Contacts of the helix formed by residues 15 - 28 (chain A) in PDB entry 1L4E
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 15 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ALA 3.8 1.0 + - - -
14A PRO* 1.3 67.9 - - - +
16A ALA* 1.3 63.2 + - - +
17A GLU* 3.1 23.6 + - - +
18A ALA* 3.2 23.6 + - + +
19A MET* 3.2 25.4 + - - +
21A ARG* 5.3 0.7 + - - -
47A ALA 4.7 0.4 - - - +
48A GLY* 2.8 18.5 + - - +
50A PRO* 4.9 11.2 - - + +
54A GLY* 5.2 3.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 16 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A PRO 3.3 7.5 + - - +
15A ASP* 1.3 72.5 + - - +
17A GLU* 1.3 56.9 + - - +
19A MET* 3.3 14.4 + - - +
20A ALA* 2.9 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 17 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ASP* 3.1 12.5 + - - +
16A ALA* 1.3 79.4 - - - +
18A ALA* 1.3 61.6 + - - +
20A ALA* 3.4 7.2 + - - +
21A ARG* 3.0 61.4 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
15A ASP* 3.2 25.0 + - - +
17A GLU* 1.3 80.5 + - - +
19A MET* 1.3 63.3 + - - +
21A ARG* 3.3 20.3 + - - +
22A THR* 2.9 33.1 + - - -
47A ALA* 3.4 23.3 - - - +
54A GLY* 3.9 14.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 19 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A PRO* 4.3 17.5 - - + -
15A ASP 3.2 18.2 + - - +
16A ALA* 3.6 12.1 - - - +
18A ALA* 1.3 77.3 - - - +
20A ALA* 1.3 56.2 + - - +
22A THR* 3.2 5.6 + - - -
23A GLN* 2.9 28.9 + - - +
44A VAL* 3.6 38.2 - - + +
45A GLN* 4.3 12.6 - - + +
47A ALA* 4.5 1.1 - - - -
48A GLY* 3.4 22.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 20 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ALA 2.9 16.1 + - - +
17A GLU* 3.7 7.6 - - - +
19A MET* 1.3 78.3 - - - +
21A ARG* 1.3 63.2 + - + +
23A GLN* 3.4 5.4 + - - +
24A GLN* 3.2 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 21 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ASP* 5.3 0.6 + - - -
17A GLU* 3.0 45.1 + - - +
18A ALA* 3.7 22.4 - - - +
20A ALA* 1.3 79.0 - - - +
22A THR* 1.3 62.9 + - - +
24A GLN* 3.5 7.3 + - - +
25A HIS* 3.1 22.9 + - - +
54A GLY* 4.2 17.1 + - - -
335A PHE* 5.6 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 22 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ALA 2.9 17.3 + - - -
19A MET* 3.5 5.8 - - - -
20A ALA 3.2 0.2 - - - -
21A ARG* 1.3 77.6 - - - +
23A GLN* 1.3 63.9 + - - +
25A HIS* 3.2 3.5 + - - +
26A ILE* 3.0 37.3 + - + +
43A ALA 4.0 2.9 - - - +
44A VAL* 3.7 19.3 - - + -
47A ALA* 2.7 29.4 - - + +
54A GLY 4.4 4.2 + - - -
56A PRO* 4.5 0.2 - - - +
335A PHE* 3.2 32.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 23 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A MET 2.9 16.0 + - - +
20A ALA* 3.8 7.2 - - - +
21A ARG 3.4 0.2 - - - -
22A THR* 1.3 75.8 - - - +
24A GLN* 1.3 63.9 + - - +
26A ILE* 3.3 5.6 + - - +
27A ASP* 2.9 61.6 + - - +
40A GLU* 4.6 10.8 + - - +
41A THR* 6.0 0.9 - - - +
44A VAL* 3.5 28.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 24 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A ALA 3.2 14.6 + - - +
21A ARG* 3.7 7.6 - - - +
22A THR 3.2 0.2 - - - -
23A GLN* 1.3 78.1 - - - +
25A HIS* 1.3 63.6 + - - +
27A ASP* 3.3 10.2 + - - +
28A GLY* 3.3 16.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 25 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ARG 3.1 11.3 + - - +
22A THR 3.2 8.0 + - - +
24A GLN* 1.3 80.0 - - - +
26A ILE* 1.3 60.8 + - - +
28A GLY* 3.1 11.8 + - - -
29A LEU* 3.4 27.2 + - + +
335A PHE* 3.1 54.3 + + + -
336A HIS* 5.3 1.8 - - - -
338A MET 5.6 1.6 - - - -
340A GLU* 3.6 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 26 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A THR* 3.0 36.8 + - + +
23A GLN* 3.7 7.2 - - - +
25A HIS* 1.3 75.7 - - - +
27A ASP* 1.3 65.8 + - - +
29A LEU* 3.2 22.2 + - + +
31A LYS* 3.0 23.9 + - - +
40A GLU* 3.4 49.8 - - + +
43A ALA* 3.7 13.2 - - + -
44A VAL* 3.7 19.1 - - + -
334A MET* 4.1 9.4 - - + -
335A PHE* 3.6 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 27 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A GLN* 2.9 49.0 + - - +
24A GLN* 3.7 7.8 - - - +
25A HIS 3.3 0.2 - - - -
26A ILE* 1.3 78.2 - - - +
28A GLY* 1.3 58.4 + - - +
29A LEU 3.5 5.2 + - - +
31A LYS* 4.6 4.5 + - - +
33A PRO* 4.3 22.6 - - + +
34A GLY 4.8 6.8 + - - -
40A GLU* 4.5 6.4 - - - +
341A LEU* 4.1 9.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 28 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A GLN 3.3 8.6 + - - -
25A HIS* 3.1 9.8 + - - -
26A ILE 3.1 0.8 - - - -
27A ASP* 1.3 75.2 - - - +
29A LEU* 1.3 60.7 + - - +
340A GLU* 3.4 11.3 - - - +
341A LEU* 3.0 31.0 + - - +
342A ALA 4.9 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