Contacts of the helix formed by residues 14 - 27 (chain A) in PDB entry 1ECX
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 14 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ARG* 3.6 5.3 + - - +
13A VAL* 1.3 76.5 - - - +
15A ASP* 1.3 68.0 + - - +
16A ARG* 2.9 53.2 + - - +
17A VAL* 2.8 32.4 + - + +
18A LEU* 3.0 10.4 + - - +
205A HIS* 3.4 17.5 + - + +
253A ILE* 4.5 6.2 - - + +
355A LYS* 4.6 2.6 + - - -
356A TYR* 2.7 35.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 15 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ARG* 2.6 35.4 + - - +
13A VAL 4.1 0.9 - - - +
14A ASP* 1.3 74.9 + - - +
16A ARG* 1.3 63.0 + - + +
18A LEU* 3.4 10.3 + - - +
19A GLU* 3.0 25.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 16 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ASP* 2.9 35.1 + - - +
15A ASP* 1.3 80.9 - - + +
17A VAL* 1.3 62.5 + - - +
19A GLU* 3.4 9.2 + - - +
20A GLU* 3.4 24.8 + - - +
249A ARG* 4.3 18.4 - - - +
253A ILE* 3.4 39.7 - - + +
257A GLU* 3.0 28.1 + - - -
355A LYS* 4.1 0.2 - - - +
356A TYR* 3.2 13.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 17 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A VAL* 3.8 14.1 - - + -
14A ASP* 2.8 28.5 + - + +
16A ARG* 1.3 77.2 - - - +
18A LEU* 1.3 61.3 + - - +
20A GLU* 3.3 5.7 + - - +
21A MET* 3.1 26.3 + - - +
205A HIS 4.0 1.6 - - - +
207A PRO* 4.4 5.6 - - + -
246A GLY* 3.2 34.7 - - - +
249A ARG* 4.3 8.7 - - + -
250A ALA* 3.8 30.1 - - + +
253A ILE* 4.3 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 18 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A VAL* 3.9 16.3 - - + +
14A ASP 3.0 11.4 + - - +
15A ASP* 3.9 12.6 - - - +
17A VAL* 1.3 74.0 - - - +
19A GLU* 1.3 67.7 + - - +
21A MET* 3.1 27.3 + - + +
22A ILE* 3.1 37.7 + - + +
25A TYR* 5.7 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 19 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ASP 3.0 17.5 + - - +
16A ARG* 3.5 9.8 - - - +
18A LEU* 1.3 77.1 - - - +
20A GLU* 1.3 65.1 + - + +
22A ILE* 3.7 19.5 + - + +
23A VAL* 4.0 10.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 20 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ARG 3.4 13.4 + - - +
17A VAL* 3.3 8.2 + - - +
18A LEU 3.1 0.4 - - - -
19A GLU* 1.3 78.2 - - + +
21A MET* 1.3 64.6 + - + +
23A VAL* 3.5 11.7 + - - +
24A PHE* 3.3 22.8 - - + -
52A LYS* 6.1 0.5 - - - -
245A VAL* 3.9 23.8 - - + +
246A GLY* 5.7 0.7 - - - -
249A ARG* 3.0 45.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 21 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A VAL* 5.0 4.5 - - - -
17A VAL* 3.1 19.6 + - - +
18A LEU* 3.1 22.0 + - + +
20A GLU* 1.3 74.6 - - - +
22A ILE* 1.3 67.3 + - - +
24A PHE* 2.9 22.8 + - - +
25A TYR* 3.5 38.8 + - + +
207A PRO* 3.5 44.2 - - + -
242A PRO* 3.2 32.9 - - - +
243A GLY* 4.1 2.0 - - - -
245A VAL* 5.6 0.2 - - - -
246A GLY* 3.8 8.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 22 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A LEU* 3.1 39.9 + - + +
19A GLU* 3.9 11.0 - - + +
21A MET* 1.3 76.8 - - - +
23A VAL* 1.3 64.9 + - + +
25A TYR* 3.0 26.5 + - + +
26A ARG* 3.1 37.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 23 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A GLU 4.1 13.0 - - - +
20A GLU* 3.5 12.3 + - - +
21A MET 3.0 1.0 + - - -
22A ILE* 1.3 79.8 - - + +
24A PHE* 1.3 63.9 + - + +
26A ARG* 5.0 0.7 - - - -
27A GLU* 3.0 32.8 + - + +
28A LYS* 2.8 58.5 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 24 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A GLU* 3.3 22.4 - - + -
21A MET* 2.9 9.3 + - - +
23A VAL* 1.3 81.7 - - + +
25A TYR* 1.3 58.8 + - - +
28A LYS* 3.3 34.5 - - + +
29A TYR* 3.2 24.9 - - - +
42A ALA* 5.3 2.9 - - - -
45A HIS* 3.4 56.8 - + + -
241A VAL* 3.8 17.9 - - + -
242A PRO* 3.8 26.6 - - + +
245A VAL* 3.6 30.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 25 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A LEU* 5.7 3.6 - - + -
21A MET* 3.5 40.1 + - + +
22A ILE* 3.0 20.9 + - + +
24A PHE* 1.3 80.2 - - - +
26A ARG* 1.3 63.8 + - + +
29A TYR* 3.8 14.9 - - - +
240A ASN* 5.0 6.0 + - - -
242A PRO* 3.7 31.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 26 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ILE* 3.1 35.9 - - + +
23A VAL* 4.8 0.7 - - - +
25A TYR* 1.3 81.7 - - + +
27A GLU* 1.3 72.3 + - + +
29A TYR* 3.6 16.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 27 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A VAL* 3.0 30.0 + - + +
26A ARG* 1.3 94.0 + - + +
28A LYS* 1.3 67.0 + - + +
29A TYR* 3.1 22.6 + - - -
38A MET* 3.6 9.2 - - - +
41A GLU* 5.0 0.2 - - - +
----------------------------------------------------------
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