Contacts of the helix formed by residues 23 - 28 (chain B) in PDB entry 4MVL
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 GLN 23 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B ASN* 2.6 37.4 + - - +
22B PHE* 1.3 79.3 + - - +
24B ASP* 1.3 66.4 + - - +
25B ASN* 3.3 9.7 - - - +
26B GLN* 3.2 34.7 + - + +
27B PHE* 3.2 23.9 + - - +
115B TYR* 2.9 19.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 24 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B PHE* 3.3 23.5 + - - -
23B GLN* 1.3 71.8 - - - +
25B ASN* 1.3 58.8 + - + +
26B GLN 3.1 5.5 + - - -
28B HIS* 3.3 12.1 + - - +
58B LEU* 3.6 30.9 - - + +
62B LYS* 4.4 22.5 - - - +
64B TYR* 2.7 24.6 + - - -
90B GLY 5.7 0.2 + - - -
92B PHE* 4.2 12.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 25 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B GLN* 4.1 18.0 - - - +
24B ASP* 1.3 74.0 + - + +
26B GLN* 1.3 64.1 + - - +
28B HIS* 3.1 29.4 + - + -
58B LEU* 3.8 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 26 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B GLN* 3.8 30.4 + - + +
24B ASP 3.1 0.6 - - - -
25B ASN* 1.3 90.1 + - - +
27B PHE* 1.3 60.4 + - - +
28B HIS* 3.2 6.4 + - - +
115B TYR* 3.5 43.1 - - + +
140B ARG* 2.9 21.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 27 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B PHE* 3.6 33.7 - + + -
23B GLN 3.2 9.7 + - - +
26B GLN* 1.3 72.9 - - - +
28B HIS* 1.3 63.6 + - - +
31B TRP* 2.8 52.7 + + - -
56B TYR* 4.0 38.4 - + - +
64B TYR* 3.5 21.3 - + - +
92B PHE* 5.6 1.6 - + - -
110B VAL* 4.2 14.4 - - + -
113B THR* 4.3 11.7 - - + -
115B TYR* 3.4 10.2 - - + -
119B ALA* 3.9 19.7 - - + -
121B VAL* 4.0 22.0 - - + -
138B TYR* 4.9 1.3 - + - -
140B ARG* 3.6 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 28 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B ASP 3.3 11.2 + - - +
25B ASN* 3.1 36.6 + - + -
26B GLN* 3.8 6.0 - - - -
27B PHE* 1.3 79.2 - - - +
29B GLY* 1.3 57.2 + - - +
56B TYR* 3.5 15.0 + - - +
58B LEU* 4.4 14.5 + - + +
64B TYR* 3.7 14.1 + - + -
140B ARG* 2.7 28.8 + - - -
----------------------------------------------------------
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