Contacts of the helix formed by residues 30 - 48 (chain A) in PDB entry 4Y1W
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 SER 30 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A ARG* 1.3 78.5 - - - +
31A GLU* 1.3 64.6 + - - +
32A GLU* 3.5 9.5 + - - +
33A GLU* 3.1 24.4 + - - +
34A VAL* 2.9 22.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 31 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A SER* 1.3 72.8 - - - +
32A GLU* 1.3 58.4 + - - +
34A VAL* 3.9 5.4 - - - +
35A THR* 2.9 45.3 + - - +
152A ARG* 6.2 3.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 32 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A SER* 3.2 8.7 + - - +
31A GLU* 1.3 77.6 - - - +
33A GLU* 1.3 58.5 + - - +
35A THR* 3.8 5.7 - - - -
36A GLN* 3.0 29.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 33 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A ARG* 3.6 35.0 + - + +
30A SER* 3.1 21.0 + - - +
32A GLU* 1.3 76.0 - - - +
34A VAL* 1.3 66.3 + - - +
36A GLN* 3.2 6.2 + - + +
37A LEU* 2.9 40.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 34 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A ARG* 4.0 15.0 - - + +
30A SER 2.9 19.7 + - - +
31A GLU* 3.9 6.5 - - - +
33A GLU* 1.3 75.8 - - - +
35A THR* 1.3 58.9 + - - +
37A LEU* 3.3 9.6 + - + +
38A ALA* 2.9 27.2 + - - +
146A LEU* 3.9 19.1 - - + +
148A GLU* 3.9 35.0 - - + +
149A VAL* 4.6 8.3 - - + -
152A ARG* 4.4 19.5 - - - +
189A GLU* 4.9 8.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 35 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A GLU* 2.9 30.6 + - - +
32A GLU* 3.8 6.1 - - - -
34A VAL* 1.3 79.2 - - - +
36A GLN* 1.3 57.1 + - - +
38A ALA* 3.3 7.6 + - + +
39A GLU* 2.9 28.8 + - + +
189A GLU* 5.5 4.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 36 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A GLU* 3.0 18.0 + - + +
33A GLU* 3.2 7.8 + - + +
35A THR* 1.3 76.1 - - - +
37A LEU* 1.3 59.3 + - + +
39A GLU* 3.1 16.6 + - - +
40A ASP* 2.8 63.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 37 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A ARG* 3.4 37.5 - - - +
33A GLU* 2.9 40.0 + - + +
34A VAL* 3.6 6.1 - - - +
36A GLN* 1.3 76.7 - - + +
38A ALA* 1.3 57.5 + - - +
40A ASP* 3.3 15.6 + - + +
41A PHE* 3.0 28.3 + - - +
146A LEU* 4.0 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 38 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A VAL 2.9 16.9 + - - +
35A THR* 3.6 6.7 - - - +
37A LEU* 1.3 76.2 - - - +
39A GLU* 1.3 57.5 + - - +
41A PHE* 3.2 8.5 + - - +
42A LYS* 2.9 28.4 + - - +
146A LEU* 4.3 5.3 - - + +
181A ALA* 5.6 0.5 - - - +
189A GLU* 3.6 38.6 - - + -
190A ALA 4.4 4.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 39 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A THR* 2.9 17.0 + - + +
36A GLN* 3.5 22.4 - - - +
38A ALA* 1.3 72.7 - - - +
40A ASP* 1.3 66.1 + - - +
42A LYS* 3.2 37.8 + - - +
43A ASP* 2.9 42.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 40 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A GLN* 2.8 47.8 + - - +
37A LEU* 3.6 17.2 - - + +
39A GLU* 1.3 76.5 - - - +
41A PHE* 1.3 55.9 + - - +
43A ASP* 3.3 11.1 + - - +
44A TRP* 2.9 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 41 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A LEU 3.0 17.4 + - - +
38A ALA 3.6 4.9 - - - +
39A GLU 3.2 0.2 - - - -
40A ASP* 1.3 74.0 - - - +
42A LYS* 1.3 60.6 + - - +
44A TRP* 3.4 26.2 + + + +
45A SER* 2.8 34.1 + - - -
111A TYR* 3.7 28.9 - + - -
145A THR* 3.7 22.9 - - + +
179A THR* 3.4 21.3 - - - -
181A ALA* 3.6 11.2 - - + -
190A ALA* 3.5 37.2 - - + -
191A GLU 4.3 0.4 - - - -
192A VAL* 3.8 14.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 42 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A ALA 2.9 14.4 + - - +
39A GLU* 3.5 39.8 + - - +
41A PHE* 1.3 77.4 - - - +
43A ASP* 1.3 65.4 + - - +
45A SER* 3.2 2.9 + - - -
46A LYS* 3.0 51.0 + - + +
181A ALA* 3.4 32.1 - - + +
182A GLY 5.4 0.2 - - - +
184A SER 5.3 9.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 43 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A GLU* 2.9 42.5 + - - +
40A ASP* 3.6 9.9 - - - +
42A LYS* 1.3 82.0 - - - +
44A TRP* 1.3 62.7 + - - +
46A LYS* 3.4 12.4 + - - +
47A ALA* 3.0 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 44 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A ASP 2.9 16.9 + - - +
41A PHE* 3.7 33.2 - + + +
43A ASP* 1.3 76.0 - - - +
45A SER* 1.3 81.2 + - - +
47A ALA* 3.2 7.4 + - + +
48A SER* 2.8 54.8 + - - -
109A PRO* 4.9 0.2 - - + -
110A LYS 3.5 25.1 - - - -
111A TYR* 4.3 13.5 - + - -
179A THR* 3.8 23.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 45 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A PHE* 2.8 26.6 + - - -
42A LYS* 3.5 5.4 - - - -
43A ASP 3.2 0.4 - - - -
44A TRP* 1.3 90.0 - - - +
46A LYS* 1.3 61.6 + - - +
48A SER* 3.2 9.2 + - - -
49A ASN* 3.7 4.0 + - - +
109A PRO* 3.5 19.3 - - - +
179A THR* 2.7 37.1 + - - +
181A ALA* 3.8 1.6 - - - +
182A GLY* 3.6 18.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 46 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A LYS* 3.0 43.1 + - + +
43A ASP* 3.7 11.6 + - - +
45A SER* 1.3 75.6 - - - +
47A ALA* 1.3 62.0 + - - +
48A SER 3.1 1.3 + - - -
49A ASN* 3.4 28.5 + - - +
182A GLY* 3.5 29.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 47 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A ASP 3.0 18.1 + - - +
44A TRP* 3.2 9.2 + - + +
46A LYS* 1.3 77.0 - - - +
48A SER* 1.3 60.2 + - - +
49A ASN 3.5 3.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 48 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A TRP* 2.8 51.7 + - - -
45A SER 3.8 5.2 - - - -
46A LYS 3.1 1.0 - - - -
47A ALA* 1.3 76.3 - - - +
49A ASN* 1.3 68.6 + - - +
50A GLY* 3.4 2.8 + - - -
109A PRO* 3.6 24.1 - - - +
----------------------------------------------------------
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