Contacts of the helix formed by residues 45 - 54 (chain A) in PDB entry 4FE1
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 THR 45 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A THR* 1.3 70.2 - - - +
46A THR* 1.3 67.2 + - - +
48A ILE* 2.9 31.9 + - + +
49A TRP* 3.5 16.7 + - - -
717A ILE* 3.3 20.4 - - + +
718A GLN 2.9 7.8 + - - +
719A PRO* 3.6 22.9 - - + -
720A ARG 2.8 34.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 46 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A THR* 3.4 15.5 + - - -
45A THR* 1.3 78.1 + - - +
47A TRP* 1.3 51.4 + - - +
49A TRP* 3.0 15.3 + - + +
50A ASN* 2.7 61.0 + - - +
694A ARG* 5.5 0.7 + - - -
720A ARG* 3.6 19.4 + - - +
721A ALA 4.6 5.2 + - - -
723A SER* 5.7 11.2 - - - +
726A GLN* 6.2 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 47 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A PRO* 3.1 39.5 - - + -
37A THR 4.8 2.5 - - - -
38A LEU* 3.0 58.9 + - + +
41A GLY* 3.4 18.1 - - - +
42A PRO* 3.4 43.3 - - + -
43A GLN 4.8 0.9 - - - +
44A THR* 3.2 16.8 + - - +
45A THR 3.0 0.2 + - - -
46A THR* 1.3 76.5 - - - +
48A ILE* 1.3 66.5 + - + +
50A ASN* 3.0 9.5 + - - +
51A LEU* 2.7 56.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 48 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A PRO* 5.5 0.2 - - + -
44A THR 5.0 0.7 - - - +
45A THR* 2.9 28.5 + - + +
47A TRP* 1.3 94.2 - - + +
49A TRP* 1.3 74.7 + - + +
51A LEU* 3.1 12.2 + - - +
52A HIS* 2.9 38.1 + - + +
717A ILE* 4.6 20.6 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
45A THR* 3.5 30.4 + - - -
46A THR* 3.0 14.8 + - + +
48A ILE* 1.3 85.5 - - + +
50A ASN* 1.3 69.4 + - - +
52A HIS* 3.0 13.1 + + + +
53A ALA* 2.9 23.5 + - - +
720A ARG 5.2 3.1 + - - -
722A LEU* 3.5 26.4 - - + +
726A GLN* 3.3 38.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 50 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A THR* 5.5 3.0 + - - -
38A LEU* 4.0 15.9 - - + +
46A THR* 2.7 39.4 + - - +
47A TRP* 3.4 9.8 - - - +
49A TRP* 1.3 77.7 - - - +
51A LEU* 1.3 63.1 + - - +
53A ALA* 3.0 8.4 + - - +
54A LEU* 2.8 42.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 51 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A PRO* 3.6 9.0 - - + -
32A GLY* 3.5 24.5 - - - +
34A PHE* 3.2 24.5 - - + -
38A LEU* 4.1 11.8 - - + +
47A TRP* 2.7 51.6 + - + +
48A ILE* 3.1 14.6 + - + +
50A ASN* 1.3 72.7 - - - +
52A HIS* 1.3 79.4 + - + +
55A ALA* 3.2 21.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 52 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A ILE* 2.9 42.2 + - + +
49A TRP* 3.0 12.2 + + + +
51A LEU* 1.3 92.7 - - + +
53A ALA* 1.3 65.0 + - - +
54A LEU 3.1 2.0 - - - -
55A ALA* 3.1 23.3 + - + +
56A HIS 4.8 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 53 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A TRP* 2.9 16.8 + - + +
50A ASN* 3.6 9.9 - - - +
52A HIS* 1.3 76.9 - - - +
54A LEU* 1.3 63.1 + - + +
55A ALA 3.9 0.2 + - - -
56A HIS 5.2 0.9 + - - -
57A ASP* 4.6 6.4 + - - +
575A ARG* 4.1 32.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 54 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A PHE* 3.8 14.4 - - + -
35A ASP* 3.3 31.0 - - + +
37A THR* 3.9 7.0 - - + +
38A LEU* 4.8 1.8 - - + -
50A ASN* 2.8 35.2 + - + +
53A ALA* 1.3 82.2 - - + +
55A ALA* 1.3 66.2 + - - +
56A HIS 3.4 2.2 - - - -
57A ASP* 3.0 37.3 + - + +
60A THR* 4.5 10.3 - - + +
61A HIS* 3.5 11.4 - - - -
575A ARG* 4.2 16.4 - - - +
----------------------------------------------------------
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