Contacts of the helix formed by residues 4 - 21 (chain P) in PDB entry 1NJI
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 ASN 4 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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656A G 2.7 23.9 + - - +
657A G 3.5 7.7 + - - -
27E ARG* 3.0 38.7 + - - +
29E ASP* 4.0 4.9 - - - -
2P LYS* 4.8 1.6 - - - +
3P THR* 1.3 73.1 + - - +
5P PRO* 1.3 70.9 - - - +
6P ARG* 2.7 30.3 + - - +
7P LEU* 3.6 24.1 - - + +
8P SER* 3.0 21.0 + - - -
37P ARG* 6.1 0.4 - - - +
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Residues in contact with PRO 5 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26E VAL 5.7 3.8 - - - +
27E ARG* 3.9 6.3 - - - -
28E SER* 4.4 17.3 - - - +
29E ASP* 3.0 25.6 - - + +
3P THR 3.2 7.9 - - - +
4P ASN* 1.3 90.1 - - - +
6P ARG* 1.3 58.0 + - + +
8P SER* 3.4 7.9 - - - -
9P SER* 3.1 31.4 + - - -
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Residues in contact with ARG 6 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25E PRO* 3.4 42.0 - - - +
26E VAL 5.2 6.0 + - - +
27E ARG* 4.1 20.0 - - - +
4P ASN* 2.7 17.4 + - - +
5P PRO* 1.3 77.0 - - + +
7P LEU* 1.3 66.2 + - - +
8P SER 3.0 1.1 - - - -
9P SER* 3.0 7.5 + - - -
10P LEU* 2.8 24.5 + - - +
99P GLU* 5.2 8.8 + - - +
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Residues in contact with LEU 7 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
656A G 4.1 17.0 - - - +
2P LYS* 3.9 33.4 - - + +
4P ASN* 3.4 23.8 + - + +
6P ARG* 1.3 77.9 - - - +
8P SER* 1.3 64.2 + - - +
10P LEU* 3.4 7.3 + - + +
11P ILE* 3.1 31.5 + - + +
33P LEU* 4.3 30.5 - - + +
37P ARG* 5.9 2.0 - - + +
40P HIS* 4.9 7.2 - - + -
79P VAL* 4.4 18.6 - - + -
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Residues in contact with SER 8 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2P LYS* 5.1 11.7 - - - +
4P ASN 3.0 16.9 + - - -
5P PRO* 3.4 10.8 - - - -
6P ARG 3.0 0.2 - - - -
7P LEU* 1.3 79.5 - - - +
9P SER* 1.3 63.2 + - - +
11P ILE* 3.2 11.5 + - - +
12P ALA* 3.1 19.4 + - - +
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Residues in contact with SER 9 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5P PRO 3.1 15.1 + - - -
6P ARG* 3.0 7.0 + - - -
8P SER* 1.3 75.0 - - - +
10P LEU* 1.3 60.6 + - - +
12P ALA* 3.0 9.1 + - - +
13P ASP* 2.8 39.7 + - - +
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Residues in contact with LEU 10 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6P ARG 2.8 15.8 + - - +
7P LEU* 3.6 9.2 - - + +
9P SER* 1.3 74.8 - - - +
11P ILE* 1.3 59.5 + - - +
13P ASP* 3.1 7.7 + - + +
14P LEU* 2.8 47.4 + - + +
33P LEU* 4.2 18.6 - - + -
79P VAL* 4.3 21.1 - - + -
98P LEU* 4.2 19.5 - - + -
99P GLU* 3.8 45.5 - - + +
102P ILE* 4.3 8.5 - - + -
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Residues in contact with ILE 11 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2P LYS* 4.9 9.0 - - + -
7P LEU* 3.1 25.7 + - + +
8P SER* 3.4 10.5 - - - +
9P SER 3.1 0.2 - - - -
10P LEU* 1.3 80.7 - - - +
12P ALA* 1.3 62.7 + - - +
14P LEU* 3.5 9.3 + - - +
15P LYS* 3.2 37.3 + - - +
30P ALA* 4.2 6.9 - - + +
33P LEU* 3.7 50.7 - - + +
34P GLU* 3.9 26.9 - - + +
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Residues in contact with ALA 12 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1277A C 3.3 47.0 - - - +
8P SER 3.1 10.6 + - - +
9P SER* 3.0 11.7 + - - +
11P ILE* 1.3 75.1 - - - +
13P ASP* 1.3 69.9 + - - +
15P LYS* 3.2 6.6 + - - +
16P SER* 3.0 19.6 + - - -
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Residues in contact with ASP 13 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9P SER* 2.8 26.0 + - - +
10P LEU* 3.5 11.0 - - + +
12P ALA* 1.3 79.3 - - - +
14P LEU* 1.3 64.0 + - - +
15P LYS 3.1 0.3 + - - -
16P SER* 3.1 8.5 + - - +
17P ALA* 3.0 23.4 + - - +
99P GLU* 5.2 7.0 - - + +
102P ILE* 4.0 14.9 - - + +
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Residues in contact with LEU 14 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10P LEU* 2.8 32.2 + - + +
11P ILE* 3.6 7.6 - - - +
13P ASP* 1.3 73.2 - - - +
15P LYS* 1.3 60.9 + - - +
17P ALA* 3.5 0.9 + - - +
18P ALA* 3.1 18.5 + - - +
26P TRP* 3.3 52.4 - - + +
29P VAL* 3.8 15.3 - - + -
30P ALA* 3.9 11.7 - - + +
33P LEU* 3.8 29.4 - - + -
98P LEU* 4.3 7.6 - - + -
102P ILE* 3.2 30.7 - - + -
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Residues in contact with LYS 15 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1277A C 3.5 24.2 + - - +
1278A A 2.8 28.9 + - - +
1279A U 5.6 1.2 + - - -
11P ILE* 3.2 22.1 - - - +
12P ALA* 3.2 7.8 + - - +
13P ASP 3.1 0.8 - - - -
14P LEU* 1.3 73.1 - - - +
16P SER* 1.3 67.3 - - - +
17P ALA 2.9 3.4 + - - -
18P ALA* 2.9 15.4 + - - +
19P ARG* 2.9 39.6 + - - +
27P GLY* 5.3 2.0 - - - -
30P ALA* 4.1 13.7 - - + -
31P GLU* 6.4 1.1 - - - -
34P GLU* 3.0 36.0 + - - -
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Residues in contact with SER 16 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1277A C 3.3 32.4 + - - -
12P ALA 3.0 9.6 + - - -
13P ASP* 3.6 11.9 - - - -
15P LYS* 1.3 79.1 - - - +
17P ALA* 1.3 57.5 + - - +
19P ARG* 4.0 2.1 - - - +
20P SER* 3.1 39.7 + - - -
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Residues in contact with ALA 17 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13P ASP 3.0 10.0 + - - +
14P LEU 3.8 4.9 - - - +
15P LYS 3.0 0.8 - - - -
16P SER* 1.3 76.1 - - - +
18P ALA* 1.3 60.0 + - - +
19P ARG 3.2 0.4 - - - -
20P SER* 4.9 0.4 - - - -
21P SER* 3.0 38.5 + - - +
26P TRP* 3.9 14.1 - - + -
102P ILE* 3.5 32.1 - - + -
106P PRO* 3.7 10.8 - - + +
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Residues in contact with ALA 18 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14P LEU 3.1 9.8 + - - +
15P LYS* 2.9 6.3 + - - +
17P ALA* 1.3 77.6 - - - +
19P ARG* 1.3 62.0 + - + +
21P SER 3.0 13.2 - - - +
22P GLY 4.4 0.3 - - - -
23P GLY 3.1 28.2 - - - +
24P ALA* 5.0 0.9 - - - -
26P TRP* 4.0 4.7 - - + +
27P GLY* 3.3 36.8 - - - +
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Residues in contact with ARG 19 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1276A U 3.2 56.5 + - - +
1277A C 2.6 40.9 + - - +
1278A A 2.8 41.6 + - - -
15P LYS* 2.9 35.7 + - - +
16P SER* 4.1 2.7 - - - +
18P ALA* 1.3 79.7 - - + +
20P SER* 1.3 69.8 + - - +
21P SER 3.3 3.8 - - - +
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Residues in contact with SER 20 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1276A U 5.1 4.7 + - - -
16P SER* 3.1 22.5 + - - -
17P ALA* 4.9 0.4 - - - -
19P ARG* 1.3 77.7 - - - +
21P SER* 1.3 71.8 + - - +
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Residues in contact with SER 21 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17P ALA* 3.0 9.3 + - - +
18P ALA 3.0 20.4 - - - +
19P ARG 3.3 2.4 - - - +
20P SER* 1.3 86.0 - - - +
22P GLY* 1.3 60.5 + - - +
23P GLY 3.1 2.9 - - - -
106P PRO* 2.9 53.3 - - - +
107P GLU* 3.9 10.5 + - - -
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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) + - + + + + + -
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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