Contacts of the helix formed by residues 19 - 29 (chain O) 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 ASP 19 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2368A A 3.7 34.3 - - - +
2369A A 4.4 4.4 + - - -
17O ARG 4.2 1.0 + - - -
18O THR* 1.3 73.8 - - - +
20O TYR* 1.3 55.2 + - - +
21O HIS* 2.9 10.5 + - - +
22O GLN* 2.6 50.9 + - + +
23O ARG* 2.9 23.9 + - - +
25O ARG* 5.7 0.3 + - - -
105O GLY* 5.3 2.6 - - - +
106O LEU* 4.0 21.3 - - + +
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Residues in contact with TYR 20 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2368A A 4.7 2.8 + - - -
3007B G 5.0 0.2 - - - -
3008B G 2.6 37.7 + - - -
3010B C 3.5 14.3 + - - -
10O MET* 3.4 34.8 - - + -
12O ARG* 3.5 31.2 + - + +
13O ARG* 4.3 9.8 - - + +
18O THR* 3.4 33.6 + - + -
19O ASP* 1.3 70.0 - - - +
21O HIS* 1.3 66.1 + - + +
23O ARG* 3.6 8.8 - - + +
24O LEU* 3.2 21.5 + - - +
23R THR* 5.5 9.4 - - + +
24R SER 5.8 0.2 - - - +
26R PRO* 3.5 32.8 - - + +
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Residues in contact with HIS 21 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2366A C 5.5 0.2 + - - -
2367A A 5.0 1.6 - - - -
2368A A 5.0 10.3 - + + -
2369A A 3.4 51.4 + - - +
2370A A 4.8 16.9 + - - -
19O ASP* 2.9 6.5 + - - +
20O TYR* 1.3 77.3 - - + +
22O GLN* 1.3 65.9 + - - +
24O LEU* 3.5 8.7 + - - +
25O ARG* 3.4 39.1 + - - +
23R THR* 3.3 37.6 + - + +
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Residues in contact with GLN 22 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2413A A 3.7 24.7 + - - +
2414A A 4.2 6.6 + - - -
2415A A 4.0 6.7 - - + -
19O ASP* 2.6 32.8 + - - +
21O HIS* 1.3 70.7 - - - +
23O ARG* 1.3 65.7 + - - +
25O ARG* 3.1 28.4 + - - +
26O LEU* 2.9 39.4 + - + +
103O ASP* 4.2 0.7 - - - +
104O ILE* 4.6 7.0 - - - +
105O GLY* 3.3 35.4 + - - +
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Residues in contact with ARG 23 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3007B G 2.7 40.7 + - - -
3008B G 2.7 29.9 + - - -
18O THR* 4.1 12.6 - - + -
19O ASP 2.9 17.4 + - - +
20O TYR* 3.6 13.5 - - - +
21O HIS 3.2 0.2 - - - -
22O GLN* 1.3 77.5 - - - +
24O LEU* 1.3 57.8 + - - +
26O LEU* 3.1 11.7 + - + +
27O LEU* 2.8 49.2 + - + +
33O ARG* 3.8 12.6 - - - +
50O LEU* 3.5 13.3 - - - +
55O ASP* 2.7 38.0 + - - -
103O ASP* 5.8 0.7 - - - +
26R PRO* 4.8 8.6 - - + +
27R GLN* 4.7 3.6 + - - +
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Residues in contact with LEU 24 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20O TYR 3.2 13.8 + - - +
21O HIS* 3.8 8.5 - - - +
22O GLN 3.2 0.2 - - - -
23O ARG* 1.3 75.0 - - - +
25O ARG* 1.3 65.7 + - + +
27O LEU* 3.3 3.1 + - - -
28O LYS* 2.9 48.9 + - + +
26R PRO* 3.9 22.2 - - + +
29R ALA* 4.4 16.2 - - + +
30R VAL* 3.8 26.9 - - + -
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Residues in contact with ARG 25 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2326A U 5.9 1.6 - - - -
2327A A 5.8 2.4 + - - -
2369A A 5.0 4.9 + - - -
2414A A 4.8 2.2 + - - +
2415A A 2.9 68.5 + - + +
2416A G 3.2 28.7 - - - +
2417A C 5.3 3.8 - - - -
19O ASP* 5.7 0.4 + - - -
21O HIS* 3.4 31.2 + - - +
22O GLN* 3.1 29.6 + - - +
24O LEU* 1.3 79.5 - - + +
26O LEU* 1.3 58.9 + - - +
28O LYS* 3.3 20.3 - - + +
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Residues in contact with LEU 26 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2414A A 4.9 3.4 - - + +
2415A A 2.9 34.6 + - + +
22O GLN* 2.9 37.2 + - + +
23O ARG* 3.1 12.1 + - - +
25O ARG* 1.3 76.9 - - - +
27O LEU* 1.3 60.5 + - - +
28O LYS 2.9 3.5 + - - -
29O SER* 3.1 11.6 + - - -
31O LYS 5.3 0.7 - - - +
33O ARG* 4.0 23.8 - - + +
101O VAL* 3.9 21.4 - - + +
102O LEU 3.9 18.8 - - - +
103O ASP* 3.5 35.0 - - + +
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Residues in contact with LEU 27 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23O ARG* 2.8 53.0 + - + +
24O LEU 3.3 5.6 + - - +
26O LEU* 1.3 73.6 - - - +
28O LYS* 1.3 62.6 + - - +
29O SER* 3.3 0.7 - - - -
30O GLY* 3.1 16.1 + - - +
31O LYS 5.7 5.4 - - - +
33O ARG* 4.2 26.5 - - + +
50O LEU* 3.7 36.2 - - + +
26R PRO* 4.6 9.9 - - + +
27R GLN* 5.3 1.1 - - - +
30R VAL* 3.9 36.1 - - + +
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Residues in contact with LYS 28 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2416A G 3.4 25.8 + - - +
2417A C 3.0 28.6 + - - +
24O LEU* 2.9 48.0 + - + +
25O ARG* 3.3 21.3 - - - +
26O LEU 2.9 0.6 + - - -
27O LEU* 1.3 77.8 - - - +
29O SER* 1.3 63.0 + - - +
30O GLY* 3.0 2.8 + - - -
30R VAL* 5.6 3.8 - - + -
69R ASP* 5.5 8.9 + - - +
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Residues in contact with SER 29 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2415A A 3.2 28.7 + - - -
2416A G 3.8 5.6 - - - -
26O LEU 3.1 13.2 + - - -
28O LYS* 1.3 79.3 - - - +
30O GLY* 1.3 61.8 + - - +
31O LYS* 3.0 29.8 + - - +
33O ARG* 6.1 0.2 - - - +
101O VAL* 3.4 25.3 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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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