Contacts of the helix formed by residues 24 - 38 (chain A) in PDB entry 2UZ3
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 GLY 24 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A PHE 3.5 2.2 - - - -
23A ALA* 1.3 79.6 - - - +
25A LYS* 1.3 62.8 + - - -
26A THR 3.3 2.2 - - - -
27A ALA* 3.3 10.9 + - - +
28A GLU* 2.9 24.3 + - - +
149A LEU* 3.9 2.9 - - - +
1220A TTP 2.8 16.3 + - - -
31B ARG* 4.0 15.7 - - - -
35B ARG* 4.8 1.1 - - - +
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Residues in contact with LYS 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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17A ILE* 3.8 7.3 - - + +
18A THR* 3.7 20.6 - - - +
19A GLY 3.7 12.8 - - - +
20A PRO 2.7 27.7 + - - +
23A ALA* 3.5 4.5 - - + -
24A GLY* 1.3 72.6 - - - +
26A THR* 1.3 55.8 + - - +
28A GLU* 3.1 5.2 + - - +
29A LEU* 2.9 27.2 + - - +
122A SER* 3.6 14.1 - - - +
123A GLY* 3.4 39.5 - - - +
124A LEU* 4.0 7.0 - - - +
149A LEU* 3.7 14.8 - - + -
1220A TTP 2.4 57.4 + - - +
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Residues in contact with THR 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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24A GLY 3.3 0.4 - - - -
25A LYS* 1.3 77.1 - - - +
27A ALA* 1.3 58.0 + - - +
29A LEU* 3.2 10.2 + - + +
30A ILE* 2.8 48.2 + - + +
96A ASP* 3.6 25.5 + - - +
97A GLU* 5.7 0.3 + - - -
122A SER* 4.3 2.5 + - - -
1220A TTP 3.3 22.4 + - - -
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Residues in contact with ALA 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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24A GLY* 3.3 14.8 + - - +
25A LYS 3.2 0.4 - - - -
26A THR* 1.3 79.9 - - - +
28A GLU* 1.3 55.7 + - - +
30A ILE* 3.3 11.9 + - - +
31A ARG* 2.8 29.5 + - - +
1220A TTP 5.3 0.4 + - - -
27B ALA* 6.0 0.2 - - - +
31B ARG* 4.2 20.9 - - + -
34B HIS* 6.3 2.5 - - + -
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Residues in contact with GLU 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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17A ILE* 3.7 20.9 - - + -
24A GLY 2.9 13.7 + - - +
25A LYS 3.1 6.9 + - - +
27A ALA* 1.3 73.9 - - - +
29A LEU* 1.3 64.7 + - - +
31A ARG* 2.7 42.8 + - - -
32A ARG* 2.9 52.2 + - - +
147A THR* 4.9 4.3 - - + +
149A LEU* 4.1 17.7 - - + -
28B GLU* 3.8 11.9 - - - +
31B ARG* 4.4 7.5 - - - +
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Residues in contact with LEU 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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17A ILE* 3.7 12.7 - - + +
25A LYS 2.9 12.0 + - - +
26A THR* 3.3 11.7 - - + +
28A GLU* 1.3 75.5 - - - +
30A ILE* 1.3 66.5 + - + +
32A ARG* 3.2 4.7 + - - +
33A LEU* 3.0 47.9 + - + +
45A VAL* 5.3 5.8 - - + -
94A GLY* 4.8 4.9 - - - -
95A ILE 4.8 1.8 - - - +
96A ASP* 3.5 42.0 - - + +
120A ILE* 3.8 33.4 - - + +
122A SER* 3.8 11.7 - - - -
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Residues in contact with ILE 30 (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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26A THR* 2.8 37.8 + - + +
27A ALA* 3.5 8.7 - - - +
29A LEU* 1.3 78.0 - - + +
31A ARG* 1.3 59.2 + - - +
33A LEU* 3.2 13.7 + - + +
34A HIS* 2.8 41.3 + - + +
62B THR* 3.2 28.3 - - + +
63B GLY* 6.0 3.8 - - - +
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Residues in contact with ARG 31 (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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27A ALA 2.8 17.2 + - - +
28A GLU* 2.7 44.5 + - - +
29A LEU 3.3 0.2 - - - -
30A ILE* 1.3 79.1 - - - +
32A ARG* 1.3 76.7 + - - +
34A HIS* 3.4 9.2 + - + +
35A ARG* 3.3 36.4 + - - +
23B ALA 2.9 22.4 + - - +
24B GLY* 3.5 33.0 - - - +
27B ALA* 4.2 15.5 - - + -
28B GLU* 4.3 12.2 + - - +
62B THR* 5.9 1.1 - - + -
149B LEU* 3.7 29.9 - - - +
150B THR 4.7 1.6 + - - +
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Residues in contact with ARG 32 (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 GLU* 2.9 43.0 + - - +
16A PHE 5.1 0.4 - - - +
17A ILE* 3.6 31.3 - - - +
28A GLU* 2.9 33.9 + - - +
29A LEU* 3.6 8.3 - - - +
31A ARG* 1.3 90.9 - - - +
33A LEU* 1.3 63.3 + - - +
35A ARG* 3.3 37.4 + - - +
36A LEU* 3.7 11.3 - - - +
120A ILE* 4.4 15.1 - - + +
145A LYS* 5.8 1.4 + - - +
147A THR* 2.8 36.0 + - - +
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Residues in contact with LEU 33 (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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29A LEU* 3.0 41.5 + - + +
30A ILE* 3.2 15.2 + - + +
32A ARG* 1.3 74.1 - - - +
34A HIS* 1.3 64.6 + - - +
36A LEU* 3.1 28.0 + - + +
37A GLU 3.7 1.0 + - - -
43A TYR* 3.6 56.6 - - + +
45A VAL* 3.7 25.8 - - + -
92A VAL* 4.7 8.5 - - + -
94A GLY* 5.2 4.3 - - - -
120A ILE* 4.8 4.7 - - + -
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Residues in contact with HIS 34 (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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30A ILE* 2.8 33.9 + - + +
31A ARG* 3.6 8.3 - - - +
33A LEU* 1.3 73.1 - - - +
35A ARG* 1.3 63.2 + - - +
37A GLU* 3.1 42.9 + - - +
38A TYR* 3.5 22.3 + + + -
43A TYR* 5.8 0.9 + - - -
61B ARG 3.6 14.0 + - - -
62B THR* 3.0 43.0 + - + -
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Residues in contact with ARG 35 (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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31A ARG* 3.3 28.5 + - - +
32A ARG* 3.3 29.1 + - - +
33A LEU 3.2 0.4 - - - -
34A HIS* 1.3 78.2 - - - +
36A LEU* 1.3 65.2 + - - +
37A GLU 3.4 0.5 + - - -
38A TYR* 3.4 24.1 + - - +
39A ALA 4.0 2.6 + - - -
22B PHE 4.0 17.4 - - - +
23B ALA 4.2 7.2 - - - +
24B GLY* 5.8 0.2 - - - -
150B THR* 2.8 44.0 + - - +
151B ALA* 3.4 9.2 + - - +
152B ILE* 3.3 50.8 + - + +
159B GLU* 4.6 7.7 + - - +
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Residues in contact with LEU 36 (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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32A ARG 3.7 14.1 - - - +
33A LEU* 3.1 19.8 + - + +
35A ARG* 1.3 79.2 - - - +
37A GLU* 1.3 54.6 + - - +
39A ALA* 3.2 3.6 + - - +
40A ASP 3.1 7.3 + - - -
41A VAL* 2.7 64.6 + - + +
43A TYR* 4.1 11.9 - - + -
92A VAL* 3.7 40.6 - - + -
120A ILE* 4.9 3.4 - - + -
152B ILE* 4.2 25.6 - - + -
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Residues in contact with GLU 37 (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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33A LEU 3.7 0.4 + - - -
34A HIS* 3.1 38.4 + - - +
36A LEU* 1.3 79.6 - - - +
38A TYR* 1.3 62.0 + - + +
39A ALA 3.1 0.2 - - - -
40A ASP* 3.1 19.0 + - - +
41A VAL 4.7 2.7 - - - +
43A TYR* 3.1 37.0 + - + -
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Residues in contact with TYR 38 (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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34A HIS* 3.5 34.9 + - + +
35A ARG* 3.4 14.0 + - - +
36A LEU 3.3 1.0 - - - -
37A GLU* 1.3 79.9 - - + +
39A ALA* 1.3 57.9 + - - +
40A ASP 3.4 0.7 - - - -
22B PHE* 4.2 34.3 - + + -
61B ARG* 2.7 57.4 + - - +
152B ILE 5.7 2.5 - - - +
154B ASN* 4.0 13.7 + - - -
184B GLN* 3.8 39.8 - - - +
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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
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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