Contacts of the helix formed by residues 289 - 295 (chain 1) 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 1).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1661 TYR* 3.7 39.0 - - + -
1711 LEU* 3.6 32.5 - - + -
2851 CYS* 4.0 7.6 - - + -
2861 ASP* 3.1 42.8 + - + +
2871 ILE 3.2 1.0 - - - -
2881 ASP* 1.4 75.8 - - - +
2901 ARG* 1.3 65.6 + - - +
2911 LYS* 3.3 5.8 - - - +
2921 ASP* 3.0 15.6 + - - +
2931 LEU* 3.3 30.6 + - + +
633 GLY 4.8 0.2 - - - -
643 ILE* 4.0 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 290 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2821 ILE* 3.4 36.3 + - + +
2831 MET* 3.9 44.0 + - - +
2851 CYS* 2.4 33.4 + - + -
2861 ASP 3.3 11.8 + - - +
2871 ILE* 3.8 25.9 - - - +
2881 ASP 3.4 1.4 - - - -
2891 ILE* 1.3 78.1 - - - +
2911 LYS* 1.4 61.5 + - - +
2921 ASP 3.3 0.3 + - - -
2931 LEU* 4.1 8.2 - - - +
2941 TYR* 3.1 32.3 + - + -
3251 MET* 4.7 5.6 - - + -
2023 THR* 2.8 38.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 291 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2871 ILE 4.7 2.5 + - - +
2881 ASP* 3.0 30.7 + - - +
2891 ILE* 3.2 1.2 + - - +
2901 ARG* 1.4 75.8 - - - +
2921 ASP* 1.4 96.7 + - - +
2941 TYR* 3.4 3.1 + - - +
2951 ALA* 3.2 22.9 + - - +
3251 MET* 3.7 25.1 - - + +
3261 LYS* 4.5 2.1 + - - +
443 MET* 5.3 8.2 - - - +
603 SER 4.4 14.6 - - - +
613 LYS* 5.3 11.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 292 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1491 THR* 3.9 23.5 - - + +
1661 TYR* 4.0 20.1 + - - -
2891 ILE* 3.0 9.4 + - - +
2911 LYS* 1.4 103.3 + - - +
2931 LEU* 1.3 68.5 + - - +
2951 ALA* 3.1 5.5 + - - -
2961 ASN* 2.9 31.5 + - - +
443 MET* 4.4 19.8 - - - +
643 ILE* 5.9 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 293 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1491 THR* 3.8 22.7 - - + -
1501 GLY* 3.8 20.0 - - - +
1511 ILE* 3.4 30.8 - - + +
1641 PRO* 4.4 6.3 - - + -
1651 ILE 4.3 4.9 - - - +
2821 ILE* 4.5 17.7 - - + -
2851 CYS* 4.0 22.0 - - + -
2891 ILE* 3.3 42.1 + - + +
2901 ARG* 4.1 7.0 - - - +
2921 ASP* 1.3 78.0 - - - +
2941 TYR* 1.3 62.4 + - - +
2961 ASN 3.0 21.0 + - - -
2971 ASN* 3.7 1.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 294 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2791 TYR* 3.4 19.8 - + - -
2821 ILE* 3.6 36.8 - - + +
2831 MET* 3.4 32.1 - - + +
2901 ARG* 3.1 28.5 + - + +
2911 LYS 3.7 3.4 - - - +
2921 ASP 3.2 1.2 - - - -
2931 LEU* 1.3 79.3 - - - +
2951 ALA* 1.3 59.6 + - - +
2961 ASN 3.1 1.1 + - - -
2971 ASN* 4.6 2.1 + - - +
3171 ILE* 4.0 20.5 - - + +
3211 ALA* 3.6 20.9 - - + +
3221 PRO* 4.7 0.2 - - + -
3251 MET* 3.4 31.6 - - + -
3261 LYS 3.2 15.3 - - - +
3271 ILE* 3.4 16.6 - - + -
3281 LYS 2.8 21.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 295 (chain 1).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1471 ARG* 4.6 0.2 + - - -
2911 LYS 3.2 11.7 + - - +
2921 ASP* 3.1 3.9 + - - +
2941 TYR* 1.3 77.9 - - - +
2961 ASN* 1.3 75.3 + - - +
3261 LYS* 3.8 32.1 - - + +
3281 LYS* 3.2 33.7 - - + +
3301 ILE* 3.8 1.4 - - - +
----------------------------------------------------------
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