Contacts of the helix formed by residues 9 - 29 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A LEU* 1.3 78.8 - - - +
10A LYS* 1.3 65.7 + - - +
11A GLU* 3.9 4.5 + - - +
12A GLN* 3.0 40.9 + - - +
13A HIS* 2.8 22.1 + - - +
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Residues in contact with LYS 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A THR* 1.3 73.7 - - - +
11A GLU* 1.3 61.3 + - - +
13A HIS* 3.3 5.1 + - - +
14A GLU* 2.9 44.2 + - + +
21F G 4.0 22.1 + - - +
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Residues in contact with GLU 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A THR* 3.3 5.6 + - - +
10A LYS* 1.3 80.0 - - - +
12A GLN* 1.3 64.9 + - + +
14A GLU* 3.4 6.5 + - - +
15A TRP* 2.9 30.5 + - + +
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Residues in contact with GLN 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A LEU* 3.8 17.8 - - + +
9A THR* 3.0 43.0 + - - +
11A GLU* 1.3 78.3 - - + +
13A HIS* 1.3 57.6 + - - +
15A TRP* 3.7 5.5 - - - +
16A LEU* 2.9 32.6 + - - +
142A TYR* 3.2 54.7 + - + +
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Residues in contact with HIS 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A LEU* 4.0 19.5 - - + +
9A THR 2.8 19.0 + - - +
10A LYS* 3.7 5.4 + - - +
12A GLN* 1.3 77.4 - - - +
14A GLU* 1.3 62.4 + - - +
16A LEU* 3.8 1.5 - - - +
17A ASN* 2.8 48.1 + - + +
135A ASN* 4.8 16.9 + - - -
138A LEU* 3.7 28.4 - - + +
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Residues in contact with GLU 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A LYS* 2.9 34.7 + - + +
11A GLU* 4.0 7.1 - - - +
13A HIS* 1.3 82.3 + - - +
15A TRP* 1.3 58.6 + - - +
17A ASN* 3.7 6.4 + - + +
18A GLY* 2.9 26.0 + - - -
21C GLU* 5.1 7.4 - - - +
56C PRO* 5.7 0.2 - - - +
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Residues in contact with TRP 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A GLU* 2.9 22.4 + - + +
12A GLN* 3.7 2.2 - - - +
14A GLU* 1.3 76.6 - - - +
16A LEU* 1.3 82.0 + - + +
18A GLY* 3.2 3.3 + - - -
19A TRP* 3.0 45.4 + + - +
142A TYR* 3.6 42.2 - + - -
145A LEU* 4.3 8.7 - - + -
146A ASP* 4.1 25.1 - - + -
149A PHE* 3.9 22.0 - + + -
54C THR* 3.2 27.7 + - - +
55C ARG* 4.1 9.4 - - + -
56C PRO* 3.9 22.5 - - + +
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Residues in contact with LEU 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A LEU* 4.0 3.4 - - + -
12A GLN 2.9 18.1 + - - +
13A HIS 4.0 2.7 - - - +
15A TRP* 1.3 88.6 - - + +
17A ASN* 1.3 57.8 + - - +
19A TRP* 3.4 2.1 + - - -
20A LEU* 2.9 54.5 + - + +
138A LEU* 3.1 46.7 - - + +
141A ILE* 4.1 11.0 - - + -
142A TYR* 3.7 20.6 - - + +
145A LEU* 3.6 30.1 - - + -
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Residues in contact with ASN 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A HIS* 2.8 35.9 + - + +
14A GLU* 3.7 8.2 + - - +
16A LEU* 1.3 75.2 - - - +
18A GLY* 1.3 63.0 + - - +
20A LEU* 3.7 1.0 - - - +
21A GLU* 2.7 62.6 + - - +
87A TYR* 4.5 6.6 + - - -
88A TYR* 2.7 35.4 + - - +
138A LEU* 4.7 2.7 - - + +
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Residues in contact with GLY 18 (chain A).
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 2.9 15.9 + - - -
15A TRP 3.7 2.7 - - - -
17A ASN* 1.3 79.8 - - - +
19A TRP* 1.3 61.4 + - - +
21A GLU* 3.3 9.6 + - - +
22A LEU* 3.1 26.7 + - - +
22C LEU* 6.3 0.4 - - - -
56C PRO* 4.0 17.0 - - - -
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Residues in contact with TRP 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A TRP* 3.0 45.9 + + - +
16A LEU* 3.7 7.9 - - + +
18A GLY* 1.3 75.2 - - - +
20A LEU* 1.3 57.5 + - - +
22A LEU* 3.4 13.0 + - + +
23A TRP* 2.9 29.3 + - - +
58A CYS* 4.3 6.3 - - + -
62A ASP* 3.3 39.9 - - + -
66A ILE* 3.5 16.8 - - + +
145A LEU* 4.4 13.7 - - + -
149A PHE* 3.4 29.2 - + - -
152A ARG* 5.8 0.2 - - - -
54C THR* 2.8 35.7 + - + -
55C ARG 3.4 9.2 - - - -
56C PRO* 3.5 24.4 - - + +
57C MET* 3.9 13.2 - - + -
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Residues in contact with LEU 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A LEU* 2.9 49.3 + - + +
18A GLY 3.2 0.2 - - - -
19A TRP* 1.3 73.2 - - - +
21A GLU* 1.3 60.7 + - - +
23A TRP* 3.5 25.4 - - + -
24A GLY* 2.8 25.6 + - - -
66A ILE* 4.1 10.8 - - + -
70A VAL* 4.1 20.6 - - + -
84A LEU* 4.8 4.7 - - + -
88A TYR* 3.7 30.5 - - + -
138A LEU* 3.7 26.7 - - + -
141A ILE* 4.9 8.5 - - + -
145A LEU* 5.3 0.9 - - + -
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Residues in contact with GLU 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A ASN* 2.7 43.5 + - - +
18A GLY* 3.3 8.0 + - - +
20A LEU* 1.3 74.3 - - - +
22A LEU* 1.3 66.4 + - + +
24A GLY* 3.3 0.7 + - - -
25A ALA* 3.0 24.6 + - - +
55A ARG* 5.3 1.7 + - - -
56A PRO 4.3 1.2 - - - +
87A TYR* 5.4 3.3 + - + -
88A TYR* 3.7 23.2 - - + +
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Residues in contact with LEU 22 (chain A).
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 3.1 12.9 + - - +
19A TRP* 3.6 13.2 - - + +
21A GLU* 1.3 77.6 - - + +
23A TRP* 1.3 56.4 + - - +
25A ALA* 3.3 3.1 + - - +
26A TRP* 2.9 28.4 + - - +
56A PRO* 3.4 42.0 - - + +
57A MET* 3.7 9.9 - - - +
58A CYS* 3.9 14.6 - - + +
22C LEU* 3.7 19.7 - - + -
56C PRO* 3.5 31.6 - - + -
57C MET 3.5 23.3 - - - +
58C CYS* 5.2 1.3 - - - -
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Residues in contact with TRP 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A TRP 2.9 18.3 + - - +
20A LEU* 3.5 26.0 - - + +
22A LEU* 1.3 76.4 - - - +
24A GLY* 1.3 72.3 + - - +
26A TRP* 3.2 4.9 + + - +
27A VAL* 2.9 45.3 + - + +
40A ILE* 4.1 15.7 - - + -
58A CYS* 4.1 9.8 - - - -
63A GLY* 3.7 6.5 - - - -
66A ILE* 3.3 39.0 - - + -
67A SER* 2.8 32.1 + - - +
70A VAL* 3.9 28.5 - - + -
84A LEU* 4.6 13.2 - - + -
85A LEU* 3.9 22.0 - - + -
88A TYR* 4.3 15.7 - - + -
89A ALA* 5.3 0.7 - - + -
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Residues in contact with GLY 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A LEU 2.8 16.2 + - - -
23A TRP* 1.3 83.2 - - - +
25A ALA* 1.3 64.6 + - - +
27A VAL* 3.3 1.9 + - - -
28A TYR* 2.9 26.5 + - - +
88A TYR 3.4 27.6 - - - -
89A ALA* 3.5 9.5 - - - -
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Residues in contact with ALA 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A GLU 3.0 12.4 + - - +
22A LEU 3.6 1.3 - - - +
24A GLY* 1.3 76.1 - - - +
26A TRP* 1.3 63.9 + - - +
28A TYR* 3.4 0.6 + - - -
29A SER 3.4 4.5 + - - -
53A MET* 3.3 23.4 - - + +
55A ARG* 3.9 36.3 - - + +
56A PRO 3.1 28.0 - - - +
57A MET* 3.5 11.3 - - + +
88A TYR 3.9 1.6 + - - -
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Residues in contact with TRP 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A LEU 2.9 14.1 + - - +
23A TRP* 3.5 7.2 - + - +
25A ALA* 1.3 77.0 - - - +
27A VAL* 1.3 78.0 + - + +
29A SER* 2.7 24.1 + - - -
31A ARG* 3.4 53.1 + - + +
32A LEU* 3.9 22.0 - - + -
57A MET* 3.6 13.4 - - + +
58A CYS* 3.7 26.9 - - - -
59A ASN 3.7 2.7 + - - -
60A ASP* 3.0 40.1 + - + -
63A GLY* 3.3 39.3 - - - -
64A MET* 3.6 11.0 - - + -
67A SER* 3.5 12.3 - - - -
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Residues in contact with VAL 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A TRP* 2.9 50.4 + - + +
24A GLY* 3.3 6.7 + - - +
26A TRP* 1.3 90.4 - - + +
28A TYR* 1.3 63.3 + - - +
30A GLY* 3.0 14.7 + - - -
31A ARG 4.3 0.4 + - - +
32A LEU* 4.4 13.1 + - + +
40A ILE* 3.6 28.3 - - + -
44A MET* 3.4 17.8 - - + +
67A SER* 4.0 4.9 - - - +
85A LEU* 4.8 3.4 - - + -
89A ALA* 4.5 13.2 - - + -
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Residues in contact with TYR 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A GLY 2.9 9.9 + - - +
25A ALA 4.0 4.5 - - - +
26A TRP 3.4 0.4 - - - -
27A VAL* 1.3 79.5 - - - +
29A SER* 1.3 59.2 + - - +
30A GLY 3.1 1.1 + - - -
43A PHE* 5.0 0.7 - + - -
44A MET* 3.7 23.2 - - + +
47A VAL* 3.8 35.7 - - + +
48A GLU* 4.4 9.0 + - - -
51A ARG* 3.6 27.6 + - + -
53A MET* 4.4 10.8 - - + -
55A ARG* 3.8 18.4 - - - +
89A ALA 3.1 31.0 - - - +
90A HIS* 3.3 44.4 + + + -
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Residues in contact with SER 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A ALA 3.4 2.2 + - - -
26A TRP 2.7 22.8 + - - -
28A TYR* 1.3 76.6 - - - +
30A GLY* 1.3 59.0 + - - +
31A ARG* 3.0 38.1 + - - +
51A ARG* 4.0 20.2 + - - +
53A MET* 3.9 15.2 - - - -
57A MET* 3.7 18.1 - - - +
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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