Contacts of the helix formed by residues 15 - 36 (chain B) in PDB entry 1UAZ
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 GLU 15 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B ARG* 2.9 28.9 - - - +
14B PRO* 1.3 79.8 - - - +
16B THR* 1.3 63.0 + - - +
17B LEU 2.8 6.1 - - - -
18B TRP* 2.7 25.2 + - + +
19B LEU* 2.8 21.4 + - + +
85B TYR* 2.4 39.8 + - + +
207B LEU* 3.3 25.7 - - - +
208B GLY* 4.4 6.3 - - - -
211B THR* 3.8 29.6 - - - +
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Residues in contact with THR 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B ALA 3.0 16.3 + - - -
7B ASP* 4.0 2.0 - - - +
8B LEU* 3.3 18.1 + - - +
9B LEU* 4.0 7.7 + - + -
13B ARG* 3.4 55.7 + - + +
15B GLU* 1.3 77.8 - - - +
17B LEU* 1.3 52.1 + - - +
19B LEU* 3.8 11.4 - - + -
20B GLY* 2.6 29.0 + - - -
67B PHE* 3.2 29.7 - - - +
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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
----------------------------------------------------------
79A SER* 5.4 4.9 - - - +
5B GLY* 3.7 23.6 - - - -
6B ALA* 3.3 27.6 + - + +
8B LEU* 3.5 25.4 - - + +
14B PRO 3.9 1.6 - - - +
15B GLU 2.7 1.6 + - - -
16B THR* 1.3 83.2 + - - +
18B TRP* 1.3 89.2 + - + +
20B GLY* 3.5 1.0 - - - -
21B ILE* 3.0 36.5 + - + +
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Residues in contact with TRP 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A SER* 4.7 15.7 - - - -
4B VAL* 2.9 32.0 + - + +
5B GLY* 3.3 16.6 - - - -
15B GLU* 2.7 17.8 + - - +
17B LEU* 1.3 91.4 - - + +
19B LEU* 1.3 64.2 + - - +
21B ILE* 3.3 21.9 + - + +
22B GLY* 2.9 21.5 + - - -
208B GLY 3.3 23.4 + - - -
211B THR* 4.3 5.8 - - + +
212B LEU* 3.6 55.5 - - + +
215B MET* 3.8 14.1 - - + +
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Residues in contact with LEU 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B ARG* 4.4 1.3 - - - +
15B GLU* 2.8 24.6 + - + +
16B THR* 3.7 11.9 - - - +
18B TRP* 1.3 73.4 - - - +
20B GLY* 1.3 64.6 + - - +
23B THR* 3.1 21.3 + - - -
63B TYR* 3.5 25.3 - - + +
66B MET* 3.5 56.8 - - + +
67B PHE* 4.1 10.3 - - - +
85B TYR* 3.7 21.5 - - + +
88B ARG* 4.9 2.5 - - - +
211B THR* 3.6 25.1 - - + +
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Residues in contact with GLY 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B LEU* 5.0 2.5 - - - -
16B THR 2.6 22.8 + - - -
17B LEU 3.5 1.3 - - - -
18B TRP 3.1 0.2 - - - -
19B LEU* 1.3 71.0 - - - +
21B ILE* 1.3 56.0 + - - +
23B THR* 2.7 34.7 + - - -
24B LEU* 3.2 5.9 + - - +
67B PHE* 3.5 19.5 - - - -
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Residues in contact with ILE 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B LEU* 3.0 25.8 + - + +
18B TRP* 3.8 26.0 - - + +
20B GLY* 1.3 72.2 - - - +
22B GLY* 1.3 63.3 + - - +
24B LEU* 3.1 10.6 + - + +
25B LEU* 2.9 38.4 + - + +
215B MET* 3.5 21.1 - - + -
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Residues in contact with GLY 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B TRP 2.9 11.3 + - - -
20B GLY 3.0 0.6 + - - -
21B ILE* 1.3 76.2 - - - +
23B THR* 1.3 57.4 + - - +
25B LEU* 3.8 4.0 - - - +
26B MET* 2.9 34.4 + - - +
63B TYR* 3.7 17.9 - - - -
215B MET* 3.4 27.7 - - - +
219B VAL* 4.8 1.6 - - - -
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Residues in contact with THR 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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19B LEU 3.1 14.9 + - - -
20B GLY* 2.7 17.3 + - - -
22B GLY* 1.3 71.5 - - - -
24B LEU* 1.3 64.1 + - - +
26B MET* 3.2 4.0 + - - +
27B LEU* 2.8 46.4 + - + +
60B SER* 4.5 6.5 - - - +
63B TYR* 3.2 28.6 + - - -
64B LEU* 3.5 30.6 + - + -
67B PHE* 4.5 3.6 - - - +
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Residues in contact with LEU 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B GLY 3.2 5.6 + - - +
21B ILE* 3.1 14.5 + - + +
23B THR* 1.3 79.8 - - - +
25B LEU* 1.3 63.8 + - + +
27B LEU* 3.5 11.1 - - + +
28B ILE* 2.9 56.3 + - + +
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Residues in contact with LEU 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B ILE* 2.9 40.3 + - + +
22B GLY 3.9 2.7 - - - +
24B LEU* 1.3 78.3 - - + +
26B MET* 1.3 67.9 + - - +
28B ILE* 3.9 8.5 - - + +
29B GLY* 3.0 21.3 + - - -
215B MET* 4.0 10.8 - - + -
219B VAL* 3.7 37.2 - - + -
223B VAL* 4.1 6.0 - - - +
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Residues in contact with MET 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B GLY 2.9 18.5 + - - +
23B THR* 3.6 3.4 - - - +
25B LEU* 1.3 76.9 - - - +
27B LEU* 1.3 62.2 + - - +
29B GLY* 3.9 0.7 - - - -
30B THR* 2.8 27.5 + - - -
56B PRO* 3.6 9.5 - - - +
59B ALA* 3.1 32.1 - - + -
60B SER* 3.1 17.7 - - - +
63B TYR* 4.2 15.7 - - + -
218B ASP* 3.6 33.0 - - + -
219B VAL* 3.7 28.3 - - + +
222B LYS* 3.9 16.8 - - + -
223B VAL* 4.3 12.1 - - - -
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Residues in contact with LEU 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B THR* 2.8 40.7 + - + +
24B LEU* 3.5 9.0 - - + +
26B MET* 1.3 73.8 - - - +
28B ILE* 1.3 53.0 + - + +
30B THR* 2.7 12.0 + - + -
31B PHE* 2.7 34.8 + - - +
60B SER* 3.0 32.5 + - - +
64B LEU* 5.5 4.0 - - + -
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Residues in contact with ILE 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B LEU* 2.9 39.7 + - + +
25B LEU* 3.9 9.6 - - + +
27B LEU* 1.3 78.8 - - + +
29B GLY* 1.3 66.3 + - - +
31B PHE* 3.1 10.2 + - + +
32B TYR* 2.7 34.2 + - + +
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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 LEU 3.0 16.0 + - - -
26B MET 3.9 1.1 - - - -
28B ILE* 1.3 78.6 - - - +
30B THR* 1.3 62.8 + - - +
32B TYR* 3.3 7.0 + - - +
33B PHE* 2.9 33.5 + - - -
56B PRO* 4.6 3.8 - - - -
223B VAL* 4.0 25.4 - - - -
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Residues in contact with THR 30 (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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26B MET 2.8 12.1 + - - -
27B LEU* 2.7 16.9 + - + +
29B GLY* 1.3 74.7 - - - +
31B PHE* 1.3 64.5 + - - +
33B PHE* 3.0 13.2 + - - +
34B ILE* 3.1 29.9 + - + +
53B ILE* 4.0 7.6 - - + +
56B PRO* 2.8 43.9 + - - +
57B GLY* 3.4 15.4 - - - +
60B SER* 3.7 1.6 + - - +
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Residues in contact with PHE 31 (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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27B LEU 2.7 15.2 + - - +
28B ILE* 3.5 11.7 - - + +
30B THR* 1.3 72.2 - - - +
32B TYR* 1.3 54.0 + - - +
34B ILE* 2.7 41.2 + - + +
35B VAL* 2.7 40.5 + - + +
38B TRP* 6.4 2.0 - + - -
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Residues in contact with TYR 32 (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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28B ILE* 2.7 28.3 + - + +
29B GLY* 3.4 8.3 - - - +
31B PHE* 1.3 74.9 - - + +
33B PHE* 1.3 78.6 + + - +
35B VAL* 3.6 13.4 + - + +
36B LYS* 3.3 56.5 + - + +
223B VAL* 6.4 0.2 - - + -
227B PHE* 4.7 18.0 - + + -
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Residues in contact with PHE 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B GLY 2.9 17.7 + - - -
30B THR 3.0 8.5 + - - +
32B TYR* 1.3 92.5 - + - +
34B ILE* 1.3 67.0 + - - +
36B LYS* 3.2 9.3 + - + -
37B GLY* 3.0 18.0 + - - -
49B TYR* 3.8 9.1 - - + -
52B THR* 3.4 42.4 - - + -
53B ILE* 3.4 16.1 - - + +
56B PRO* 3.9 18.8 - - + -
222B LYS 4.9 0.9 - - - -
223B VAL* 3.6 38.1 - - + -
226B GLY* 3.8 2.9 - - - -
227B PHE* 3.7 19.1 - - + -
230B LEU* 3.6 20.2 - - + -
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Residues in contact with ILE 34 (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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30B THR* 3.1 29.4 + - + +
31B PHE* 2.7 28.5 + - + +
33B PHE* 1.3 72.7 - - - +
35B VAL* 1.3 54.6 + - - +
37B GLY* 2.7 25.0 + - - +
38B TRP* 3.3 27.9 + - + -
53B ILE* 3.3 22.9 - - + -
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Residues in contact with VAL 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B PHE* 2.7 58.1 + - + +
32B TYR* 3.7 13.9 - - + +
34B ILE* 1.3 76.0 - - + +
36B LYS* 1.3 63.0 + - + +
37B GLY 3.2 2.8 + - - -
38B TRP* 3.4 24.8 + - + +
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Residues in contact with LYS 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B TYR* 3.3 49.6 + - + +
33B PHE* 3.2 9.4 + - + +
35B VAL* 1.3 80.7 - - + +
37B GLY* 1.3 61.9 + - - +
38B TRP 3.4 2.9 - - - -
39B GLY* 4.2 4.1 + - - -
40B VAL* 3.8 11.3 - - - +
49B TYR* 3.2 37.6 + - + +
227B PHE* 4.5 17.8 + - - +
230B LEU* 4.5 18.9 + - - +
231B ARG* 4.9 5.9 - - - +
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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