Contacts of the helix formed by residues 13 - 30 (chain A) in PDB entry 2LY4
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 13 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LYS 3.5 2.6 + - - -
12A MET* 1.3 79.8 - - - +
14A SER* 1.3 67.5 + - - +
15A TYR* 3.0 13.0 - - - -
16A ALA* 3.0 14.4 + - - +
17A PHE* 3.2 9.2 + - - -
60A GLU* 4.8 5.6 - - - -
63A ALA* 4.4 0.7 - - - -
33B SER* 5.3 5.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 14 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A SER* 1.3 73.5 - - - +
15A TYR* 1.3 63.7 + - - +
17A PHE* 3.1 5.8 + - - +
18A PHE* 2.9 24.1 + - - +
48A TRP* 3.3 23.9 - - - -
56A LYS 4.2 0.2 + - - -
59A PHE* 3.5 13.9 - - - +
60A GLU* 3.3 56.8 + - - +
63A ALA* 4.2 2.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 15 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A SER* 4.1 10.0 - - - +
14A SER* 1.3 80.8 + - - +
16A ALA* 1.3 61.2 + - - +
18A PHE* 3.2 18.1 - + - +
19A VAL* 3.5 2.6 + - - +
44A CYS 4.4 0.4 - - - -
45A SER* 2.8 23.6 + - - -
48A TRP* 3.3 52.0 - + + -
49A LYS* 2.7 32.0 + - - -
43B LEU* 3.7 16.2 - - + +
44B MET* 3.2 45.9 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
12A MET* 3.7 24.7 - - + -
13A SER* 3.0 5.4 + - - +
15A TYR* 1.3 77.3 - - - +
17A PHE* 1.3 54.8 + - - +
19A VAL* 3.2 1.9 + - - +
20A GLN* 2.7 36.4 + - - +
44B MET* 3.5 28.0 - - + +
45B LEU* 3.5 22.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 17 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ARG* 4.5 2.2 - - + -
10A GLY 4.5 5.6 - - - -
11A LYS 4.8 0.4 - - - -
12A MET* 3.0 52.9 - - + -
13A SER 3.2 6.6 + - - +
14A SER* 3.1 12.7 + - - +
16A ALA* 1.3 73.4 - - - +
18A PHE* 1.3 60.0 + - - +
20A GLN* 3.4 27.7 - - - +
21A THR* 2.8 35.2 + - - +
59A PHE* 4.1 13.0 - - + +
62A MET* 4.0 12.8 - - + -
63A ALA* 3.6 25.4 - - + -
66A ASP* 3.4 41.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 18 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A SER 2.9 6.5 + - - +
15A TYR* 3.2 13.2 - + - +
17A PHE* 1.3 78.8 - - - +
19A VAL* 1.3 63.4 + - + +
21A THR* 3.6 3.1 - - - +
22A CYS* 3.4 29.3 + - + +
44A CYS* 3.1 52.0 - - + -
47A ARG* 4.2 28.3 - - + -
48A TRP* 3.5 36.6 - + + -
51A MET* 3.9 19.7 - - + -
59A PHE* 3.4 33.4 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 19 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A TYR 3.9 1.1 - - - +
16A ALA 3.2 7.0 + - - +
18A PHE* 1.3 74.7 - - + +
20A GLN* 1.3 57.8 + - - +
22A CYS 3.3 0.2 + - - -
23A ARG* 2.8 38.6 + - - +
40A PHE* 3.5 28.5 - - + -
41A SER* 4.8 8.7 - - - +
44A CYS* 3.5 27.6 - - + -
44B MET* 3.6 34.3 - - + -
45B LEU* 3.7 23.1 - - + -
54B PHE* 4.5 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 20 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ARG* 3.3 44.9 + - - +
12A MET* 4.5 1.5 - - + +
16A ALA 2.7 22.4 + - - +
17A PHE* 3.2 34.3 + - - +
19A VAL* 1.3 72.1 - - - +
21A THR* 1.3 78.2 + - - +
23A ARG* 2.8 34.4 + - - +
24A GLU* 3.0 16.3 + - - +
66A ASP* 5.0 1.0 + - - -
45B LEU* 3.8 12.5 - - + +
53B TRP* 3.7 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 21 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A PHE* 2.8 23.5 + - - +
18A PHE 3.6 7.2 - - - +
20A GLN* 1.3 83.8 - - - +
22A CYS* 1.3 62.8 + - + +
24A GLU* 3.9 4.2 - - - +
25A GLU* 3.0 31.0 + - - +
59A PHE* 3.6 23.6 - - + -
62A MET* 4.9 9.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 22 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A PHE* 3.4 21.7 + - + +
19A VAL* 3.3 0.8 + - - -
20A GLN 3.2 0.4 - - - -
21A THR* 1.3 81.0 - - + +
23A ARG* 1.3 64.2 + - - +
25A GLU* 3.5 5.6 + - - +
26A HIS* 3.3 22.9 + - - +
40A PHE* 3.6 25.9 - - + -
44A CYS* 5.2 4.5 - - - -
47A ARG* 5.4 10.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 23 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A VAL 2.8 18.6 + - - +
20A GLN* 2.8 48.8 + - - +
22A CYS* 1.3 73.3 - - - +
24A GLU* 1.3 102.6 + - - +
26A HIS* 3.7 7.0 + - - +
27A LYS* 3.3 22.0 + - - +
35A VAL* 4.8 10.2 - - + +
40A PHE* 3.3 26.6 - - + -
45B LEU* 4.0 4.5 - - - -
53B TRP* 2.7 44.6 + - - +
54B PHE* 3.3 52.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 24 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ARG* 2.6 42.6 + - - -
20A GLN* 3.0 14.7 + - - +
21A THR* 3.9 3.7 - - - +
23A ARG* 1.3 116.7 + - - +
25A GLU* 1.3 55.6 + - - +
26A HIS 3.1 0.2 - - - -
27A LYS* 2.8 6.9 + - + +
28A LYS* 2.8 60.2 + - + +
53B TRP* 5.1 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 25 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A THR* 3.0 22.1 + - - +
22A CYS* 3.5 6.7 + - - +
24A GLU* 1.3 75.0 - - - +
26A HIS* 1.3 62.1 + - - +
28A LYS* 2.7 39.5 + - - +
29A LYS* 3.2 56.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 26 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A CYS* 3.3 13.6 + - - +
23A ARG* 3.8 5.1 + - - +
24A GLU 3.1 0.4 - - - -
25A GLU* 1.3 79.1 - - - +
27A LYS* 1.3 60.4 + - - +
29A LYS* 3.6 7.0 + - + +
30A HIS* 3.0 41.8 + + - +
33A ALA* 3.7 24.5 - - + +
34A SER* 3.5 22.2 + - - -
35A VAL* 3.8 18.8 - - + +
40A PHE* 6.1 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 27 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A ARG* 3.3 16.5 + - - +
24A GLU* 2.8 9.7 + - + +
26A HIS* 1.3 80.6 - - - +
28A LYS* 1.3 64.0 + - + +
30A HIS 3.0 21.3 - - - +
31A PRO* 3.3 29.1 + - + +
32A ASP 5.0 0.2 - - - -
33A ALA 2.7 32.1 + - - +
34A SER* 5.0 5.9 - - - +
35A VAL* 6.4 0.7 - - + -
53B TRP 5.8 2.5 - - - +
54B PHE 4.5 14.4 - - - +
55B THR* 4.7 4.1 + - - +
56B GLU* 3.8 43.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 28 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A GLU* 2.8 47.4 + - + +
25A GLU* 2.7 30.8 + - - +
26A HIS 3.3 0.2 - - - -
27A LYS* 1.3 77.7 - - + +
29A LYS* 1.3 65.1 + - + +
30A HIS 3.6 0.2 + - - -
31A PRO* 4.0 11.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 29 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A GLU* 3.2 47.9 + - - +
26A HIS* 4.0 7.0 - - + +
28A LYS* 1.3 78.3 - - + +
30A HIS* 1.3 73.9 + - + +
31A PRO* 3.4 8.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 30 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A HIS* 3.0 27.6 + + - +
27A LYS* 3.0 13.0 - - - +
29A LYS* 1.3 92.4 + - + +
31A PRO* 1.3 58.3 - - - +
32A ASP* 3.0 29.0 + - - +
33A ALA* 3.0 35.6 + - + +
----------------------------------------------------------
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