Contacts of the helix formed by residues 7 - 29 (chain B) in PDB entry 3KZ3
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 7 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B SER 3.9 2.9 + - - +
6B LEU* 1.3 78.1 - - - +
8B GLN* 1.3 63.2 + - - +
9B GLU* 3.5 8.1 + - - +
10B GLN* 3.0 38.0 + - - +
11B LEU* 3.0 21.0 + - - +
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Residues in contact with GLN 8 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B THR* 1.3 74.6 - - - +
9B GLU* 1.3 58.7 + - - +
11B LEU* 3.2 13.7 + - + +
12B GLU* 2.9 49.9 + - + +
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Residues in contact with GLU 9 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B THR* 3.2 7.3 + - - +
8B GLN* 1.3 82.7 - - - +
10B GLN* 1.3 60.7 + - + +
12B GLU* 3.7 7.7 - - - +
13B ASP* 2.9 36.2 + - - +
16B ARG* 3.5 19.8 + - - -
77B PRO* 4.9 4.9 - - - +
78B SER* 3.6 29.2 - - - +
81B ARG* 4.4 6.6 + - - -
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Residues in contact with GLN 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B SER 4.5 1.6 - - - +
6B LEU* 3.4 25.6 - - + +
7B THR* 3.0 44.0 + - - +
9B GLU* 1.3 80.0 - - + +
11B LEU* 1.3 61.0 + - - +
13B ASP* 3.3 13.5 + - - +
14B ALA* 3.1 22.7 + - - +
55B ALA* 3.4 27.7 - - + +
56B LEU 5.0 4.0 + - - +
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Residues in contact with LEU 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B LEU* 4.0 20.6 - - + +
7B THR 3.0 18.1 + - - +
8B GLN* 3.5 13.0 - - + +
10B GLN* 1.3 77.9 - - - +
12B GLU* 1.3 57.4 + - + +
14B ALA* 3.4 4.4 + - - +
15B ARG* 2.9 27.7 + - - +
51B ASN 5.6 0.2 - - - +
52B GLY* 3.7 27.8 - - - +
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Residues in contact with GLU 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B GLN* 2.9 41.5 + - + +
9B GLU* 3.3 9.8 + - - +
11B LEU* 1.3 73.6 - - + +
13B ASP* 1.3 67.0 + - - +
15B ARG* 3.3 24.9 + - - +
16B ARG* 3.0 49.4 + - - +
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Residues in contact with ASP 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B GLU* 2.9 26.2 + - - +
10B GLN* 3.5 15.3 - - - +
12B GLU* 1.3 76.1 - - - +
14B ALA* 1.3 57.7 - - - +
16B ARG* 2.7 29.3 + - - -
17B LEU* 2.9 29.6 + - - +
56B LEU* 4.2 13.2 - - + +
75B PHE* 3.2 17.8 - - - +
76B SER* 2.6 37.1 + - - -
77B PRO* 4.1 0.5 - - - +
78B SER* 3.8 6.9 + - - -
79B ILE* 4.7 4.9 - - - +
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Residues in contact with ALA 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B LEU* 5.3 1.1 - - + -
10B GLN 3.1 12.6 + - - +
11B LEU 3.7 4.9 - - - +
13B ASP* 1.3 80.5 - - - +
15B ARG* 1.3 58.7 + - - +
17B LEU* 3.2 6.6 + - - +
18B LYS* 2.9 26.3 + - - +
49B LEU 3.4 23.8 - - - +
50B PHE 3.4 9.7 - - - +
51B ASN 4.7 0.4 - - - -
52B GLY* 3.7 25.4 - - - +
54B ASN 5.7 0.7 - - - +
56B LEU* 5.0 3.6 - - + +
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Residues in contact with ARG 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B LEU 2.9 17.9 + - - +
12B GLU* 3.3 24.7 + - - +
14B ALA* 1.3 76.8 - - - +
16B ARG* 1.3 65.9 + - - +
18B LYS* 3.5 6.3 + - - +
19B ALA* 3.1 24.3 + - + +
50B PHE 5.1 0.2 - - - -
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Residues in contact with ARG 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B GLU* 3.5 16.6 + - - -
12B GLU* 3.0 31.6 + - - +
13B ASP* 2.7 38.1 + - - +
15B ARG* 1.3 78.1 - - + +
17B LEU* 1.3 67.2 + - - +
19B ALA* 3.3 6.8 + - - +
20B ILE* 3.0 27.5 + - - +
23B LYS* 4.8 0.7 + - - -
74B GLU 3.8 13.7 - - - +
75B PHE* 2.8 30.6 + - - -
77B PRO* 3.8 14.5 - - - +
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Residues in contact with LEU 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B ASP 2.9 16.6 + - - +
14B ALA* 3.6 4.7 - - - +
16B ARG* 1.3 75.0 - - - +
18B LYS* 1.3 65.5 + - - +
20B ILE* 3.1 5.1 + - + +
21B TRP* 2.9 20.5 + - - +
49B LEU 4.3 10.8 - - - +
50B PHE* 3.6 29.8 - - + -
56B LEU* 3.9 22.9 - - + -
64B LEU* 3.8 21.1 - - + -
68B LEU* 3.7 26.2 - - + -
75B PHE* 3.7 31.2 - - + +
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Residues in contact with LYS 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B ALA 2.9 10.2 + - - +
15B ARG* 3.9 6.1 - - - +
17B LEU* 1.3 77.0 - - - +
19B ALA* 1.3 57.9 + - - +
21B TRP* 3.4 10.6 + - + +
22B GLU* 2.9 47.5 + - + +
50B PHE* 3.5 31.4 + - + +
51B ASN* 3.1 28.9 + - - +
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Residues in contact with ALA 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B ARG* 3.1 20.8 + - + +
16B ARG* 3.6 7.2 - - - +
17B LEU 3.2 0.2 - - - -
18B LYS* 1.3 74.5 - - - +
20B ILE* 1.3 60.3 + - - +
22B GLU* 3.9 5.4 - - - +
23B LYS* 2.9 53.0 + - - +
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Residues in contact with ILE 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B ARG 3.0 20.4 + - - +
17B LEU* 3.1 5.8 + - - +
19B ALA* 1.3 74.7 - - - +
21B TRP* 1.3 67.8 + - - +
23B LYS* 3.1 18.9 + - - +
24B LYS* 2.9 46.3 + - + +
68B LEU* 4.2 15.9 - - + -
70B VAL* 4.0 15.3 - - + -
74B GLU* 3.9 42.4 - - + +
75B PHE* 4.0 20.0 - - + -
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Residues in contact with TRP 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B LEU 2.9 12.1 + - - +
18B LYS* 3.5 11.0 - - + +
20B ILE* 1.3 77.8 - - - +
22B GLU* 1.3 84.7 + - + +
25B LYS* 2.9 69.8 + - + +
30B LEU* 3.8 12.6 - - + -
31B SER 3.4 23.8 - - - -
32B TYR* 3.9 13.0 - - + +
35B VAL* 3.3 40.4 - - + -
50B PHE* 3.4 44.4 - + + -
68B LEU* 3.8 24.6 - - + +
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Residues in contact with GLU 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B LYS* 2.9 38.6 + - + +
19B ALA* 4.0 5.8 - - - +
20B ILE 3.2 0.2 - - - -
21B TRP* 1.3 100.2 + - + +
23B LYS* 1.3 62.4 + - + +
25B LYS* 3.3 34.6 - - - +
26B ASN* 5.2 1.7 + - - -
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Residues in contact with LYS 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B ARG 4.8 0.4 + - - -
19B ALA* 2.9 48.4 + - - +
20B ILE* 3.6 20.5 - - - +
22B GLU* 1.3 79.6 - - + +
24B LYS* 1.3 64.0 + - + +
26B ASN* 5.0 3.5 + - - +
27B GLU* 4.6 5.9 + - - +
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Residues in contact with LYS 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B ILE* 2.9 26.4 + - + +
23B LYS* 1.3 80.9 - - + +
25B LYS* 1.3 66.6 + - - +
26B ASN 3.3 2.7 - - - -
27B GLU* 3.2 37.2 + - - +
28B LEU* 3.0 37.2 + - + +
68B LEU* 2.9 29.8 + - + +
69B LYS* 3.2 23.2 + - - +
70B VAL* 3.8 15.8 - - + +
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Residues in contact with LYS 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B TRP* 2.9 69.7 + - + +
22B GLU* 3.3 34.5 - - - +
23B LYS 3.7 0.2 - - - -
24B LYS* 1.3 75.8 - - - +
26B ASN* 1.3 84.1 + - - +
28B LEU* 3.3 2.8 + - - -
29B GLY 3.0 3.5 + - - -
30B LEU* 2.9 37.8 + - - +
31B SER* 5.8 0.9 - - - -
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Residues in contact with ASN 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B GLU 5.2 1.9 + - - -
23B LYS 5.0 3.7 + - - +
24B LYS 3.3 0.8 - - - -
25B LYS* 1.3 107.0 + - - +
27B GLU* 1.3 64.4 + - - +
29B GLY* 3.0 14.8 + - - -
30B LEU 5.1 2.2 + - - -
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Residues in contact with GLU 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B LYS 4.6 3.7 + - - +
24B LYS* 3.2 48.4 + - - +
26B ASN* 1.3 78.3 - - - +
28B LEU* 1.3 72.9 + - + +
29B GLY 3.2 0.6 + - - -
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Residues in contact with LEU 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B LYS* 3.0 37.6 + - + +
25B LYS 3.9 1.6 - - - +
27B GLU* 1.3 91.8 - - + +
29B GLY* 1.3 63.2 - - - +
30B LEU* 3.4 29.1 + - + +
67B ILE 3.9 5.8 - - - +
68B LEU* 3.7 38.6 - - + +
69B LYS* 4.2 28.9 - - + -
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Residues in contact with GLY 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B LYS 3.0 0.6 + - - -
26B ASN* 3.0 16.3 + - - -
27B GLU 3.2 0.8 + - - -
28B LEU* 1.3 79.2 - - - +
30B LEU* 1.3 64.3 + - - +
34B SER* 4.3 3.3 + - - -
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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
------------------------------------------------------------
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