Contacts of the helix formed by residues 25 - 37 (chain A) in PDB entry 1I4W
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 ASN 25 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A LEU* 3.8 2.1 - - + +
24A TRP* 1.3 87.0 - - + +
26A PRO* 1.3 70.0 - - - +
27A THR* 3.1 32.7 + - - +
28A VAL* 3.0 29.5 + - + +
29A TYR* 3.5 8.0 + - - -
233A GLU* 2.8 40.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 26 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A ILE 5.3 5.2 - - - +
24A TRP* 3.0 15.9 - - + +
25A ASN* 1.3 89.0 - - - +
27A THR* 1.3 63.0 + - - +
29A TYR* 3.2 3.8 + - + +
30A ASN* 3.1 31.1 + - - +
59A ILE* 4.9 2.9 - - + -
63A ILE* 3.9 28.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 27 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ASN* 3.1 22.0 + - - +
26A PRO* 1.3 78.6 - - - +
28A VAL* 1.3 64.1 + - + +
30A ASN* 3.5 8.8 + - - +
31A LYS* 3.3 32.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 28 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A LEU* 3.5 27.1 - - + -
25A ASN* 3.0 31.3 + - + +
27A THR* 1.3 76.0 - - + +
29A TYR* 1.3 66.6 + - - +
31A LYS* 2.8 26.8 + - - +
32A ILE* 2.9 23.1 + - + +
227A ILE* 4.3 10.5 - - + -
229A PHE* 4.2 26.7 - - + -
233A GLU* 3.8 12.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 29 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A TYR* 5.5 4.0 - - - +
23A LEU* 3.3 55.8 + - + +
25A ASN 3.5 8.3 + - - -
26A PRO 3.2 7.7 + - - +
28A VAL* 1.3 78.3 - - - +
30A ASN* 1.3 51.9 + - - +
32A ILE* 3.1 11.8 + - + +
33A PHE* 2.7 56.0 + + + -
57A VAL* 6.1 0.2 - - - +
59A ILE* 3.6 16.3 - - + +
60A GLN* 3.0 52.5 + - + +
63A ILE* 3.7 28.0 - - + -
171A TRP* 4.2 10.5 + + - -
343A XE 4.6 4.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 30 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A PRO* 3.1 20.2 + - - +
27A THR* 3.6 11.4 - - - +
28A VAL 3.1 0.8 - - - -
29A TYR* 1.3 75.5 - - - +
31A LYS* 1.3 57.0 + - + +
33A PHE* 3.3 1.0 + - - +
34A ASP* 2.8 44.2 + - - +
63A ILE* 4.3 8.1 - - - +
67A LYS* 3.1 34.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 31 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A THR* 3.3 24.1 + - + +
28A VAL* 2.8 17.6 + - - +
30A ASN* 1.3 79.0 - - + +
32A ILE* 1.3 56.3 + - - +
34A ASP* 3.5 7.6 + - - +
35A LYS* 3.0 23.4 + - - +
227A ILE* 3.1 34.4 - - + +
228A LEU 4.0 18.6 + - - +
229A PHE* 6.0 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 32 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A LEU* 4.3 4.5 - - + -
28A VAL* 2.9 28.4 + - + +
29A TYR* 3.3 14.4 - - + +
31A LYS* 1.3 74.4 - - - +
33A PHE* 1.3 58.9 + - + +
35A LYS* 3.0 6.0 + - - +
36A LEU* 2.7 50.0 + - + +
171A TRP* 4.2 14.6 - - + -
205A ILE* 4.2 4.3 - - + -
206A ALA* 3.8 17.9 - - + -
227A ILE* 3.4 17.7 - - + -
244A LEU* 3.6 35.0 - - + -
343A XE 4.3 6.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 33 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A TYR* 2.7 44.4 + + + +
30A ASN 3.9 2.9 - - - +
32A ILE* 1.3 74.3 - - + +
34A ASP* 1.3 61.6 + - - +
36A LEU* 3.9 9.4 - - + +
37A ASP* 3.1 20.8 + - - -
38A LEU* 4.1 20.4 - - + -
60A GLN* 4.3 11.9 - - + -
63A ILE* 4.0 24.5 - - + -
64A PHE* 3.6 40.6 - + + -
67A LYS* 4.2 18.8 - - + +
68A TYR* 4.1 23.1 + + - +
169A LEU* 6.4 0.4 - - + -
343A XE 4.0 21.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 34 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A ASN* 2.8 33.3 + - - +
31A LYS* 3.6 9.2 - - - +
33A PHE* 1.3 76.9 - - - +
35A LYS* 1.3 61.9 + - - +
37A ASP* 3.8 15.3 + - - +
67A LYS* 4.8 5.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 35 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A LYS 3.0 15.1 + - - +
32A ILE* 3.0 8.7 + - - +
34A ASP* 1.3 76.8 - - - +
36A LEU* 1.3 64.2 + - - +
37A ASP* 4.3 2.9 - - - +
203A LYS* 4.7 5.5 - - - +
205A ILE* 3.9 47.6 - - + +
224A TRP 3.0 16.4 + - - -
225A ASP* 3.0 30.2 + - - +
226A PRO* 4.3 0.7 - - - -
227A ILE* 4.0 14.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 36 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A ILE* 2.7 40.4 + - + +
33A PHE* 3.9 20.0 - - + +
35A LYS* 1.3 75.5 - - - +
37A ASP* 1.3 68.6 + - - +
38A LEU* 3.2 22.9 + - + +
41A THR* 6.0 0.3 - - - +
169A LEU* 4.0 23.8 - - + -
205A ILE* 4.1 22.4 - - + -
244A LEU* 5.1 1.1 - - + -
246A GLU* 3.9 34.2 - - - +
343A XE 4.3 9.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 37 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A PHE 3.1 14.5 + - - -
34A ASP* 3.8 12.2 + - - +
35A LYS 3.3 3.3 - - - +
36A LEU* 1.3 79.5 - - - +
38A LEU* 1.3 66.3 + - - +
39A THR* 3.3 7.5 + - - -
40A LYS* 2.9 43.9 + - + +
41A THR* 4.8 1.4 - - - +
68A TYR* 5.5 0.7 - - - -
----------------------------------------------------------
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