Contacts of the helix formed by residues 47 - 52 (chain A) in PDB entry 4GUP
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 ALA 47 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A HIS* 6.0 0.4 - - + -
32A PRO 3.8 12.8 - - - +
33A ILE* 3.9 1.2 + - - -
45A PRO* 3.6 5.6 - - - +
46A ARG* 1.4 79.3 - - - +
48A PRO* 1.4 74.3 - - + +
49A TRP* 3.5 29.2 - - + +
50A MET* 3.3 27.6 - - + +
51A ALA* 3.5 5.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 48 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A ALA* 1.4 81.0 - - + +
49A TRP* 1.3 71.6 + - + +
50A MET 3.0 5.4 - - - -
51A ALA* 3.0 23.2 + - + +
52A GLU* 3.1 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 49 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A VAL* 4.8 4.9 - - + -
31A HIS* 4.5 19.1 + + + -
33A ILE* 3.5 22.2 - - + -
47A ALA* 3.7 17.5 - - + +
48A PRO* 1.3 88.4 - - + +
50A MET* 1.3 87.4 + - + +
52A GLU* 2.9 17.6 - - - +
53A ASN* 2.7 26.9 + - - +
168A PHE* 3.9 20.6 - - + -
171A TYR* 3.3 41.8 - - + +
174A ASP* 3.9 22.5 + - - -
175A THR* 3.9 25.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 50 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A ILE* 3.8 17.9 - - + +
34A THR* 3.8 28.9 - - + -
45A PRO* 3.7 14.6 - - + -
47A ALA* 3.3 24.0 - - + +
48A PRO 3.0 0.2 - - - -
49A TRP* 1.3 108.7 - - + +
51A ALA* 1.3 65.8 + - - +
52A GLU 3.0 8.0 - - - +
54A LEU* 3.5 41.6 - - + +
58A HIS* 5.5 0.4 - - + -
59A TRP* 3.6 7.1 - - + -
168A PHE* 3.7 29.8 - - + -
171A TYR* 5.2 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 51 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A PRO* 3.9 20.7 - - + +
47A ALA 3.5 4.8 + - - +
48A PRO* 3.0 14.0 + - + +
50A MET* 1.3 80.5 - - - +
52A GLU* 1.4 59.3 - - - +
54A LEU 3.5 14.0 - - - +
59A TRP* 4.7 4.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 52 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A PRO* 3.1 29.4 - - - +
49A TRP* 2.9 16.0 - - - +
50A MET 3.0 5.4 - - - +
51A ALA* 1.4 74.0 - - - +
53A ASN* 1.3 81.2 + - - +
54A LEU 2.9 13.0 + - - -
----------------------------------------------------------
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