.6 36.8 - - + +
2833 MET* 3.4 32.9 - - + +
2903 ARG* 3.1 28.8 + - + +
2913 LYS 3.7 3.4 - - - +
2923 ASP 3.2 1.2 - - - -
2933 LEU* 1.3 77.3 - - - +
2953 ALA* 1.3 59.7 + - - +
2963 ASN 3.1 1.1 + - - -
2973 ASN* 4.6 1.8 + - - +
3173 ILE* 4.0 20.8 - - + +
3213 ALA* 3.6 21.1 - - + +
3223 PRO* 4.7 0.4 - - + -
3253 MET* 3.4 31.0 - - + -
3263 LYS 3.2 16.4 - - - +
3273 ILE* 3.4 16.2 - - + -
3283 LYS 2.8 22.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 295 (chain 3).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2913 LYS 3.2 11.2 + - - +
2923 ASP* 3.1 3.7 + - - +
2943 TYR* 1.3 78.3 - - - +
2963 ASN* 1.4 75.3 + - - +
3263 LYS* 3.8 32.3 - - + +
3283 LYS* 3.2 33.6 - - - +
3303 ILE* 3.8 0.9 - - - +
----------------------------------------------------------
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