Contacts of the helix formed by residues 21 - 31 (chain D) in PDB entry 1NUE
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 VAL 21 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ILE* 4.1 11.9 - - + -
29A GLU* 3.0 18.6 + - - +
35A LEU* 5.1 7.9 - - + -
38A MET* 4.6 8.5 - - + -
11D ILE* 4.0 14.3 - - + +
15D GLY 4.4 0.4 - - - +
16D VAL* 4.0 38.1 - - + -
20D LEU* 1.3 77.2 - - - +
22D GLY* 1.3 64.0 + - - +
24D ILE* 3.4 1.7 + - - +
25D ILE* 3.1 42.0 + - + +
74D VAL* 4.0 21.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 22 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A GLY* 3.3 30.4 - - - -
25A ILE* 3.9 5.6 - - - +
26A LYS* 4.0 9.0 - - - -
29A GLU* 2.8 20.5 + - - -
21D VAL* 1.3 72.8 - - - +
23D GLU* 1.3 57.3 + - - +
25D ILE* 3.4 1.1 + - - -
26D LYS* 2.9 31.9 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
26A LYS* 3.7 34.3 + - + +
29A GLU* 4.6 0.8 + - - -
19D GLY 5.4 1.3 + - - +
20D LEU* 3.4 20.7 + - + +
21D VAL 3.3 0.6 - - - -
22D GLY* 1.3 76.7 - - - +
24D ILE* 1.3 61.9 + - - +
26D LYS* 3.5 16.7 + - - +
27D ARG* 3.3 38.4 + - - +
108D PHE* 3.4 34.3 - - + -
30F GLN* 5.4 3.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 24 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D ILE* 4.0 35.2 - - + -
15D GLY* 5.3 0.2 - - - -
20D LEU* 3.0 30.9 + - + +
21D VAL 3.9 2.9 - - - +
23D GLU* 1.3 73.7 - - - +
25D ILE* 1.3 67.3 + - - +
27D ARG* 3.2 16.7 + - - +
28D PHE* 3.3 25.7 - - + -
76D MET* 5.1 3.8 - - + -
104D ILE* 4.2 19.7 - - + -
108D PHE* 5.1 6.5 - - + -
116D ILE* 4.2 24.9 - - + +
117D ILE* 3.8 24.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 25 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A VAL* 4.1 9.2 - - + -
22A GLY* 3.8 11.2 - - - +
25A ILE* 4.0 16.6 - - + -
38A MET* 5.1 0.2 - - + -
11D ILE* 4.6 3.8 - - + -
21D VAL* 3.1 38.7 + - + +
22D GLY 3.9 3.1 - - - +
24D ILE* 1.3 75.5 - - - +
26D LYS* 1.3 63.9 + - - +
28D PHE* 3.0 14.9 + - - +
29D GLU* 3.0 28.6 + - - +
35D LEU* 5.5 2.0 - - + -
38D MET* 3.8 28.0 - - + -
74D VAL* 5.0 1.1 - - + -
76D MET* 3.9 19.7 - - - -
78D TRP* 4.2 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 26 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A GLY* 4.0 5.6 - - - -
23A GLU* 3.7 32.9 + - + +
26A LYS* 4.1 17.8 - - + +
26B LYS* 5.8 4.2 - - - +
22D GLY 2.9 17.5 + - - +
23D GLU* 3.6 21.3 + - - +
24D ILE 3.2 0.2 - - - -
25D ILE* 1.3 78.8 - - - +
27D ARG* 1.3 61.3 + - + +
29D GLU* 3.2 13.4 + - + +
30D GLN* 3.0 56.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 27 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D GLU* 3.3 29.0 + - - +
24D ILE* 3.2 11.0 + - - +
26D LYS* 1.3 78.4 - - + +
28D PHE* 1.3 60.6 + - + +
30D GLN* 4.0 17.3 + - - +
31D LYS* 3.4 22.0 + - - +
90D MET* 3.6 16.6 - - + +
102D GLY 3.1 19.6 + - - -
103D THR 3.6 13.7 + - - -
104D ILE* 3.8 20.1 - - + +
107D ASP* 2.8 30.1 + - - +
108D PHE* 3.4 32.1 - - - -
107E ASP 4.6 2.1 - - - +
30F GLN* 5.9 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 28 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D ILE* 4.3 29.2 - - + -
24D ILE* 3.3 29.6 - - + -
25D ILE* 3.0 3.1 + - - +
27D ARG* 1.3 75.6 - - + +
29D GLU* 1.3 66.0 + - - +
31D LYS* 3.5 7.2 + - - +
33D PHE* 3.4 42.2 + + - +
76D MET* 5.9 0.7 - - + -
78D TRP* 3.5 46.9 - + + -
83D VAL* 5.6 2.0 - - + -
87D GLY* 4.3 14.6 - - - -
90D MET* 4.1 23.6 - - + -
91D LEU* 4.3 13.9 - - + -
104D ILE* 3.9 21.5 - - + -
117D ILE* 4.5 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 29 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A VAL 4.6 1.6 - - - +
19A GLY* 3.1 37.0 - - - +
21A VAL* 3.0 34.2 + - - +
22A GLY* 2.8 29.5 + - - -
23A GLU 4.5 0.7 + - - -
25D ILE* 3.0 16.1 + - + +
26D LYS* 3.7 12.2 - - + +
28D PHE* 1.3 78.1 - - - +
30D GLN* 1.3 63.2 + - + +
32D GLY* 3.1 15.6 + - - -
33D PHE 4.4 4.1 + - - +
35D LEU* 6.2 0.4 - - + -
78D TRP* 3.9 18.8 - - + -
18E ARG* 4.8 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 30 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26D LYS* 3.0 52.0 + - + +
27D ARG* 4.0 18.3 + - - +
29D GLU* 1.3 77.9 - - + +
31D LYS* 1.3 58.0 + - - +
18E ARG* 3.0 21.4 + - - +
20E LEU* 5.4 2.5 - - + +
23E GLU* 5.5 3.5 - - - +
27E ARG* 6.1 0.2 - - - +
107E ASP* 3.8 9.3 + - - +
108E PHE* 3.4 43.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 31 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D ARG 3.4 15.5 + - - +
28D PHE 3.7 6.5 - - - +
29D GLU 3.1 0.4 - - - -
30D GLN* 1.3 79.6 - - - +
32D GLY* 1.3 57.9 + - - +
33D PHE* 3.5 23.6 - - + -
86D THR* 3.8 28.1 - - - +
90D MET* 4.2 11.9 - - + -
150D VAL* 5.0 0.3 - - - +
18E ARG* 4.0 1.8 + - - -
96E PRO 4.3 9.7 + - - -
97E ALA* 6.0 0.2 - - - +
99E SER 5.5 0.6 + - - -
105E ARG 3.6 5.5 + - - -
106E GLY* 2.8 31.9 + - - +
107E ASP 3.4 13.2 - - - +
108E PHE 3.6 11.5 - - - +
109E CYS* 2.8 27.9 + - - +
110E ILE* 3.4 21.7 - - + +
----------------------------------------------------------
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