Contacts of the helix formed by residues 9 - 29 (chain P) in PDB entry 6P18
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 THR 9 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8P LEU* 1.3 80.2 - - + +
10P LYS* 1.3 69.1 + - - +
11P GLU* 3.5 30.5 + - + +
12P GLN* 3.7 17.7 - - + +
13P HIS* 3.1 23.2 + - - +
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Residues in contact with LYS 10 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9P THR* 1.3 82.3 + - - +
11P GLU* 1.3 63.6 + - - +
13P HIS* 3.3 13.9 + - + +
14P GLU* 3.1 38.3 + - + +
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Residues in contact with GLU 11 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9P THR* 3.5 14.6 + - + +
10P LYS* 1.3 79.1 - - - +
12P GLN* 1.3 101.6 + - - +
14P GLU* 2.9 30.9 - - - +
15P TRP* 3.0 20.1 + - - +
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Residues in contact with GLN 12 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8P LEU* 4.0 18.8 - - + -
9P THR* 3.7 15.3 - - + +
10P LYS 3.3 0.2 - - - -
11P GLU* 1.3 115.8 + - - +
13P HIS* 1.3 59.5 + - - +
15P TRP* 3.3 32.6 - - - +
16P LEU* 3.0 38.2 + - + +
142P TYR* 3.2 37.6 - - + +
146P ASP* 5.0 0.2 - - - +
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Residues in contact with HIS 13 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8P LEU* 4.6 10.0 - - + +
9P THR 3.1 20.3 + - - +
10P LYS* 3.3 18.4 + - + +
12P GLN* 1.3 77.9 - - - +
14P GLU* 1.3 60.4 + - - +
16P LEU* 3.6 2.7 + - - +
17P ASN* 2.9 41.6 + - + +
135P ASN* 5.1 13.1 + - - -
138P LEU* 4.3 22.9 - - + +
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Residues in contact with GLU 14 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10P LYS* 3.1 30.1 + - - +
11P GLU* 2.9 27.9 - - - +
13P HIS* 1.3 76.9 + - - +
15P TRP* 1.3 75.1 + - - +
17P ASN* 3.8 6.7 + - - +
18P GLY* 3.0 24.9 + - - -
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Residues in contact with TRP 15 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11P GLU* 3.0 19.7 + - - +
12P GLN* 3.3 30.7 - - - +
13P HIS 3.3 0.2 - - - -
14P GLU* 1.3 86.1 - - - +
16P LEU* 1.3 67.7 + - + +
18P GLY* 3.4 1.7 + - - -
19P TRP* 3.0 69.9 + + - +
145P LEU* 3.8 20.4 - - + -
146P ASP* 4.4 9.0 - - - -
149P PHE* 3.7 28.7 - + - -
150P LYS* 4.7 7.0 - - - -
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Residues in contact with LEU 16 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8P LEU* 6.0 1.8 - - + -
12P GLN* 3.0 47.2 + - - +
13P HIS* 4.1 2.2 - - - +
15P TRP* 1.3 85.8 - - + +
17P ASN* 1.3 61.1 + - - +
19P TRP* 4.6 3.8 - - + +
20P LEU* 3.0 40.0 + - + +
138P LEU* 4.9 19.5 - - + +
141P ILE* 3.7 29.2 - - + -
142P TYR* 3.8 25.6 - - + -
145P LEU* 3.8 22.7 - - + -
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Residues in contact with ASN 17 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13P HIS* 2.9 33.7 + - + +
14P GLU* 3.8 7.1 + - - +
16P LEU* 1.3 77.3 - - - +
18P GLY* 1.3 58.3 + - - +
20P LEU 3.4 0.5 + - - -
21P GLU* 3.0 36.0 + - - +
87P TYR* 4.2 10.7 + - - -
88P TYR* 2.4 41.8 + - - +
138P LEU* 5.4 1.9 - - + +
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Residues in contact with GLY 18 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14P GLU 3.0 16.6 + - - -
15P TRP 3.9 0.9 - - - -
17P ASN* 1.3 79.5 - - - +
19P TRP* 1.3 55.9 + - - +
21P GLU* 3.2 21.4 - - - +
22P LEU* 3.0 30.4 + - - +
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Residues in contact with TRP 19 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15P TRP* 3.0 73.2 + + - +
16P LEU* 4.1 7.4 - - + +
18P GLY* 1.3 76.6 - - - +
20P LEU* 1.3 62.5 + - + +
22P LEU* 3.5 16.2 + - + +
23P TRP* 3.0 27.2 + - - +
58P CYS* 5.3 6.1 - - + -
62P ASP* 4.3 27.4 - - + -
66P ILE* 4.9 20.5 - - + +
145P LEU* 5.6 5.4 - - + -
149P PHE* 4.8 20.0 - + - -
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Residues in contact with LEU 20 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16P LEU* 3.0 43.4 + - + +
17P ASN 3.9 0.2 - - - +
18P GLY 3.3 0.2 - - - -
19P TRP* 1.3 80.7 - - + +
21P GLU* 1.3 58.2 + - - +
23P TRP* 3.4 33.8 + - + +
24P GLY* 2.7 24.6 + - - -
66P ILE* 5.2 9.2 - - + -
70P VAL* 5.6 4.7 - - + -
84P LEU* 4.8 12.1 - - + -
88P TYR* 3.7 43.7 - - + +
138P LEU* 4.9 8.5 - - + -
141P ILE* 4.4 15.0 - - + -
145P LEU* 5.1 4.9 - - + -
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Residues in contact with GLU 21 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17P ASN* 3.0 28.5 + - - +
18P GLY* 3.2 25.0 - - - +
20P LEU* 1.3 74.1 - - - +
22P LEU* 1.3 77.4 + - - +
24P GLY* 3.8 2.4 - - - +
25P ALA* 2.9 26.9 + - - +
55P ARG* 4.7 17.3 + - - +
56P PRO* 4.7 13.9 - - - +
88P TYR* 3.9 17.9 - - + +
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Residues in contact with LEU 22 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18P GLY 3.0 18.4 + - - +
19P TRP* 3.7 17.9 - - + +
21P GLU* 1.3 105.4 + - - +
23P TRP* 1.3 57.4 + - - +
25P ALA* 3.4 2.9 + - - +
26P TRP* 3.0 26.2 + - - +
56P PRO* 3.3 34.3 - - + +
57P MET 3.9 3.1 - - - +
58P CYS* 3.5 39.7 + - + +
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Residues in contact with TRP 23 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19P TRP* 3.0 18.1 + - + +
20P LEU* 3.7 29.2 - - + +
21P GLU 3.3 0.2 - - - -
22P LEU* 1.3 76.3 - - - +
24P GLY* 1.3 63.9 + - - +
26P TRP* 3.2 7.4 + + - +
27P VAL* 3.0 51.4 + - + +
32P LEU* 5.3 3.6 - - + -
40P ILE* 5.3 4.0 - - + -
58P CYS* 4.9 3.6 - - - -
63P GLY* 3.6 22.2 + - - -
66P ILE* 3.5 25.6 - - + -
67P SER* 3.4 30.0 - - - +
70P VAL* 3.6 32.5 - - + -
81P PHE* 4.5 4.7 - + - -
84P LEU* 5.5 4.5 - - + -
85P LEU* 3.7 32.1 - - + -
88P TYR* 5.3 5.8 - - + -
89P ALA* 5.5 1.8 - - + -
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Residues in contact with GLY 24 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20P LEU 2.7 18.5 + - - -
21P GLU 3.8 0.9 - - - -
22P LEU 3.3 0.2 - - - -
23P TRP* 1.3 78.1 - - - +
25P ALA* 1.3 57.0 + - - +
27P VAL* 3.6 1.2 + - - -
28P TYR* 3.0 29.8 + - - +
55P ARG* 4.3 0.7 - - - -
88P TYR 3.4 24.9 - - - -
89P ALA* 3.4 17.8 - - - +
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Residues in contact with ALA 25 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21P GLU 2.9 16.1 + - - +
22P LEU 3.7 2.5 - - - +
23P TRP 3.3 0.2 - - - -
24P GLY* 1.3 75.7 - - - +
26P TRP* 1.3 62.7 + - - +
28P TYR* 3.8 8.2 + - - +
29P SER* 3.8 6.1 + - - -
53P MET* 5.0 4.7 - - - +
55P ARG* 3.8 31.3 - - + +
56P PRO 3.3 28.5 - - - +
57P MET* 3.6 18.1 - - + +
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Residues in contact with TRP 26 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22P LEU 3.0 13.4 + - - +
23P TRP* 3.2 11.6 + - + +
25P ALA* 1.3 77.9 - - - +
27P VAL* 1.3 74.7 + - + +
29P SER* 3.1 23.6 + - - -
30P GLY 4.1 0.9 + - - -
31P ARG* 3.3 37.4 + - + +
32P LEU* 3.7 37.0 - - + -
57P MET* 3.6 18.6 - - + +
58P CYS* 3.4 25.4 - - - -
59P ASN 3.1 28.5 + - - -
60P ASP* 3.8 34.0 - - - +
63P GLY* 4.4 15.9 - - - -
64P MET* 4.5 14.8 - - + -
67P SER* 4.7 1.1 - - - -
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Residues in contact with VAL 27 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23P TRP* 3.0 50.4 + - + +
24P GLY 4.3 2.7 - - - +
26P TRP* 1.3 90.6 - - + +
28P TYR* 1.3 60.6 + - - +
30P GLY* 2.9 19.1 + - - +
31P ARG 5.1 2.0 - - - +
32P LEU* 4.1 14.8 - - + -
40P ILE* 3.8 28.7 - - + -
43P PHE* 5.4 0.4 - - + -
44P MET* 3.5 20.9 - - + +
85P LEU* 5.9 0.4 - - + -
89P ALA* 4.9 12.1 - - + -
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Residues in contact with TYR 28 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24P GLY 3.0 19.5 + - - +
25P ALA* 4.1 6.1 - - - +
26P TRP 3.3 0.6 - - - -
27P VAL* 1.3 76.9 - - - +
29P SER* 1.3 51.3 + - - +
30P GLY 3.2 0.2 - - - -
43P PHE* 6.2 0.7 - + - -
44P MET* 4.2 10.7 - - - +
47P VAL* 4.4 7.0 - - + +
51P ARG* 2.6 64.2 + - + +
52P VAL* 3.7 27.5 + - + +
53P MET* 4.3 7.2 - - - +
54P THR 6.2 0.2 - - - -
55P ARG* 3.4 18.6 - - - +
89P ALA* 3.4 16.1 - - + +
90P HIS* 3.9 40.9 + + + -
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Residues in contact with SER 29 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25P ALA 3.8 2.4 + - - -
26P TRP 3.1 15.1 + - - -
27P VAL 3.2 0.2 - - - -
28P TYR* 1.3 78.9 - - - +
30P GLY* 1.3 57.3 + - - +
31P ARG* 3.2 38.3 + - - +
49P PRO 5.1 0.2 - - - +
51P ARG* 2.7 18.1 + - - -
53P MET* 3.8 23.8 - - - +
57P MET* 3.3 15.7 - - - +
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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