Contacts of the helix formed by residues 5 - 25 (chain B) in PDB entry 2NS8
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 ASP 5 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B LEU* 1.3 84.5 + - - +
6B LYS* 1.3 68.4 + - - +
7B SER* 2.8 35.3 + - - +
8B LYS* 3.1 17.8 + - - +
9B VAL* 3.3 12.3 + - - +
44B HIS* 3.7 7.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 6 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B ASP* 1.3 75.8 - - + +
7B SER* 1.3 61.6 + - - +
9B VAL* 3.4 5.7 + - + +
10B ILE* 3.2 45.5 + - + +
44B HIS* 2.6 54.0 + - + +
45B VAL* 4.5 9.3 - - + +
50B ALA 5.8 0.2 + - - -
54B ALA* 4.8 10.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 7 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B ASP* 2.8 19.8 + - - +
6B LYS* 1.3 78.7 - - - +
8B LYS* 1.3 66.1 + - - +
10B ILE* 3.4 5.3 + - - +
11B ASN* 3.0 37.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 8 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B LEU* 5.0 10.3 - - + +
5B ASP* 3.1 21.3 + - - +
7B SER* 1.3 80.9 + - - +
9B VAL* 1.3 63.4 + - + +
11B ASN* 3.8 10.9 - - + +
12B SER* 2.9 45.6 + - - +
15B GLU* 5.3 7.5 + - - -
34B LEU* 4.3 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 9 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B LEU* 4.4 9.9 - - + -
5B ASP 3.3 12.8 + - - +
6B LYS* 3.6 9.2 - - + +
7B SER 3.2 0.4 - - - -
8B LYS* 1.3 76.0 - - + +
10B ILE* 1.3 58.5 + - + +
12B SER* 3.7 1.7 - - - -
13B ALA* 2.7 34.9 + - - +
30B LEU* 4.0 13.7 - - + +
34B LEU* 4.3 15.3 - - + -
41B LEU* 3.7 28.5 - - + -
44B HIS* 3.9 30.5 - - + -
45B VAL* 4.1 14.4 - - + -
51B LEU* 5.4 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 10 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B LYS* 3.2 34.2 + - + +
7B SER* 3.8 6.5 - - - +
9B VAL* 1.3 77.3 - - + +
11B ASN* 1.3 66.8 + - - +
13B ALA* 3.6 4.3 - - - +
14B LEU* 3.0 25.1 + - + +
45B VAL* 5.5 2.2 - - + -
51B LEU* 4.9 5.6 - - + -
54B ALA* 3.3 35.9 - - + +
55B LEU* 3.8 17.4 - - + +
58B GLU* 3.1 39.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 11 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B SER* 3.0 30.2 + - - +
8B LYS* 3.8 11.3 - - + +
10B ILE* 1.3 79.6 - - - +
12B SER* 1.3 63.6 + - - +
14B LEU* 3.3 4.4 + - - +
15B GLU* 3.0 38.1 + - - +
58B GLU* 4.7 4.0 + - - -
62B ARG* 2.9 31.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 12 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B LYS* 2.9 37.0 + - - -
9B VAL 3.8 1.8 - - - -
11B ASN* 1.3 74.9 - - - +
13B ALA* 1.3 60.3 + - - +
15B GLU* 3.2 14.4 + - - +
16B LEU* 2.7 30.1 + - - +
30B LEU* 4.0 8.3 - - - -
33B LYS* 3.8 14.1 - - - +
34B LEU* 3.4 27.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 13 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B VAL 2.7 22.4 + - - +
10B ILE* 3.6 1.1 - - - +
11B ASN 3.3 0.2 - - - -
12B SER* 1.3 72.4 - - - +
14B LEU* 1.3 51.0 + - - +
16B LEU* 3.1 5.5 + - - +
17B LEU* 2.7 34.3 + - - +
25B LEU* 4.4 5.0 - - + +
30B LEU* 3.9 17.2 - - + +
51B LEU* 3.8 19.7 - - + -
55B LEU* 3.6 30.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 14 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B ILE* 3.0 15.0 + - + +
11B ASN* 3.4 8.7 - - - +
13B ALA* 1.3 73.8 - - - +
15B GLU* 1.3 64.2 + - + +
17B LEU* 3.3 9.6 + - + +
18B ASN* 3.3 18.6 + - - -
55B LEU* 3.6 31.4 - - + +
58B GLU* 4.1 17.9 - - + -
59B MET* 4.5 11.4 - - + -
62B ARG* 3.4 41.3 - - - +
93B HIS* 3.3 44.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 15 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B LYS* 5.3 6.6 + - - -
11B ASN* 3.0 33.5 + - - +
12B SER* 3.6 14.7 + - - +
14B LEU* 1.3 75.1 - - + +
16B LEU* 1.3 61.8 + - - +
18B ASN* 3.3 12.1 + - - +
19B GLU* 3.2 27.2 + - - +
33B LYS* 4.1 19.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 16 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B SER 2.7 17.4 + - - +
13B ALA* 3.3 9.4 - - - +
15B GLU* 1.3 70.6 - - - +
17B LEU* 1.3 66.3 + - - +
19B GLU* 3.2 21.2 + - + +
20B VAL* 3.0 47.5 + - + +
25B LEU* 3.3 26.5 - - + -
29B LYS* 3.8 17.7 - - + +
30B LEU* 3.5 39.0 - - + +
33B LYS* 4.1 12.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 17 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B ALA 2.7 16.1 + - - +
14B LEU* 3.5 20.9 - - + +
15B GLU 3.3 0.2 - - - -
16B LEU* 1.3 74.3 - - - +
18B ASN* 1.3 57.1 + - - +
20B VAL* 4.7 2.2 - - - -
21B GLY* 2.7 35.2 + - - +
22B ILE* 3.7 33.2 - - + +
25B LEU* 4.2 16.4 - - + -
55B LEU* 4.7 7.6 - - + -
59B MET* 4.9 4.3 - - - -
93B HIS* 4.0 20.0 - - + -
94B ARG* 3.3 27.8 - - - +
96B GLY* 5.3 0.2 - - - -
99B VAL* 4.0 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 18 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B LEU 3.3 8.7 + - - -
15B GLU* 3.5 11.3 - - - +
16B LEU 3.3 0.2 - - - -
17B LEU* 1.3 79.6 - - - +
19B GLU* 1.3 57.4 + - + +
92B SER 4.7 2.5 + - - +
93B HIS* 3.6 23.5 + - - +
94B ARG* 3.1 52.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 19 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B GLU* 3.2 17.7 - - - +
16B LEU* 3.5 22.8 - - + +
18B ASN* 1.3 79.1 - - - +
20B VAL* 1.3 62.7 + - + +
33B LYS* 3.4 32.3 + - - -
94B ARG* 2.8 11.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 20 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B LEU* 3.0 40.1 + - + +
19B GLU* 1.3 83.6 - - + +
21B GLY* 1.3 75.3 + - - +
23B GLU* 5.7 0.3 - - - +
24B GLY* 3.6 18.8 + - - +
25B LEU* 3.5 21.5 - - + +
29B LYS* 4.4 16.6 - - + -
94B ARG* 3.5 13.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 21 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B LEU* 2.7 29.7 + - - -
20B VAL* 1.3 81.7 - - - +
22B ILE* 1.3 60.2 + - - -
23B GLU* 3.5 1.6 - - - -
25B LEU* 3.1 20.6 + - - +
94B ARG* 3.3 16.3 - - - -
95B ASP* 3.1 14.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 22 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B LEU* 3.7 11.7 - - + +
21B GLY* 1.3 69.9 - - - -
23B GLU* 1.3 87.2 + - + +
24B GLY 3.3 0.3 + - - -
25B LEU* 3.3 8.2 + - + +
48B LYS* 3.0 26.1 + - - +
49B ARG* 5.4 0.4 - - - +
52B LEU* 3.9 36.1 - - + -
95B ASP* 2.9 33.0 + - + +
98B LYS* 4.1 29.4 - - + +
99B VAL* 3.9 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 23 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B VAL 5.7 0.4 - - - +
21B GLY 3.5 0.6 - - - -
22B ILE* 1.3 93.5 - - + +
24B GLY* 1.3 57.9 + - - +
25B LEU 3.7 1.9 + - - +
26B THR* 4.8 3.8 - - - +
48B LYS* 3.8 12.9 + - - +
95B ASP* 5.3 2.2 - - - +
98B LYS* 3.4 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 24 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B VAL* 3.6 19.0 + - - +
21B GLY 3.5 5.0 + - - -
22B ILE 3.2 0.6 - - - -
23B GLU* 1.3 76.9 - - - +
25B LEU* 1.3 61.4 + - - +
26B THR* 4.2 2.2 - - - -
29B LYS* 3.1 39.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 25 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B ALA* 4.4 4.5 - - - +
16B LEU* 3.3 40.2 - - + -
17B LEU* 4.2 18.8 - - + +
20B VAL* 3.8 5.2 - - + -
21B GLY 3.1 15.8 + - - +
22B ILE* 3.3 8.2 + - - +
23B GLU 4.0 0.5 - - - +
24B GLY* 1.3 76.1 - - - +
26B THR* 1.3 67.7 + - - +
30B LEU* 5.0 2.9 - - + -
48B LYS* 3.1 27.1 + - - -
51B LEU* 4.1 22.9 - - + -
52B LEU* 4.3 14.1 - - + -
55B LEU* 3.9 27.4 - - + -
----------------------------------------------------------
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