Contacts of the helix formed by residues 23 - 34 (chain D) in PDB entry 4UJ3
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 23 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21D GLY 3.2 0.8 - - - -
22D VAL* 1.3 80.9 - - - +
24D LYS* 1.3 66.4 + - - +
26D ASN* 3.2 3.3 + - - +
27D LEU* 2.9 28.0 + - - +
124D ASN* 3.6 9.5 + - - -
200D GNP 3.1 38.1 + - - -
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Residues in contact with LYS 24 (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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16D LEU* 3.5 26.0 - - + +
17D ILE* 3.5 31.4 - - - +
18D GLY 3.0 23.6 + - - +
19D ASP 3.1 11.1 + - - -
22D VAL* 3.8 11.1 - - + +
23D GLY* 1.3 75.2 - - - +
25D SER* 1.3 57.4 + - - +
27D LEU* 2.8 29.5 + - - +
28D LEU 3.0 9.4 + - - -
66D ASP* 4.0 8.1 - - - +
67D THR* 3.5 17.0 - - - -
69D GLY* 3.5 4.4 - - - -
90D VAL* 4.1 13.9 - - + -
200D GNP 2.6 46.3 + - - +
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Residues in contact with SER 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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24D LYS* 1.3 78.2 - - - +
26D ASN* 1.3 59.0 + - - +
28D LEU* 3.3 7.7 - - - +
29D SER* 2.9 27.7 + - - -
40D SER* 5.7 1.8 - - - -
41D LYS 5.8 1.6 - - - -
43D THR* 2.5 13.6 + - - +
66D ASP* 2.6 18.4 + - - -
200D GNP 3.2 14.7 + - - -
201D MG 1.9 31.9 - - - -
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Residues in contact with ASN 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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23D GLY 3.2 7.1 + - - +
24D LYS 3.1 1.2 - - - -
25D SER* 1.3 76.2 - - - +
27D LEU* 1.3 61.8 + - - +
28D LEU 3.1 1.6 - - - -
29D SER* 3.2 8.0 + - - -
30D ARG* 2.9 32.7 + - - +
35D GLU 4.3 0.2 - - - +
36D PHE* 3.1 19.0 - - + -
37D ASN* 2.9 31.6 + - - +
40D SER* 3.3 22.6 + - - -
155D ALA* 3.8 18.2 - - + +
200D GNP 2.7 36.6 + - + +
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Residues in contact with LEU 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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16D LEU* 4.7 8.3 - - + -
23D GLY 2.9 17.7 + - - +
24D LYS* 2.8 10.4 + - - +
26D ASN* 1.3 76.2 - - - +
28D LEU* 1.3 63.5 + - - +
30D ARG* 3.9 2.5 - - - +
31D PHE* 3.1 25.1 + - - +
88D LEU* 5.8 2.5 - - + -
90D VAL* 3.7 37.7 - - + -
122D VAL* 4.5 13.0 - - + -
124D ASN* 4.1 10.8 - - - +
153D THR* 3.5 23.1 - - + +
155D ALA* 4.1 4.9 - - + +
161D VAL* 4.0 24.2 - - + +
164D ALA* 6.2 1.1 - - + -
165D PHE* 3.6 17.7 - - + -
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Residues in contact with LEU 28 (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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16D LEU* 4.0 9.3 - - + +
24D LYS 3.0 10.6 + - - +
25D SER* 3.3 9.9 - - - +
27D LEU* 1.3 75.0 - - - +
29D SER* 1.3 62.4 + - - +
31D PHE* 3.3 3.6 + - - +
32D THR* 2.9 47.5 + - + +
33D ARG* 5.5 3.4 - - - +
47D GLU* 4.4 12.1 - - + +
48D PHE* 5.2 2.9 - - - -
49D ALA* 3.9 14.6 - - + +
64D ILE* 3.5 42.6 - - + +
66D ASP* 3.4 34.3 - - + +
165D PHE* 4.8 2.9 - - - -
755F VAL* 5.9 1.6 - - + -
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Residues in contact with SER 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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25D SER 2.9 10.5 + - - -
26D ASN* 3.2 21.7 + - - -
28D LEU* 1.3 76.9 - - - +
30D ARG* 1.3 57.7 + - - +
32D THR* 3.7 6.3 - - - -
33D ARG* 2.9 58.8 + - - +
34D ASN 3.0 5.7 + - - -
35D GLU* 2.7 28.5 + - - -
36D PHE* 4.5 0.3 - - - -
37D ASN 5.2 0.2 + - - -
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Residues in contact with ARG 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 ASN 2.9 20.0 + - - +
27D LEU 3.9 2.9 - - - +
29D SER* 1.3 76.8 + - - +
31D PHE* 1.3 59.6 + - - +
34D ASN* 2.9 64.5 + - - +
35D GLU* 3.6 7.4 - - - +
36D PHE* 3.0 36.1 - - + +
155D ALA* 2.9 24.9 + - + +
156D LEU 3.5 12.9 + - - -
158D SER* 3.3 23.9 + - - +
161D VAL* 3.6 27.8 - - + -
162D GLU* 5.5 1.9 - - - +
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Residues in contact with PHE 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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27D LEU 3.1 17.5 + - - +
28D LEU 3.3 2.9 + - - +
30D ARG* 1.3 79.6 - - - +
32D THR* 1.3 74.1 + - + +
34D ASN 4.6 0.9 + - - -
51D ARG* 2.9 76.3 + - + +
53D ILE* 4.5 7.4 - - + -
62D ALA* 4.7 7.6 - - + -
64D ILE* 4.3 12.8 - - + -
161D VAL* 4.3 4.5 - - + +
162D GLU* 3.6 19.3 - - - +
165D PHE* 3.3 59.9 - + + -
166D GLN* 5.0 2.7 - - + -
169D LEU* 4.4 13.9 - - + -
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Residues in contact with THR 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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28D LEU* 2.9 29.4 + - + +
29D SER* 3.7 6.8 + - - -
31D PHE* 1.3 93.1 - - + +
33D ARG* 1.3 77.1 + - - +
49D ALA* 3.5 38.4 - - + +
50D THR 4.5 12.3 - - - +
51D ARG* 4.8 10.5 - - + +
64D ILE* 5.2 0.9 - - + -
756F LYS* 5.7 3.1 - - - -
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Residues in contact with ARG 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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28D LEU* 5.4 5.3 - - - +
29D SER* 2.9 38.1 + - - +
32D THR* 1.3 89.0 + - - +
34D ASN* 1.3 72.1 + - - +
35D GLU* 2.8 42.3 + - + +
755F VAL* 4.4 20.9 - - - +
756F LYS* 6.6 0.2 - - - +
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Residues in contact with ASN 34 (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 SER 3.0 2.6 + - - -
30D ARG* 2.9 54.2 + - - +
31D PHE 4.5 0.8 + - - +
32D THR 3.7 1.4 - - - -
33D ARG* 1.3 79.4 - - - +
35D GLU* 1.3 60.7 + - - +
158D SER* 4.5 1.9 + - - -
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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
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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