Contacts of the strand formed by residues 45 - 53 (chain D) in PDB entry 4IHB
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 VAL 45 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7D LEU 3.6 12.6 - - - +
8D TYR* 4.0 16.2 - - + -
36D LYS* 4.6 1.6 + - - -
38D ILE* 3.6 18.3 - - - +
43D ASN* 3.4 17.0 + - - +
44D PRO* 1.3 73.2 - - - +
46D TRP* 1.3 62.5 + - - +
47D ASN* 4.3 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 46 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6D ILE* 3.6 22.0 - - + +
7D LEU 2.9 4.9 + - - -
8D TYR* 4.0 8.7 - - - -
9D ALA* 3.6 20.0 - - + -
22D ALA* 3.3 16.4 + - + -
23D TYR* 3.7 19.7 - - - -
24D CYS* 4.0 10.1 - - + -
35D THR* 3.1 26.7 + - + -
36D LYS* 3.0 52.4 + - + +
38D ILE* 3.6 16.3 - - + +
44D PRO* 3.7 28.9 - - + -
45D VAL* 1.3 72.9 - - - +
47D ASN* 1.3 70.2 + - - +
48D GLU* 3.3 8.5 + - + +
69D VAL* 4.4 9.6 - - + -
117D LEU* 3.6 25.8 - - + -
204D FMT 3.1 9.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 47 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5D PHE* 5.8 3.7 - - - -
6D ILE 3.1 7.8 + - - -
7D LEU* 2.9 32.0 + - + +
45D VAL* 4.3 14.8 - - + -
46D TRP* 1.3 77.5 - - - +
48D GLU* 1.3 57.8 + - - +
204D FMT 2.7 28.6 + - - +
205D FMT 4.7 6.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 48 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4D VAL 3.7 0.7 - - - +
5D PHE* 3.3 7.8 - - - -
6D ILE 2.9 32.2 + - - +
34D ARG 4.1 1.9 - - - +
35D THR* 3.4 22.2 - - + -
36D LYS* 2.7 48.8 + - - +
46D TRP* 3.4 17.6 - - + +
47D ASN* 1.3 75.9 - - - +
49D GLY* 1.3 60.0 + - - +
50D PHE* 3.7 23.4 - - + -
204D FMT 3.6 12.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 49 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4D VAL 3.5 4.5 - - - -
5D PHE* 4.0 18.6 - - - -
47D ASN 4.4 0.2 + - - -
48D GLU* 1.3 73.4 - - - +
50D PHE* 1.3 72.4 - - - -
51D GLU* 5.6 2.2 - - - -
203D FMT 4.5 3.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 50 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2D LEU 3.6 1.0 - - - +
3D ARG* 3.3 6.4 - - - +
4D VAL* 2.8 38.1 + - + +
6D ILE* 3.5 34.1 - - + -
24D CYS 5.5 0.2 - - - -
26D ALA* 5.5 3.1 - - + -
33D LYS* 3.7 15.7 - - + -
34D ARG* 3.6 35.0 - - - -
35D THR* 3.9 7.6 - - + -
48D GLU* 3.7 26.2 - - + -
49D GLY* 1.3 79.1 - - - -
51D GLU* 1.3 66.7 + - - +
52D TRP* 3.7 25.8 - + + -
203D FMT 3.4 24.0 - - - -
207D FMT 3.6 11.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 51 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1D MET* 3.2 41.3 - - + +
2D LEU 3.3 5.2 - - - +
3D ARG* 4.4 15.0 - - + -
33D LYS* 3.4 8.4 + - - -
49D GLY 5.6 1.1 - - - +
50D PHE* 1.3 80.2 - - - +
52D TRP* 1.3 62.6 + - - +
53D ASP* 5.3 1.9 - - - +
202D FMT 3.4 17.5 + - - -
203D FMT 3.3 13.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 52 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1D MET* 3.1 5.1 - - - -
2D LEU* 2.8 58.4 + - + +
4D VAL* 3.6 24.9 - - + -
26D ALA* 3.6 42.4 - - + -
28D PHE* 3.2 47.0 + + + -
29D ALA* 4.9 2.9 - - + -
31D VAL* 2.9 30.1 + - + +
33D LYS* 3.3 34.4 - - + +
50D PHE* 3.7 20.0 - + + -
51D GLU* 1.3 74.6 - - - +
53D ASP* 1.3 66.6 + - - +
54D LEU* 3.3 0.7 + - - +
65D LEU* 4.3 6.1 - - + -
202D FMT 3.9 6.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 53 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0D PHE 4.0 4.0 - - - +
1D MET* 3.5 26.1 - - + +
29D ALA* 5.6 1.7 - - - +
51D GLU* 5.3 2.3 - - - +
52D TRP* 1.3 71.9 - - - +
54D LEU* 1.3 60.9 + - - +
55D LYS* 2.7 33.7 + - + +
57D ILE* 5.1 1.4 - - - +
126D ALA* 5.3 1.2 - - - +
202D FMT 3.3 25.8 + - - +
----------------------------------------------------------
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