Contacts of the helix formed by residues 24 - 39 (chain A) in PDB entry 1NHX
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 PRO 24 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A SER 3.6 4.9 - - - +
23A LEU* 1.3 86.1 - - + +
25A GLN* 1.3 67.0 + - - +
26A ALA* 3.3 2.9 - - + +
27A VAL* 2.9 31.4 + - + +
28A ARG* 2.9 10.4 + - - +
181A LEU* 4.1 34.1 - - + +
184A LEU* 4.9 0.9 - - + -
185A GLY* 3.1 34.1 - - - +
186A ASP* 4.1 9.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 25 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A LEU 3.5 3.1 + - - -
24A PRO* 1.3 70.0 - - - +
26A ALA* 1.3 58.8 + - - +
28A ARG* 3.2 26.1 + - - +
29A GLU* 2.8 62.7 + - - +
32A GLU* 5.6 0.8 + - - -
186A ASP* 4.1 10.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 26 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A PRO* 3.3 3.1 - - + +
25A GLN* 1.3 78.4 - - - +
27A VAL* 1.3 56.3 + - + +
29A GLU* 4.0 12.4 - - - +
30A PHE* 3.1 27.5 + - - +
186A ASP* 5.2 6.6 + - - +
187A GLY 5.3 4.9 - - - +
189A PHE* 3.5 20.2 - - + -
191A LYS* 5.8 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 27 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A LEU* 4.3 17.0 - - + -
24A PRO* 2.9 27.0 + - + +
26A ALA* 1.3 75.4 - - + +
28A ARG* 1.3 60.6 + - - +
30A PHE* 3.4 3.4 + - - +
31A LEU* 2.9 28.5 + - + +
141A VAL* 4.9 5.8 - - + -
158A ILE* 3.8 28.0 - - + -
181A LEU* 4.3 10.3 - - + -
184A LEU* 3.7 24.2 - - + -
189A PHE* 3.6 24.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 28 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A SER* 6.0 0.6 - - - -
20A LEU* 3.4 59.4 + - + +
21A ASP* 2.8 31.1 + - - +
23A LEU* 4.1 15.3 - - + +
24A PRO 2.9 11.6 + - - +
25A GLN* 3.4 27.8 + - - +
27A VAL* 1.3 76.5 - - - +
29A GLU* 1.3 57.2 + - - +
31A LEU* 3.3 3.0 + - - +
32A GLU* 2.8 58.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 29 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A GLN* 2.8 53.3 + - - +
26A ALA* 4.0 10.4 - - - +
28A ARG* 1.3 69.9 - - - +
30A PHE* 1.3 66.3 + - - +
32A GLU* 4.2 13.5 - - - +
33A ASN* 3.0 35.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 30 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ALA 3.1 19.0 + - - +
27A VAL 3.6 4.5 - - - +
29A GLU* 1.3 75.9 - - - +
31A LEU* 1.3 61.5 + - - +
33A ASN* 3.9 3.9 - - - +
34A ASN* 2.9 55.8 + - - +
158A ILE* 3.6 33.4 - - + -
160A LEU* 3.7 23.1 - - + +
189A PHE* 3.9 18.6 - + + -
191A LYS* 3.6 37.9 - - + +
192A CYS 3.6 31.0 - - - -
193A LEU* 4.6 4.9 - - + -
227A GLU* 5.7 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 31 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LEU* 4.9 3.8 - - + -
20A LEU* 3.7 22.0 - - + -
23A LEU* 3.7 26.0 - - + -
27A VAL 2.9 17.4 + - - +
28A ARG 3.5 4.7 - - - +
30A PHE* 1.3 75.5 - - - +
32A GLU* 1.3 60.4 + - - +
34A ASN* 3.3 1.9 + - - +
35A ALA* 2.9 32.3 + - + +
43A ILE* 3.9 26.5 - - + -
45A ILE* 4.6 2.5 - - + -
139A MET* 3.6 25.6 - - - -
141A VAL* 3.7 24.5 - - + -
160A LEU* 4.2 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 32 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LEU* 3.8 30.0 - - + +
20A LEU* 5.2 1.5 - - + +
25A GLN* 5.6 0.9 + - - -
28A ARG* 2.8 58.3 + - + +
29A GLU* 3.9 16.4 - - - +
31A LEU* 1.3 72.6 - - + +
33A ASN* 1.3 66.8 + - - +
35A ALA* 4.0 1.2 - - - +
36A GLU* 3.1 25.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 33 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A GLU* 3.0 25.5 + - - +
30A PHE* 3.9 5.9 - - + +
32A GLU* 1.3 80.2 - - - +
34A ASN* 1.3 64.0 + - - +
36A GLU* 3.7 5.7 + - - +
37A LEU* 3.2 23.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 34 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A PHE* 2.9 50.0 + - - +
33A ASN* 1.3 80.9 - - - +
35A ALA* 1.3 60.5 + - - +
36A GLU 3.3 0.4 - - - -
37A LEU* 3.7 14.8 - - - +
38A CYS* 2.8 34.9 + - - +
126A PHE* 5.0 1.0 - - - -
139A MET* 3.7 6.5 - - + +
160A LEU* 3.7 21.7 - - + +
193A LEU* 3.5 28.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 35 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LEU* 3.9 26.7 - - + -
14A LYS* 4.9 3.1 + - + +
31A LEU* 2.9 21.0 + - + +
32A GLU 4.0 2.0 - - - +
34A ASN* 1.3 75.8 - - - +
36A GLU* 1.3 58.4 + - - +
39A GLN* 2.8 28.6 + - - -
40A PRO* 3.1 15.2 - - + +
43A ILE* 4.0 21.8 - - + -
139A MET* 4.0 5.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 36 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LEU* 5.3 2.3 - - + +
32A GLU 3.1 18.2 + - - +
33A ASN* 3.7 6.3 - - - +
35A ALA* 1.3 77.4 - - - +
37A LEU* 1.3 62.3 + - - +
39A GLN* 2.7 40.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 37 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A ASN 3.2 15.1 + - - +
34A ASN* 3.8 19.3 - - - +
35A ALA 3.3 0.2 - - - -
36A GLU* 1.3 83.5 - - - +
38A CYS* 1.3 66.9 + - - +
39A GLN* 3.6 1.9 + - - +
126A PHE* 3.3 38.8 - - + -
127A ASN* 6.0 0.2 - - - +
130A PHE* 4.0 9.2 - - + +
131A PRO* 3.5 36.9 - - + +
132A GLY* 3.0 21.0 + - - -
193A LEU* 4.7 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 38 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A ASN 2.8 23.1 + - - +
37A LEU* 1.3 80.5 - - - +
39A GLN* 1.3 67.8 + - - +
40A PRO* 4.1 2.5 - - + -
130A PHE* 3.7 24.0 - - - -
132A GLY* 3.3 7.1 - - - -
133A CYS* 3.7 20.0 - - - -
134A MET* 2.9 50.4 + - + -
139A MET* 4.2 0.7 - - + -
193A LEU* 4.2 17.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 39 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A LYS* 3.6 18.1 + - - +
35A ALA 2.8 11.6 + - - -
36A GLU* 2.7 50.1 + - - +
37A LEU 4.3 3.8 - - - +
38A CYS* 1.3 79.1 - - - +
40A PRO* 1.3 68.3 - - - +
41A ASP* 4.3 1.4 - - - +
132A GLY* 4.4 10.3 - - - -
134A MET 4.2 0.2 - - - -
135A LYS* 3.3 41.8 + - + +
----------------------------------------------------------
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