Contacts of the helix formed by residues 13 - 26 (chain A) in PDB entry 1CEZ
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 ASP 13 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A PHE 5.1 1.6 - - - +
12A SER* 1.3 75.6 + - - +
14A ILE* 1.3 62.4 + - + +
16A LEU* 4.0 6.3 - - - +
17A ALA* 3.2 23.6 + - - +
153A ARG* 2.7 49.6 + - - +
154A ILE* 3.4 31.4 - - + +
157A LEU* 3.7 16.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 14 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A SER* 2.9 11.8 - - - +
13A ASP* 1.3 80.9 - - + +
15A GLU* 1.3 64.3 + - + +
17A ALA* 3.7 6.5 + - - +
18A ALA* 3.5 19.8 + - + +
157A LEU* 4.7 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 15 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ASP 5.1 0.7 - - - +
11A PHE* 3.7 28.7 - - + -
12A SER* 2.9 37.0 + - - +
14A ILE* 1.3 78.8 - - + +
16A LEU* 1.3 60.4 + - - +
17A ALA 3.2 0.2 - - - -
18A ALA* 3.2 2.6 + - - +
19A ILE* 2.7 38.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 16 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A ALA* 4.1 24.0 - - + +
9A ASN 5.9 0.4 - - - +
11A PHE* 3.7 28.0 - - + +
12A SER 2.8 20.8 + - - +
13A ASP* 4.3 5.2 - - - +
15A GLU* 1.3 76.5 - - - +
17A ALA* 1.3 63.8 + - - +
19A ILE* 4.0 3.6 - - + -
20A PRO* 3.0 22.5 - - - +
154A ILE* 4.0 26.9 - - + -
194A GLY* 3.7 29.4 - - - +
289A ASN* 3.2 21.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 17 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ASP 3.2 18.9 + - - +
14A ILE* 3.7 7.6 - - - +
15A GLU 3.2 0.4 - - - -
16A LEU* 1.3 79.3 - - - +
18A ALA* 1.3 57.8 + - + +
20A PRO* 4.1 0.9 - - - +
21A PHE* 5.1 1.4 - - - +
154A ILE* 4.0 8.4 - - + +
157A LEU* 3.6 15.5 - - + +
158A GLU* 3.2 60.4 - - - +
161A HIS* 4.3 5.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 18 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ILE 3.5 12.7 + - - +
15A GLU* 3.2 3.6 + - - +
16A LEU 3.1 0.2 - - - -
17A ALA* 1.3 77.5 - - + +
19A ILE* 1.3 67.5 + - - +
20A PRO* 3.1 4.2 - - - -
21A PHE* 3.3 1.8 + - - +
22A ASN* 3.2 31.4 + - - +
161A HIS* 3.2 39.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 19 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A PHE* 4.8 13.5 - - + -
15A GLU* 2.7 23.7 + - + +
16A LEU* 3.4 7.0 - - - +
18A ALA* 1.3 73.3 - - - +
20A PRO* 1.4 66.3 - - + +
22A ASN* 4.3 5.4 - - + +
23A THR* 2.6 36.8 + - + +
192A SER* 3.6 33.4 - - - +
194A GLY* 3.6 11.7 - - - +
195A LEU* 3.5 13.0 - - + -
289A ASN* 3.2 17.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 20 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A LEU 3.0 10.3 - - - +
17A ALA 4.1 0.9 - - - +
18A ALA 3.4 4.0 - - - -
19A ILE* 1.4 95.5 - - + +
21A PHE* 1.3 54.3 + - - +
23A THR* 3.3 6.9 + - + +
24A LEU* 2.7 39.7 + - - +
37A LEU* 4.4 7.6 - - + -
158A GLU* 3.7 17.5 - - - +
195A LEU* 3.6 10.8 - - + -
287A TRP* 3.5 26.5 - - + +
289A ASN* 3.2 26.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 21 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A ALA 5.1 2.4 + - - +
18A ALA* 3.3 2.4 + - - +
20A PRO* 1.3 79.7 - - - +
22A ASN* 1.3 58.3 + - - +
24A LEU* 3.6 2.2 - - - +
25A ALA* 2.7 39.1 + - + +
30A GLU* 4.4 15.0 - - + -
33A ALA* 4.1 9.6 - - + +
34A ARG* 3.8 31.4 - - + -
37A LEU* 3.7 22.4 - - + +
158A GLU* 5.4 0.2 + - - -
161A HIS* 3.3 39.0 - + + -
162A PHE* 3.2 37.2 - - + -
164A LYS 4.1 17.0 - - - -
166A VAL* 4.3 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 22 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ALA* 3.2 25.4 - - - +
19A ILE* 4.3 5.7 - - + +
21A PHE* 1.3 84.6 - - - +
23A THR* 1.3 52.5 + - - +
25A ALA* 3.2 5.6 + - - +
26A ASP* 2.7 34.7 + - - +
161A HIS* 3.0 25.9 + - - -
166A VAL* 5.5 6.5 - - - +
167A GLU* 5.3 6.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 23 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ILE* 2.6 32.3 - - + +
20A PRO* 3.4 10.5 - - + +
22A ASN* 1.3 70.2 - - - +
24A LEU* 1.3 64.9 + - - +
25A ALA 3.0 1.6 - - - -
26A ASP* 3.1 11.8 + - - -
27A HIS* 2.7 38.6 + - - -
186A VAL* 5.2 1.0 - - - +
190A MET 5.1 6.6 + - - -
191A LEU* 5.4 1.2 - - - +
192A SER* 5.9 2.0 - - - -
195A LEU* 3.6 25.7 - - + +
287A TRP* 4.2 15.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 24 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A PRO 2.7 20.7 + - - +
21A PHE* 3.7 1.3 - - - +
23A THR* 1.3 73.7 + - - +
25A ALA* 1.3 53.4 + - - +
27A HIS 2.1 27.6 - - - +
28A TYR* 3.4 27.8 - - + +
33A ALA* 3.6 23.4 - - + +
36A GLN* 4.0 18.6 - - + -
37A LEU* 4.2 17.5 - - + -
186A VAL* 5.8 0.2 - - + -
273A VAL* 4.5 4.7 - - + -
287A TRP* 3.2 70.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 25 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A PHE* 2.7 26.3 + - + +
22A ASN* 3.5 7.2 - - - +
24A LEU* 1.3 74.6 - - - +
26A ASP* 1.3 67.0 + - - +
27A HIS 2.9 8.1 - - - +
29A GLY* 3.0 18.3 + - - -
30A GLU* 4.2 17.4 + - + +
33A ALA* 3.7 13.7 - - + -
166A VAL* 4.8 13.0 - - + -
172A LYS* 4.2 5.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 26 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ASN 2.7 18.3 + - - +
23A THR* 3.3 13.9 - - - +
25A ALA* 1.3 73.2 - - - +
27A HIS* 1.3 77.5 + - + +
29A GLY 4.9 0.2 + - - -
172A LYS* 5.0 9.3 - - - +
----------------------------------------------------------
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