Contacts of the helix formed by residues 13 - 28 (chain A) in PDB entry 1DNY
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 ASN 13 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A PRO* 3.6 2.1 - - - +
12A THR* 1.3 105.2 + - - +
14A ALA* 1.3 65.5 + - - +
15A VAL* 2.9 22.3 + - + +
16A GLU* 2.7 25.6 + - + +
17A SER* 2.9 19.3 + - - -
82A ALA* 5.4 3.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 14 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ASN* 1.3 73.3 - - - +
15A VAL* 1.3 63.8 + - + +
17A SER* 3.0 18.8 - - - +
18A LYS* 3.0 22.0 + - - +
59A TYR* 4.7 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 15 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ASN* 2.9 14.6 + - + +
14A ALA* 1.3 81.7 - - + +
16A GLU* 1.3 62.1 + - - +
18A LYS* 3.3 2.9 + - - +
19A LEU* 3.1 21.3 + - - +
59A TYR* 4.0 16.8 + - + +
78A ALA* 3.0 35.0 - - + +
81A VAL* 3.7 11.2 - - + -
82A ALA* 2.8 38.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 16 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A PRO* 3.9 10.8 - - + -
12A THR* 3.1 16.6 + - - -
13A ASN* 2.7 48.0 + - + +
15A VAL* 1.3 74.0 - - - +
17A SER* 1.3 57.2 + - - +
19A LEU* 3.6 0.6 - - - -
20A ALA* 2.7 37.4 + - - +
34A ILE* 3.1 26.1 - - + +
74A ILE* 3.7 20.6 - - + +
75A LYS* 3.8 11.9 - - - +
78A ALA* 3.0 23.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 17 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A PRO* 3.3 21.3 - - - +
13A ASN 2.9 9.2 + - - -
14A ALA* 3.0 32.4 + - - +
16A GLU* 1.3 77.7 - - - +
18A LYS* 1.3 60.6 + - - +
20A ALA* 3.1 7.6 - - - +
21A GLU* 3.1 22.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 18 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ALA 3.0 10.0 + - - +
15A VAL 3.8 1.1 - - - +
17A SER* 1.3 72.5 - - - +
19A LEU* 1.3 52.7 + - + +
20A ALA 2.7 9.7 + - - -
21A GLU* 2.8 27.6 + - + +
22A ILE* 2.6 30.8 + - + +
54A GLN* 3.0 31.9 + - + -
58A GLU* 3.4 30.6 + - + +
59A TYR* 3.3 20.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 19 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A VAL* 3.1 15.5 + - + +
16A GLU* 4.4 0.4 - - - -
18A LYS* 1.3 78.9 - - + +
20A ALA* 1.3 55.5 + - - +
22A ILE* 3.0 10.3 - - + -
23A TRP* 2.6 42.4 + - - +
51A VAL* 3.4 29.4 - - + -
54A GLN* 6.0 0.4 - - + -
55A VAL* 4.2 14.1 - - + -
59A TYR* 4.8 5.2 - - + +
74A ILE* 3.8 15.5 - - + +
77A LEU* 3.0 35.9 - - + -
78A ALA* 3.3 32.1 - - - +
81A VAL* 3.9 11.4 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
8A TYR* 3.7 28.0 - - + +
16A GLU 2.7 20.5 + - - +
17A SER* 3.1 8.5 - - - +
18A LYS 2.7 0.8 + - - -
19A LEU* 1.3 75.7 - - - +
21A GLU* 1.3 67.9 + - - +
23A TRP* 3.2 6.1 - - - +
24A GLU* 3.1 21.5 + - - +
31A GLY 5.1 4.2 - - - +
32A ILE* 4.0 2.9 - - - +
74A ILE* 4.2 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 21 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A SER 3.1 9.0 + - - +
18A LYS* 2.8 27.2 + - + +
20A ALA* 1.3 76.7 - - - +
22A ILE* 1.3 67.2 + - - +
24A GLU* 2.9 34.2 + - - +
25A ARG* 3.0 13.0 + - - +
----------------------------------------------------------
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 LYS* 2.6 32.5 + - + +
19A LEU* 3.0 20.0 - - + -
21A GLU* 1.3 72.3 - - - +
23A TRP* 1.3 64.8 + - - +
25A ARG* 2.8 18.4 + - - +
26A VAL* 2.8 56.9 + - + -
50A ALA 4.2 0.2 - - - -
51A VAL* 3.1 39.3 - - + -
54A GLN* 3.3 42.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 23 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A LEU* 2.6 38.9 + - + +
20A ALA* 3.2 7.9 - - - +
21A GLU 3.0 0.2 + - - -
22A ILE* 1.3 78.2 - - - +
24A GLU* 1.3 55.8 + - - +
27A LEU* 2.6 60.7 + - + +
32A ILE* 3.0 31.6 - - + -
36A ASP* 3.2 30.3 - - + -
37A ASN 4.2 3.4 - - - -
38A PHE* 2.7 59.7 - + - -
40A GLN* 6.2 0.2 - - + -
51A VAL* 3.3 19.4 - - + +
73A THR* 3.1 29.4 - - - -
74A ILE* 3.1 13.9 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
20A ALA 3.1 2.9 + - - +
21A GLU* 2.9 39.1 + - - +
23A TRP* 1.3 76.9 - - - +
25A ARG* 1.3 60.5 + - + +
28A GLY* 2.8 8.7 + - - -
29A VAL 2.7 44.3 + - - +
30A SER* 4.6 4.9 + - - -
31A GLY* 4.1 12.9 + - - +
32A ILE* 3.0 24.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 25 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A GLU* 3.0 17.5 + - - +
22A ILE* 2.8 12.2 + - - +
24A GLU* 1.3 78.6 - - + +
26A VAL* 1.3 76.6 + - + +
27A LEU 3.1 1.1 - - - -
28A GLY* 2.8 14.6 + - - -
54A GLN* 5.6 5.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 26 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ILE* 2.8 41.7 + - + -
25A ARG* 1.3 83.6 - - + +
27A LEU* 1.3 55.6 + - - +
47A LYS* 2.7 56.2 - - + +
50A ALA* 2.9 37.7 - - + +
51A VAL* 4.2 1.8 - - + -
54A GLN* 5.1 4.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 27 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A TRP* 2.6 66.0 + - + +
26A VAL* 1.3 79.2 - - - +
28A GLY* 1.3 62.0 + - - +
29A VAL* 3.2 17.4 + - + +
38A PHE* 4.0 22.4 - - + +
41A ILE 5.4 3.3 - - - +
42A GLY* 5.5 4.2 - - - -
47A LYS* 3.4 40.3 - - + -
48A ALA* 3.8 12.8 - - - +
51A VAL* 4.1 6.7 - - + -
----------------------------------------------------------
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 GLU 2.8 11.7 + - - -
25A ARG 2.8 10.6 + - - -
27A LEU* 1.3 80.4 - - - +
29A VAL* 1.3 61.1 + - - +
47A LYS* 5.8 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