Contacts of the helix formed by residues 13 - 28 (chain A) in PDB entry 1N3G
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 THR 13 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A MET* 5.5 8.1 - - + -
11A GLU* 3.6 16.3 + - + +
12A ILE* 1.3 76.4 - - - +
14A PRO* 1.3 66.7 - - - +
15A ALA* 3.7 5.9 + - - +
16A ILE* 2.8 45.4 + - + +
17A ARG* 2.7 36.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 14 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ILE 4.5 1.6 - - - +
13A THR* 1.3 87.6 - - - +
15A ALA* 1.3 62.3 + - + +
17A ARG* 3.3 38.6 + - - +
18A GLN* 3.2 24.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 15 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A THR* 3.2 6.2 - - - +
14A PRO* 1.3 82.8 - - + +
16A ILE* 1.3 65.4 + - + +
18A GLN* 3.5 4.5 + - - +
19A HIS* 3.1 15.9 + - - -
71A TYR* 2.8 36.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 16 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A MET* 5.3 1.3 - - + -
11A GLU 5.0 0.9 - - - +
12A ILE* 4.8 3.6 - - + -
13A THR* 2.8 43.8 + - + +
15A ALA* 1.3 74.1 - - + +
17A ARG* 1.3 68.0 + - - +
19A HIS* 2.9 16.5 + - - +
20A VAL* 3.0 18.7 + - + +
41A LEU* 3.4 39.3 - - + -
48A PHE* 4.2 23.3 - - + -
70A MET* 4.0 23.6 - - + -
71A TYR* 4.0 4.3 - - + -
74A ILE* 3.8 11.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 17 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ILE* 5.7 5.2 - - + +
12A ILE* 3.6 27.7 + - + +
13A THR 2.7 17.8 + - - +
14A PRO* 3.3 40.7 + - - +
16A ILE* 1.3 72.1 - - - +
18A GLN* 1.3 68.1 + - + +
20A VAL* 3.3 6.9 - - - +
21A ALA* 2.9 32.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 18 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A PRO 3.2 15.1 + - - +
15A ALA* 3.8 4.5 - - - +
16A ILE 3.2 0.6 - - - -
17A ARG* 1.3 85.1 - - + +
19A HIS* 1.3 64.3 + - - +
21A ALA* 4.1 7.6 - - - +
22A ASP* 2.8 37.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 19 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ALA 3.1 9.5 + - - +
16A ILE* 2.9 15.0 + - - +
18A GLN* 1.3 80.6 - - - +
20A VAL* 1.3 63.1 + - - +
22A ASP* 3.3 4.4 + - - +
23A ARG* 3.2 27.3 + - + +
71A TYR* 3.1 54.7 + + + +
74A ILE* 3.5 35.2 - - + -
75A ASN* 4.0 16.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 20 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A MET* 4.3 17.5 - - + -
5A ILE* 4.9 15.3 - - + -
12A ILE* 5.4 1.3 - - + -
16A ILE* 3.0 13.8 + - + +
17A ARG* 3.3 16.4 - - - +
19A HIS* 1.3 79.0 - - - +
21A ALA* 1.3 65.6 + - + +
23A ARG* 2.9 6.9 + - + +
24A LEU* 2.7 37.7 + - + +
39A ILE* 3.8 31.9 - - + -
74A ILE* 3.8 21.4 - - + +
77A LEU* 6.2 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 21 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A MET* 4.7 10.3 - - - +
5A ILE* 6.3 1.6 - - + -
17A ARG* 2.9 19.6 + - + +
18A GLN* 3.8 11.7 - - - +
19A HIS 3.2 0.2 - - - -
20A VAL* 1.3 82.6 - - + +
22A ASP* 1.3 56.7 + - - +
24A LEU* 3.3 5.6 + - - +
25A ALA* 2.8 31.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 22 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A GLN* 2.8 39.9 + - - +
19A HIS* 3.6 4.3 - - - +
21A ALA* 1.3 78.7 - - - +
23A ARG* 1.3 65.8 + - + +
25A ALA* 3.4 7.0 + - - +
26A LYS* 3.3 23.0 + - - +
----------------------------------------------------------
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 HIS* 3.2 19.8 + - + +
20A VAL* 2.9 13.3 + - + +
22A ASP* 1.3 82.1 - - - +
24A LEU* 1.3 57.5 + - + +
26A LYS* 3.6 3.0 + - - +
27A LEU* 3.0 32.2 + - - +
74A ILE* 4.8 10.3 - - + +
75A ASN* 2.6 33.1 + - - +
78A ILE* 3.8 45.8 - - + +
79A ASN* 5.4 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 24 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 5.1 7.5 - - + +
3A MET* 3.6 35.7 - - + -
20A VAL* 2.7 22.8 + - + +
21A ALA 3.8 1.3 - - - +
23A ARG* 1.3 70.0 - - + +
25A ALA* 1.3 60.9 + - - +
27A LEU* 3.7 10.3 - - + -
28A GLU* 2.9 40.0 + - + +
34A LEU* 5.1 9.4 - - + -
37A PRO* 4.5 22.4 - - + -
39A ILE* 3.8 29.4 - - + -
54A ILE* 5.0 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 25 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 5.9 3.4 - - - -
21A ALA 2.8 17.9 + - - +
22A ASP* 3.5 11.0 - - - +
23A ARG 3.2 0.2 - - - -
24A LEU* 1.3 77.1 - - - +
26A LYS* 1.3 58.9 + - - +
28A GLU* 3.0 25.2 - - - +
29A LYS* 4.5 0.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 26 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ASP 3.3 12.0 + - - +
23A ARG* 4.2 2.7 - - - +
25A ALA* 1.3 74.9 - - - +
27A LEU* 1.3 63.3 + - - +
28A GLU 3.0 6.8 + - - -
29A LYS* 3.3 29.5 + - - +
30A TRP* 4.5 5.1 + - + -
----------------------------------------------------------
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 ARG 3.0 18.0 + - - +
24A LEU* 3.7 11.9 - - + +
26A LYS* 1.3 72.5 - - - +
28A GLU* 1.3 55.8 + - - +
29A LYS 3.0 6.1 - - - -
30A TRP* 2.9 41.5 + - + -
34A LEU* 2.9 46.7 - - + +
54A ILE* 4.9 5.4 - - + -
78A ILE* 3.4 22.2 - - + -
81A LEU* 5.2 9.0 - - + -
82A GLU* 3.1 27.1 - - - +
85A LEU* 4.5 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 28 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 3.0 55.0 + - - +
24A LEU* 2.9 13.5 + - - +
25A ALA* 3.0 18.2 - - - +
26A LYS 3.0 0.6 - - - -
27A LEU* 1.3 76.9 - - - +
29A LYS* 1.3 58.8 + - + +
30A TRP 3.4 2.6 + - - +
33A HIS* 4.3 12.2 - - - +
34A LEU* 3.6 21.8 - - - +
----------------------------------------------------------
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