Contacts of the helix formed by residues 24 - 38 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31C ARG* 3.8 16.9 - - - -
34C HIS* 6.4 2.0 - - - -
35C ARG* 4.9 1.3 - - - +
22D PHE 3.6 1.4 - - - -
23D ALA* 1.3 79.4 - - - +
25D LYS* 1.3 60.0 + - - +
26D THR 3.4 1.8 - - - -
27D ALA* 3.4 11.6 + - - +
28D GLU* 2.9 29.8 + - - +
149D LEU* 3.9 2.2 - - - -
4220D TTP 2.9 13.2 + - - -
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Residues in contact with LYS 25 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D ILE* 4.0 7.3 - - + +
18D THR* 3.6 22.9 - - - +
19D GLY 3.6 13.9 - - - +
20D PRO 2.8 24.6 + - - +
23D ALA* 4.4 4.0 - - + -
24D GLY* 1.3 72.2 - - - +
26D THR* 1.3 57.7 + - - +
28D GLU* 3.2 4.9 + - - +
29D LEU* 2.9 28.1 + - - +
122D SER* 3.6 15.4 + - - +
123D GLY* 3.5 38.4 - - - +
124D LEU* 3.4 3.3 - - - +
149D LEU* 3.7 14.8 - - + -
4220D TTP 2.7 59.7 + - - +
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Residues in contact with THR 26 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D LYS* 1.3 72.1 - - - +
27D ALA* 1.3 55.9 + - - +
29D LEU* 3.2 7.0 + - - +
30D ILE* 2.8 48.1 + - + +
58D ILE* 4.3 4.9 - - + -
59D GLN 3.5 31.0 - - - +
60D SER* 5.5 0.2 - - - -
96D ASP* 2.9 27.7 + - - +
122D SER* 4.6 0.8 + - - -
4219D MG 2.2 31.8 - - - -
4220D TTP 3.0 6.3 + - - -
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Residues in contact with ALA 27 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C ALA* 5.8 0.7 - - - +
31C ARG* 4.0 18.2 - - + -
24D GLY* 3.4 14.9 - - - +
26D THR* 1.3 77.6 - - - +
28D GLU* 1.3 55.9 + - - +
30D ILE* 3.2 2.6 + - - +
31D ARG* 2.8 29.7 + - - +
60D SER* 3.5 19.6 - - - +
61D ARG 5.5 0.4 - - - +
62D THR* 3.8 21.0 + - - +
4220D TTP 5.6 0.2 + - - -
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Residues in contact with GLU 28 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C GLU* 3.8 13.3 - - - +
31C ARG* 4.5 6.9 - - - +
17D ILE* 3.7 23.6 - - + -
24D GLY 2.9 13.2 + - - +
25D LYS 3.2 7.8 + - - +
27D ALA* 1.3 73.8 - - - +
29D LEU* 1.3 64.7 + - - +
31D ARG* 2.7 38.2 + - - +
32D ARG* 2.6 54.0 + - - +
147D THR* 5.4 1.5 - - + +
149D LEU* 4.1 17.5 - - + -
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Residues in contact with LEU 29 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D ILE* 3.8 11.8 - - + +
25D LYS 2.9 13.7 + - - +
26D THR 3.6 6.5 - - - +
28D GLU* 1.3 74.5 - - - +
30D ILE* 1.3 64.0 + - - +
32D ARG* 3.3 4.7 + - - +
33D LEU* 3.1 42.8 + - + +
45D VAL* 4.8 3.6 - - + -
58D ILE* 3.6 26.5 - - + -
94D GLY* 4.5 1.1 - - - -
95D ILE 4.7 1.1 - - - +
96D ASP* 3.8 32.1 - - + +
120D ILE* 3.5 47.3 - - + +
121D ILE 4.5 0.4 - - - +
122D SER* 4.2 10.8 - - - -
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Residues in contact with ILE 30 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26D THR* 2.8 30.9 + - + +
27D ALA 3.6 3.8 - - - +
29D LEU* 1.3 71.8 - - - +
31D ARG* 1.3 54.6 + - - +
33D LEU* 3.2 2.3 + - - +
34D HIS* 2.7 35.1 + - + +
58D ILE* 3.7 31.6 - - + +
59D GLN* 3.6 7.2 - - - +
60D SER* 3.4 35.2 - - - +
64D THR* 3.7 38.4 - - + +
66D LEU* 3.9 18.3 - - + +
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Residues in contact with ARG 31 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C ALA 3.2 20.6 + - - +
24C GLY* 3.8 28.4 - - - +
27C ALA* 4.2 14.1 - - + -
28C GLU* 4.4 13.2 - - - +
149C LEU* 3.2 38.7 - - - +
150C THR 4.2 0.8 + - - +
27D ALA 2.8 19.7 + - - +
28D GLU* 2.7 46.6 + - - +
30D ILE* 1.3 75.5 - - - +
32D ARG* 1.3 74.2 + - - +
34D HIS* 3.3 6.2 + - - +
35D ARG* 3.3 47.7 + - - +
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Residues in contact with ARG 32 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D GLU* 2.7 50.5 + - - +
16D PHE 5.2 0.8 + - - +
17D ILE* 3.6 27.6 - - - +
28D GLU* 2.6 35.5 + - - +
29D LEU* 3.8 5.8 - - - +
31D ARG* 1.3 87.3 - - - +
33D LEU* 1.3 62.4 + - - +
35D ARG* 3.4 39.1 + - - +
36D LEU* 3.9 9.0 - - - +
120D ILE* 4.1 17.3 - - + +
145D LYS* 4.3 13.5 - - - +
147D THR* 2.9 37.4 + - - +
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Residues in contact with LEU 33 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29D LEU* 3.1 42.6 + - + +
32D ARG* 1.3 75.5 - - - +
34D HIS* 1.3 63.5 + - - +
36D LEU* 3.1 28.2 + - + +
37D GLU 3.9 0.5 + - - -
43D TYR* 3.8 27.3 - - + -
45D VAL* 3.7 28.3 - - + -
58D ILE* 4.9 1.1 - - + -
66D LEU* 3.8 20.4 - - + -
92D VAL* 3.7 29.6 - - + -
94D GLY* 4.5 10.1 - - - -
120D ILE* 4.1 11.0 - - + -
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Residues in contact with HIS 34 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30D ILE* 2.7 25.0 + - + +
31D ARG* 3.7 7.9 - - - +
33D LEU* 1.3 74.0 - - - +
35D ARG* 1.3 60.9 + - - +
37D GLU* 3.0 50.7 + - - +
38D TYR* 3.6 39.7 + + - -
64D THR* 4.0 33.4 + - + +
66D LEU* 4.2 5.6 - - + +
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Residues in contact with ARG 35 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C PHE* 3.7 24.6 - - - +
23C ALA 3.8 15.7 - - - +
24C GLY* 5.5 0.2 - - - -
150C THR* 3.3 41.3 + - - +
151C ALA* 4.4 1.4 + - - +
152C ILE* 3.0 49.6 + - + +
159C GLU* 4.7 9.1 + - - +
31D ARG* 3.4 31.4 - - - +
32D ARG* 3.4 27.5 + - - +
33D LEU 3.2 0.2 - - - -
34D HIS* 1.3 77.2 - - - +
36D LEU* 1.3 62.4 + - - +
37D GLU 3.3 0.7 + - - -
38D TYR* 3.4 17.1 + - - +
39D ALA 4.0 2.1 + - - -
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Residues in contact with LEU 36 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152C ILE* 3.8 29.6 - - + -
32D ARG 3.9 8.3 - - - +
33D LEU* 3.1 24.9 + - + +
35D ARG* 1.3 77.2 - - - +
37D GLU* 1.3 61.9 + - - +
39D ALA* 3.2 4.2 + - - -
40D ASP 3.1 3.6 + - - -
41D VAL* 2.8 59.6 + - + +
43D TYR* 3.9 16.4 - - + -
92D VAL* 3.6 41.1 - - + -
120D ILE* 5.4 2.0 - - + -
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Residues in contact with GLU 37 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D LEU 4.5 0.2 - - - +
34D HIS* 3.0 40.9 + - + +
36D LEU* 1.3 78.6 - - - +
38D TYR* 1.3 62.1 + - + +
40D ASP* 3.0 18.6 + - - +
41D VAL 4.7 2.7 - - - +
43D TYR* 2.7 42.1 + - + -
66D LEU* 3.7 9.4 - - - +
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Residues in contact with TYR 38 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C PHE* 3.7 55.0 - + + -
152C ILE 5.4 2.0 - - - +
154C ASN* 3.2 16.1 + - - +
184C GLN* 3.6 41.2 - - - +
34D HIS* 3.6 48.3 + + - -
35D ARG* 3.4 12.8 + - - +
36D LEU 3.3 0.8 - - - -
37D GLU* 1.3 80.0 - - + +
39D ALA* 1.3 57.1 + - - +
40D ASP 3.4 0.7 - - - -
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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
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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