Contacts of the helix formed by residues 22 - 37 (chain A) in PDB entry 1NPR
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 LYS 22 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A GLU* 3.0 42.2 + - + +
20A PRO 3.1 6.2 + - - +
21A GLY* 1.3 81.2 + - - +
23A GLU* 1.3 52.0 + - - +
24A ASN 3.2 2.9 - - - -
25A GLU* 2.7 49.6 + - + +
26A ALA* 2.8 18.4 + - - +
158A HIS* 4.0 27.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 23 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A VAL* 3.9 15.7 - - + -
19A GLU 3.8 1.0 + - - -
20A PRO* 3.3 1.8 - - - +
21A GLY* 2.7 25.2 + - - -
22A LYS* 1.3 77.3 - - - +
24A ASN* 1.3 62.3 + - - +
26A ALA* 3.4 2.8 + - - +
27A LYS* 3.0 23.0 + - - +
48A VAL* 3.5 28.2 - - + +
130A LEU* 6.1 0.2 - - + -
133A LYS* 2.9 36.3 + - + -
136A PRO* 3.6 4.3 - - + +
137A GLY 2.7 27.6 + - - +
138A TYR 3.8 18.8 - - - +
139A ILE* 3.8 7.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 24 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A GLY 5.4 0.2 + - - -
22A LYS 3.2 0.6 - - - -
23A GLU* 1.3 79.5 + - - +
25A GLU* 1.3 65.3 + - - +
27A LYS* 3.4 11.7 + - - +
28A GLU* 3.0 36.1 + - + +
48A VAL* 3.6 18.8 - - - +
113A PRO* 3.8 22.5 - - - +
130A LEU* 2.8 34.9 - - - +
----------------------------------------------------------
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 GLY 3.8 5.8 - - - +
22A LYS* 2.7 45.1 + - + +
24A ASN* 1.3 77.3 + - - +
26A ALA* 1.3 57.8 + - - +
28A GLU* 3.3 6.1 + - - +
29A ASN* 2.7 41.1 + - - +
158A HIS* 4.0 20.4 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
18A VAL* 3.8 16.8 - - + -
22A LYS 2.8 14.3 + - - +
23A GLU 3.6 8.3 - - - +
25A GLU* 1.3 72.4 - - - +
27A LYS* 1.3 57.2 + - - +
29A ASN* 3.4 7.0 + - - +
30A LEU* 2.8 30.7 + - - +
139A ILE* 4.5 3.8 - - + -
156A THR* 4.2 2.4 - - - +
157A PRO 4.3 0.7 - - - -
158A HIS* 3.8 22.3 - - + +
159A VAL* 3.8 22.1 - - + +
----------------------------------------------------------
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 GLU 3.0 13.6 + - - +
24A ASN* 3.5 15.7 - - - +
25A GLU 3.2 0.2 - - - -
26A ALA* 1.3 76.9 - - - +
28A GLU* 1.3 73.5 - - - +
30A LEU* 3.1 4.9 + - - +
31A LEU* 3.0 41.1 + - + +
46A VAL* 3.0 54.0 + - + +
47A ILE* 4.7 7.3 - - - +
48A VAL* 4.2 18.8 - - + +
139A ILE* 4.5 4.4 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
24A ASN* 3.0 23.6 + - + +
25A GLU* 3.7 7.0 - - - +
27A LYS* 1.3 87.2 - - - +
29A ASN* 1.3 66.9 + - - +
31A LEU* 3.4 21.9 + - - +
32A LYS* 3.1 42.1 + - - +
112A LYS* 6.2 2.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 29 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A GLU* 2.7 30.5 + - - +
26A ALA 3.5 4.5 - - - +
28A GLU* 1.3 78.9 - - - +
30A LEU* 1.3 63.3 + - - +
32A LYS* 3.2 14.1 + - - +
33A VAL* 3.0 23.7 + - - +
156A THR* 3.5 15.5 - - + -
157A PRO* 2.6 47.2 + - + +
158A HIS* 3.6 11.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 30 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A LEU* 4.2 13.9 - - + -
26A ALA 2.8 21.5 + - - +
27A LYS* 3.1 5.1 + - - +
29A ASN* 1.3 72.7 - - - +
31A LEU* 1.3 63.6 + - - +
33A VAL* 2.8 6.9 + - + +
34A LEU* 2.8 46.6 + - + +
43A VAL* 5.9 0.9 - - + -
46A VAL* 4.1 17.5 - - + -
139A ILE* 4.4 4.0 - - + -
141A ILE* 3.9 29.8 - - + -
149A LEU* 5.8 0.2 - - + -
152A ALA 4.9 0.2 - - - +
153A ILE* 4.3 24.2 - - + +
156A THR* 3.5 25.7 - - + +
159A VAL* 5.3 2.2 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
27A LYS* 3.0 28.8 + - + +
28A GLU* 3.7 28.0 - - - +
29A ASN 3.4 0.2 - - - -
30A LEU* 1.3 73.2 - - - +
32A LYS* 1.3 64.6 + - + +
34A LEU* 3.1 17.7 + - + +
35A GLU* 3.1 20.4 + - - +
40A LYS* 4.8 2.8 - - - +
46A VAL* 3.9 26.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 32 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A GLU* 3.1 31.8 + - - +
29A ASN* 3.4 13.9 - - - +
31A LEU* 1.3 78.8 - - + +
33A VAL* 1.3 61.4 + - + +
35A GLU* 3.2 9.6 + - - +
36A LEU* 3.2 29.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 33 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A ASN 3.0 16.2 + - - +
30A LEU* 2.8 10.8 + - + +
32A LYS* 1.3 75.9 - - + +
34A LEU* 1.3 61.1 + - - +
35A GLU 3.1 0.2 - - - -
36A LEU* 3.5 8.0 + - + +
37A GLU* 3.0 43.3 + - + +
152A ALA* 3.8 22.4 - - + +
155A LYS* 4.7 8.5 - - + +
156A THR* 3.6 34.3 - - + +
157A PRO* 4.6 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 34 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A LEU* 2.8 41.7 + - + +
31A LEU* 3.1 25.1 + - + +
33A VAL* 1.3 76.1 - - + +
35A GLU* 1.3 61.5 + - - +
37A GLU* 4.9 0.2 - - - -
38A GLY 3.1 1.7 + - - -
39A LEU* 2.8 44.7 + - + -
40A LYS* 3.3 22.7 - - + +
43A VAL* 4.0 28.5 - - + -
149A LEU* 3.8 29.2 - - + -
152A ALA* 5.3 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 35 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A LEU 3.1 10.9 + - - +
32A LYS* 3.2 13.9 - - - +
33A VAL 3.1 0.4 - - - -
34A LEU* 1.3 77.4 - - - +
36A LEU* 1.3 71.6 + - + +
38A GLY* 3.0 14.4 + - - -
40A LYS* 2.6 47.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 36 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A LYS* 3.2 19.5 + - + +
33A VAL* 3.5 7.8 + - + +
35A GLU* 1.3 86.7 - - + +
37A GLU* 1.3 69.1 + - - +
38A GLY 3.3 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 37 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A VAL* 3.0 33.0 + - + +
36A LEU* 1.3 85.5 - - + +
38A GLY* 1.3 65.8 + - - +
39A LEU* 3.3 31.0 - - + +
148A LYS* 3.8 23.0 + - - +
152A ALA* 4.4 4.4 - - + +
155A LYS* 3.5 26.6 + - - +
----------------------------------------------------------
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