Contacts of the helix formed by residues 22 - 37 (chain D) in PDB entry 1NPP
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 D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19D GLU* 2.9 36.8 + - + +
20D PRO 3.1 2.0 - - - +
21D GLY* 1.3 88.8 - - - +
23D GLU* 1.3 56.8 + - - +
24D ASN 3.3 2.7 - - - -
25D GLU* 3.1 28.4 + - + +
26D ALA* 2.9 28.3 + - - +
158D HIS* 4.1 29.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 23 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18D VAL* 3.7 29.6 - - + -
19D GLU 3.9 0.9 - - - -
20D PRO* 3.6 0.3 - - - +
21D GLY* 3.0 34.4 + - - +
22D LYS* 1.3 72.9 - - - +
24D ASN* 1.3 64.2 + - - +
26D ALA* 3.4 2.1 + - - +
27D LYS* 3.1 23.4 + - - +
48D VAL* 4.0 12.5 - - + +
132D ASN* 3.4 33.3 + - - +
136D PRO* 3.6 9.5 - - - +
137D GLY 2.9 25.9 + - - +
138D TYR 4.2 7.0 - - - +
139D ILE* 3.7 5.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 24 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22D LYS 3.3 0.8 - - - -
23D GLU* 1.3 78.2 + - - +
25D GLU* 1.3 71.2 + - - +
27D LYS* 3.5 5.8 + - - +
28D GLU* 3.2 28.3 + - + +
48D VAL* 4.1 14.1 - - - +
130D LEU* 3.5 39.2 + - - +
132D ASN* 5.6 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 25 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21D GLY 4.2 3.0 - - - +
22D LYS* 3.1 41.1 + - + +
24D ASN* 1.3 82.5 + - + +
26D ALA* 1.3 60.1 + - - +
28D GLU* 3.4 5.5 + - - +
29D ASN* 2.9 37.9 + - - +
158D HIS* 3.9 17.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 26 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18D VAL* 3.9 16.2 - - + -
22D LYS 2.9 15.2 + - - +
23D GLU 3.7 5.4 - - - +
24D ASN 3.4 0.2 - - - -
25D GLU* 1.3 76.4 - - - +
27D LYS* 1.3 53.3 + - - +
29D ASN* 3.2 2.3 + - - +
30D LEU* 2.7 36.2 + - - +
139D ILE* 4.0 2.9 - - + -
156D THR* 4.1 2.8 - - - +
157D PRO 4.1 4.7 - - - -
158D HIS* 3.7 32.7 - - + +
159D VAL* 3.9 11.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 27 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D GLU 3.1 16.1 + - - +
24D ASN* 3.7 6.5 - - - +
26D ALA* 1.3 78.1 - - - +
28D GLU* 1.3 67.9 + - - +
30D LEU* 3.1 5.7 + - - +
31D LEU* 2.9 44.6 + - + +
46D VAL* 3.0 46.3 + - + +
47D ILE* 4.8 2.8 - - - +
48D VAL* 3.9 22.6 - - + +
130D LEU* 6.3 1.0 - - - +
139D ILE* 3.4 14.0 - - + +
186D ARG* 6.1 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 28 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24D ASN 3.2 17.3 + - - +
25D GLU* 3.9 6.1 - - - +
27D LYS* 1.3 91.2 - - - +
29D ASN* 1.3 67.5 + - - +
31D LEU* 3.5 20.4 + - - +
32D LYS* 3.1 41.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 29 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25D GLU* 2.9 23.1 + - - +
26D ALA 3.6 1.8 - - - +
28D GLU* 1.3 77.5 - - - +
30D LEU* 1.3 62.8 + - - +
32D LYS* 3.4 17.7 + - - +
33D VAL* 3.0 26.0 + - - +
156D THR* 3.6 17.9 - - + -
157D PRO* 3.1 38.9 + - + +
158D HIS* 3.8 13.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 30 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16D LEU* 4.1 15.9 - - + -
26D ALA 2.7 21.5 + - - +
27D LYS* 3.1 7.2 + - - +
29D ASN* 1.3 70.8 - - - +
31D LEU* 1.3 65.0 + - - +
33D VAL* 3.0 5.3 + - + +
34D LEU* 2.9 48.1 + - + +
43D VAL* 6.1 0.9 - - + -
46D VAL* 4.0 31.0 - - + -
139D ILE* 5.1 2.2 - - + -
141D ILE* 4.1 17.9 - - + -
153D ILE* 4.1 21.1 - - + +
156D THR* 3.5 22.9 - - + +
159D VAL* 4.9 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 31 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D LYS* 2.9 32.6 + - + +
28D GLU* 3.9 32.1 - - - +
29D ASN 3.4 0.2 - - - -
30D LEU* 1.3 76.8 - - - +
32D LYS* 1.3 62.4 + - + +
34D LEU* 3.3 13.9 + - + +
35D GLU* 3.1 23.0 + - - +
40D LYS* 5.3 0.9 - - - +
46D VAL* 4.0 30.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 32 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28D GLU* 3.1 35.0 + - - +
29D ASN* 3.7 15.7 - - - +
31D LEU* 1.3 77.7 - - + +
33D VAL* 1.3 57.5 + - + +
35D GLU* 3.6 6.8 - - - +
36D LEU* 3.0 32.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 33 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29D ASN* 3.0 18.5 + - + +
30D LEU* 3.5 9.9 - - + +
32D LYS* 1.3 73.0 - - + +
34D LEU* 1.3 62.7 + - + +
36D LEU* 3.2 4.8 + - - +
37D GLU* 2.7 39.8 + - + +
152D ALA* 3.8 33.2 - - + +
155D LYS 5.3 1.1 - - - +
156D THR* 3.4 30.3 - - + +
157D PRO* 5.1 4.9 - - + -
860D IPA 5.2 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 34 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30D LEU* 2.9 35.4 + - + +
31D LEU* 3.7 25.4 - - + +
33D VAL* 1.3 78.0 - - + +
35D GLU* 1.3 60.9 + - - +
38D GLY* 3.2 3.1 + - - -
39D LEU* 2.8 43.9 + - + +
40D LYS* 3.6 21.6 + - + +
43D VAL* 4.0 33.0 - - + -
46D VAL* 4.6 3.1 - - + -
149D LEU* 3.7 29.8 - - + -
152D ALA* 5.5 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 35 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31D LEU 3.1 16.2 + - - +
32D LYS* 3.6 7.4 - - - +
34D LEU* 1.3 74.3 - - - +
36D LEU* 1.3 74.8 + - + +
38D GLY* 3.4 10.6 + - - -
40D LYS* 2.8 44.3 + - + +
859D IPA 4.0 40.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 36 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32D LYS 3.0 19.6 + - - +
33D VAL* 3.9 5.2 - - - +
35D GLU* 1.3 86.9 - - + +
37D GLU* 1.3 66.2 + - + +
38D GLY 3.2 1.4 + - - -
859D IPA 5.8 3.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 37 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33D VAL* 2.7 36.8 + - + +
36D LEU* 1.3 77.4 - - + +
38D GLY* 1.3 63.0 + - - +
39D LEU* 3.3 22.7 - - + +
148D LYS* 3.5 39.1 + - - -
152D ALA* 4.6 4.3 - - + -
860D IPA 3.5 33.7 + - + +
----------------------------------------------------------
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