Contacts of the helix formed by residues 9 - 29 (chain C) in PDB entry 6P1A
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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7C ASN 4.0 1.1 + - - +
8C LEU* 1.3 78.6 - - - +
10C LYS* 1.3 66.2 + - - +
11C GLU* 3.2 24.8 + - - +
12C GLN* 3.0 33.2 + - - +
13C HIS* 2.9 22.2 + - - +
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Residues in contact with LYS 10 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C THR* 1.3 74.6 - - - +
11C GLU* 1.3 64.5 + - - +
13C HIS* 3.3 4.9 + - - +
14C GLU* 2.9 58.4 + - + +
21D G 4.6 33.1 + - - +
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Residues in contact with GLU 11 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C THR* 3.2 25.0 + - - +
10C LYS* 1.3 80.9 + - - +
12C GLN* 1.3 73.3 + - + +
14C GLU* 3.3 9.1 + - - +
15C TRP* 2.9 26.2 + - - +
21D G 5.4 3.6 - - - +
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Residues in contact with GLN 12 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C LEU* 3.6 18.1 - - + +
9C THR* 3.0 40.7 + - - +
11C GLU* 1.3 81.8 - - + +
13C HIS* 1.3 63.3 + - - +
15C TRP* 3.7 6.3 - - - +
16C LEU* 2.9 27.4 + - - +
142C TYR* 3.3 49.6 + - + +
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Residues in contact with HIS 13 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C LEU* 4.3 18.8 - - + +
9C THR 2.9 19.2 + - - +
10C LYS* 3.6 5.4 - - - +
12C GLN* 1.3 77.2 - - - +
14C GLU* 1.3 64.1 + - - +
16C LEU* 3.4 2.5 + - - +
17C ASN* 2.8 44.0 + - + +
94C LYS* 5.9 4.0 + - - -
135C ASN* 4.9 14.8 + - - -
138C LEU* 3.4 33.1 - - + +
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Residues in contact with GLU 14 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C LYS* 2.9 48.2 + - + +
11C GLU* 3.9 7.0 - - - +
13C HIS* 1.3 81.9 - - - +
15C TRP* 1.3 58.0 + - - +
17C ASN* 3.7 6.7 + - - +
18C GLY* 2.9 26.7 + - - -
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Residues in contact with TRP 15 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C GLU 2.9 18.4 + - - +
12C GLN* 3.7 2.5 - - - +
14C GLU* 1.3 77.4 - - - +
16C LEU* 1.3 83.8 + - + +
18C GLY* 3.2 2.8 + - - -
19C TRP* 3.0 54.9 + + - +
142C TYR* 3.6 41.1 - + - -
145C LEU* 3.9 31.2 - - + -
146C ASP* 4.1 21.3 - - + -
149C PHE* 3.8 12.6 - + + -
201C CL 3.8 9.8 - - + +
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Residues in contact with LEU 16 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C LEU* 4.2 2.7 - - + -
12C GLN 2.9 18.7 + - - +
13C HIS* 3.9 4.0 - - - +
15C TRP* 1.3 89.4 - - + +
17C ASN* 1.3 57.4 + - - +
19C TRP* 3.4 2.6 + - - +
20C LEU* 2.9 50.9 + - + +
138C LEU* 3.0 48.9 - - + +
141C ILE* 4.1 13.2 - - + -
142C TYR* 3.7 18.6 - - + +
145C LEU* 3.5 29.8 - - + -
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Residues in contact with ASN 17 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C HIS* 2.8 35.6 + - + +
14C GLU* 3.7 7.3 + - - +
16C LEU* 1.3 75.0 - - - +
18C GLY* 1.3 61.7 + - - +
20C LEU* 3.7 1.1 - - - +
21C GLU* 2.7 57.2 + - - +
87C TYR* 4.4 8.8 + - - -
88C TYR* 2.8 35.3 + - - +
138C LEU* 4.8 1.7 - - + +
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Residues in contact with GLY 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C GLU 2.9 15.0 + - - -
15C TRP 3.7 2.7 - - - -
17C ASN* 1.3 79.8 - - - +
19C TRP* 1.3 61.1 + - - +
21C GLU* 3.2 10.9 + - - +
22C LEU* 3.0 29.3 + - - +
201C CL 4.2 10.5 - - - -
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Residues in contact with TRP 19 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A THR 5.4 4.0 - - - -
55A ARG 5.6 0.2 - - - -
56A PRO* 3.6 40.4 - - + -
15C TRP* 3.0 63.7 + + - +
16C LEU 3.6 7.6 - - - +
18C GLY* 1.3 75.0 - - - +
20C LEU* 1.3 58.9 + - - +
22C LEU* 3.3 15.9 + - + +
23C TRP* 2.9 28.3 + - - +
58C CYS* 4.4 4.0 - - + -
62C ASP* 3.6 25.8 - - + -
66C ILE* 3.5 28.4 - - + +
145C LEU* 4.1 14.4 - - + -
149C PHE* 3.6 28.9 - + - -
152C ARG* 5.8 0.4 - - - -
201C CL 3.7 13.0 - - + +
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Residues in contact with LEU 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C LEU* 2.9 38.7 + - + +
17C ASN 3.8 0.2 - - - +
18C GLY 3.2 0.4 - - - -
19C TRP* 1.3 72.8 - - - +
21C GLU* 1.3 60.5 + - - +
23C TRP* 3.6 18.0 - - + -
24C GLY* 2.8 25.3 + - - -
66C ILE* 4.3 8.7 - - + -
70C VAL* 4.1 25.1 - - + -
84C LEU* 4.6 5.2 - - + -
88C TYR* 3.4 37.1 - - + +
138C LEU* 3.6 36.1 - - + -
141C ILE* 4.9 9.6 - - + -
145C LEU* 5.5 1.1 - - + -
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Residues in contact with GLU 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A GLU* 5.1 6.6 - - - +
17C ASN* 2.7 45.4 + - - +
18C GLY* 3.2 8.1 + - - +
20C LEU* 1.3 73.9 - - - +
22C LEU* 1.3 67.5 + - + +
24C GLY* 3.3 0.9 + - - -
25C ALA* 3.0 24.9 + - - +
55C ARG* 5.4 2.1 + - - +
56C PRO 4.2 1.5 - - - +
87C TYR* 5.4 4.4 + - + -
88C TYR* 3.8 21.4 - - + +
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Residues in contact with LEU 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A GLY* 6.3 0.4 - - - -
22A LEU* 3.7 28.5 - - + -
56A PRO* 3.9 33.4 - - + -
18C GLY 3.0 19.8 + - - +
19C TRP* 3.6 20.0 - - + +
21C GLU* 1.3 78.0 - - + +
23C TRP* 1.3 57.0 + - - +
25C ALA* 3.3 3.6 + - - +
26C TRP* 2.9 27.5 + - - +
56C PRO* 3.4 27.8 - - + +
57C MET* 3.6 6.0 - - - +
58C CYS* 3.7 16.3 + - + +
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Residues in contact with TRP 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C TRP 2.9 14.6 + - - +
20C LEU* 3.6 22.0 - - + +
22C LEU* 1.3 76.7 - - - +
24C GLY* 1.3 71.2 + - - +
26C TRP* 3.2 4.2 + + - +
27C VAL* 2.9 43.9 + - + +
40C ILE* 4.2 11.9 - - + -
58C CYS* 4.1 9.6 - - - -
63C GLY 3.5 13.2 - - - -
66C ILE* 3.4 34.1 - - + -
67C SER* 2.7 34.4 + - - +
70C VAL* 4.0 25.4 - - + -
84C LEU* 4.5 17.0 - - + -
85C LEU* 3.4 33.7 - - + -
88C TYR* 4.3 16.6 - - + -
89C ALA 5.5 0.4 - - - -
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Residues in contact with GLY 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C LEU 2.8 16.3 + - - -
21C GLU 3.8 0.2 - - - -
23C TRP* 1.3 80.8 - - - +
25C ALA* 1.3 65.1 + - - +
27C VAL* 3.2 2.0 + - - +
28C TYR* 2.9 25.3 + - - +
88C TYR 3.6 27.6 - - - -
89C ALA* 3.7 10.3 - - - -
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Residues in contact with ALA 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C GLU 3.0 13.1 + - - +
22C LEU 3.6 0.7 - - - +
24C GLY* 1.3 74.8 - - - +
26C TRP* 1.3 63.3 + - - +
28C TYR* 3.3 10.6 + - - +
29C SER 3.5 4.9 + - - -
55C ARG* 3.8 32.1 - - + +
56C PRO 3.1 30.1 - - - +
57C MET* 3.3 23.8 - - + +
88C TYR 4.2 1.8 + - - -
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Residues in contact with TRP 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C LEU 2.9 14.0 + - - +
23C TRP* 3.2 7.2 + + - +
25C ALA* 1.3 75.4 - - - +
27C VAL* 1.3 72.9 + - + +
29C SER* 2.7 22.0 + - - -
30C GLY 4.0 1.6 + - - -
31C ARG* 3.8 37.6 + - + +
32C LEU* 3.7 35.4 - - + -
57C MET* 3.4 12.5 - - + +
58C CYS* 3.7 29.4 - - - -
59C ASN 3.8 1.8 - - - -
60C ASP* 3.0 42.3 + - + +
63C GLY* 3.4 19.7 - - - -
64C MET* 3.6 19.5 - - + -
67C SER* 3.2 22.4 - - - -
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Residues in contact with VAL 27 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C TRP* 2.9 51.7 + - + +
24C GLY* 3.7 6.3 - - - +
26C TRP* 1.3 90.2 - - + +
28C TYR* 1.3 64.2 + - - +
30C GLY* 3.0 14.7 + - - -
31C ARG 4.6 0.2 + - - -
32C LEU* 4.8 7.6 + - + +
40C ILE* 3.8 29.8 - - + -
43C PHE* 5.2 0.2 - - + -
44C MET* 3.1 30.5 - - + +
67C SER* 4.1 3.6 - - - +
85C LEU* 4.9 4.7 - - + -
89C ALA* 4.4 10.8 - - + -
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Residues in contact with TYR 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C GLY 2.9 16.3 + - - +
25C ALA 3.7 6.3 - - - +
26C TRP 3.3 0.2 - - - -
27C VAL* 1.3 76.5 - - - +
29C SER* 1.3 59.3 - - - +
30C GLY 3.5 0.3 + - - -
44C MET* 4.0 20.8 - - + +
47C VAL* 4.0 35.2 - - + +
48C GLU* 4.1 10.6 + - - +
50C GLY 4.8 3.8 + - - -
51C ARG* 4.8 10.1 - - + -
52C VAL* 4.2 32.5 - - + +
53C MET* 4.8 17.2 - - - -
55C ARG* 3.7 13.0 - - - +
89C ALA* 3.0 27.1 - - - +
90C HIS* 3.9 26.7 + + - -
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Residues in contact with SER 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C ALA 3.5 2.0 + - - -
26C TRP 2.7 22.2 + - - -
28C TYR* 1.3 78.3 - - - +
30C GLY* 1.3 59.9 + - - +
31C ARG* 3.2 28.0 + - - +
51C ARG* 6.0 3.4 - - - -
57C MET* 3.9 23.3 - - - -
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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
------------------------------------------------------------
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