Contacts of the helix formed by residues 11 - 24 (chain A) in PDB entry 2D2I
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 GLY 11 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A GLY 3.1 8.9 + - - -
10A PHE* 1.3 74.5 - - - +
12A ARG* 1.3 67.8 + - - -
13A ILE 3.4 2.5 - - - -
14A GLY* 4.1 1.4 - - - +
15A ARG* 2.8 42.2 + - - +
1341A NAP 3.2 30.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 12 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A GLY* 1.3 71.6 - - - +
13A ILE* 1.3 64.6 + - - +
15A ARG* 3.2 27.9 - - - +
16A ASN* 2.8 43.9 + - - +
50A ASP* 2.7 43.7 + - - -
51A SER 5.3 1.6 - - - +
52A VAL* 4.0 10.2 - - - +
53A LEU* 4.8 1.4 - - - +
186A LEU* 3.6 21.1 - - + +
319A GLU* 2.8 47.6 + - + +
1341A NAP 2.8 39.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 13 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ARG* 1.3 73.4 - - - +
14A GLY* 1.3 55.1 - - - +
17A PHE* 2.6 37.0 + - + +
96A ILE* 5.9 0.2 - - + -
98A SER* 4.3 3.8 - - - -
122A THR* 3.8 34.1 - - + +
319A GLU* 4.1 13.9 - - + +
322A TYR* 4.1 11.9 - - + -
323A SER* 3.8 19.5 - - - +
326A VAL* 4.8 3.6 - - + -
1341A NAP 2.9 75.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 14 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A ILE* 4.1 12.5 - - - +
9A GLY 3.7 20.0 - - - -
10A PHE* 4.0 9.0 - - - -
11A GLY 3.3 8.3 + - - +
13A ILE* 1.3 79.0 - - - +
15A ARG* 1.3 60.5 + - - +
17A PHE* 3.6 5.4 - - - +
18A LEU* 3.2 21.0 + - - +
96A ILE* 6.0 0.2 - - - -
98A SER* 3.8 12.0 + - - -
1341A NAP 4.7 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 15 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A PHE* 3.0 60.9 + - + +
11A GLY* 2.8 38.1 + - - +
12A ARG* 3.2 36.5 - - - +
14A GLY* 1.3 69.7 - - - -
16A ASN* 1.3 66.8 + - - +
18A LEU* 3.4 2.8 + - - +
19A ARG* 3.1 32.1 + - - +
46A LEU* 3.1 62.8 + - - +
47A LEU* 3.9 9.5 - - + +
49A TYR 5.8 0.4 + - - -
50A ASP* 4.5 4.2 + - - +
53A LEU* 5.7 0.4 - - + -
1341A NAP 5.1 0.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 16 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ARG* 2.8 52.6 + - - +
13A ILE* 3.5 1.3 - - - +
15A ARG* 1.3 74.0 - - - +
17A PHE* 1.3 67.1 + - - +
19A ARG* 3.2 6.9 + - - +
20A CYS* 2.9 25.6 + - - -
50A ASP* 4.8 0.6 + - - -
53A LEU* 3.7 17.3 - - - +
319A GLU* 3.8 16.8 + - - +
320A TRP* 3.5 35.0 + - + +
323A SER* 3.2 19.5 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
5A VAL* 4.8 3.4 - - + -
7A ILE* 3.9 25.1 - - + -
13A ILE* 2.6 23.5 + - + +
14A GLY* 3.6 4.7 - - - +
16A ASN* 1.3 73.4 - - - +
18A LEU* 1.3 66.9 + - - +
20A CYS* 3.3 3.4 + - - +
21A TRP* 2.8 27.3 + - + +
29A LEU* 4.4 18.4 - - + -
31A VAL* 4.4 16.2 - - + -
96A ILE* 3.9 35.0 - - + -
323A SER* 3.6 12.5 + - - +
326A VAL* 3.1 36.1 - - + -
327A VAL* 3.5 30.5 - - + -
330A ALA* 4.6 1.6 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
7A ILE* 3.9 15.3 - - + -
10A PHE* 3.7 25.6 - - + -
14A GLY 3.2 11.0 + - - +
15A ARG 3.6 7.6 - - - +
16A ASN 3.2 0.2 - - - -
17A PHE* 1.3 84.0 - - - +
19A ARG* 1.3 62.9 + - - +
21A TRP* 3.1 18.1 + - + +
22A PHE* 2.9 62.0 + - + -
31A VAL* 4.4 10.1 - - + -
34A ILE* 4.3 8.3 - - + -
47A LEU* 3.8 22.0 - - + -
56A PHE* 5.8 0.2 - - + -
74A MET* 4.1 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 19 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ARG* 3.1 20.5 + - - +
16A ASN* 3.8 3.8 - - - +
18A LEU* 1.3 72.5 - - - +
20A CYS* 1.3 68.4 + - - +
22A PHE* 3.1 3.8 + - - +
23A GLY* 3.0 18.2 + - - -
47A LEU* 3.2 31.5 + - + -
48A GLU 4.0 0.6 + - - -
50A ASP* 3.8 14.9 + - - +
53A LEU* 3.8 34.2 + - - +
54A GLY 2.9 29.4 + - - -
55A ARG 3.5 3.6 + - - -
56A PHE* 3.2 63.8 - - + +
320A TRP* 4.0 17.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 20 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ASN 2.9 16.7 + - - -
17A PHE 3.6 7.2 - - - +
19A ARG* 1.3 74.2 - - - +
21A TRP* 1.3 67.4 + - - +
23A GLY* 2.9 13.1 + - - +
24A ARG* 3.3 13.8 + - - +
320A TRP* 3.7 31.4 - - - -
323A SER* 3.8 18.2 - - - -
324A GLN* 3.2 46.9 + - - +
327A VAL* 3.9 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 21 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A PHE* 2.8 19.7 + + + +
18A LEU* 3.1 13.0 + - + +
20A CYS* 1.3 77.3 - - - +
22A PHE* 1.3 103.4 + + - +
24A ARG* 3.1 26.3 + - + +
27A THR* 3.0 36.0 + - + +
29A LEU* 3.1 46.1 - - + +
30A GLU* 4.0 2.5 - - + -
31A VAL* 3.7 43.1 - - + -
72A LYS* 3.6 33.7 - - + -
74A MET* 5.1 1.3 - - - -
327A VAL* 4.1 13.2 - - + +
331A GLU* 4.5 2.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 22 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A LEU* 2.9 52.4 + - + +
19A ARG 3.1 7.2 + - - +
21A TRP* 1.3 90.2 - + - +
23A GLY* 1.3 58.6 + - - +
24A ARG 3.4 3.3 - - - +
56A PHE* 3.9 22.0 - + + -
69A VAL* 3.3 48.5 - - + -
70A ASN* 4.3 14.3 - - + +
72A LYS* 4.2 21.5 - - + -
74A MET* 3.7 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 23 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ARG 3.0 7.8 + - - -
20A CYS* 2.9 10.5 + - - -
22A PHE* 1.3 77.2 - - - +
24A ARG* 1.3 63.7 + - - +
25A GLN* 3.7 2.3 + - - -
320A TRP* 6.3 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 24 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A CYS 3.3 10.6 + - - +
21A TRP* 3.1 18.7 + - + +
22A PHE 4.6 2.9 - - - +
23A GLY* 1.3 82.1 - - - +
25A GLN* 1.3 99.5 + - - +
26A ASN* 3.9 14.4 - - - +
27A THR* 5.0 5.3 - - - +
292A ASP* 5.9 0.2 - - - -
324A GLN* 2.6 54.0 + - - +
325A ARG* 5.1 1.0 - - - +
327A VAL* 3.4 21.0 - - + +
328A ASP* 2.5 31.2 + - - -
331A GLU* 5.1 6.6 + - - +
----------------------------------------------------------
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