Contacts of the helix formed by residues 20 - 28 (chain D) in PDB entry 4UC5
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 PRO 20 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219A HIS* 5.3 2.0 - - + -
20B PRO* 4.3 26.5 - - + -
22B ILE* 4.5 1.8 - - + -
220C SER* 4.3 4.7 - - - +
18D LEU 3.6 4.2 - - - +
19D LEU* 1.3 92.8 - - + +
21D PRO* 1.3 76.5 - - + +
22D ILE* 3.8 17.0 - - + -
23D ALA* 3.0 23.6 + - + +
24D HIS* 3.5 4.5 - - - -
154D TYR* 3.7 1.8 - - - +
216D LYS 3.8 2.2 - - - +
217D ALA 3.5 27.6 - - - +
218D GLY* 3.9 3.8 - - - +
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Residues in contact with PRO 21 (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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20D PRO* 1.3 84.4 - - + +
22D ILE* 1.3 62.4 + - - +
23D ALA 3.0 0.9 + - - -
24D HIS* 3.0 5.4 + - + +
25D LEU* 2.9 26.9 + - + +
153D GLN* 3.5 37.0 - - + +
154D TYR* 3.4 39.9 - - + +
214D VAL* 4.9 2.9 - - + -
215D THR 4.0 9.6 - - - +
216D LYS* 3.2 26.7 - - + +
218D GLY* 4.2 4.9 - - - +
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Residues in contact with ILE 22 (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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219A HIS* 4.3 19.5 - - - +
17B GLU* 4.5 14.1 - - + +
18B LEU 4.3 7.6 - - - +
19B LEU* 3.5 22.2 - - + +
20D PRO* 3.8 15.5 - - + -
21D PRO* 1.3 76.8 - - - +
23D ALA* 1.3 57.5 + - - +
25D LEU* 3.8 10.7 - - + +
26D TYR* 3.0 28.6 + - - +
216D LYS* 3.0 36.3 + - + +
217D ALA* 4.1 16.6 - - + +
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Residues in contact with ALA 23 (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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19B LEU* 3.9 13.0 - - + +
20B PRO* 5.5 0.2 - - + -
23B ALA* 4.0 26.0 - - + -
19D LEU* 4.3 16.2 - - + -
20D PRO* 3.0 25.2 + - + +
21D PRO 3.0 0.2 + - - -
22D ILE* 1.3 79.8 - - - +
24D HIS* 1.3 61.6 + - - +
26D TYR* 3.6 3.4 + - - +
27D GLU* 3.4 26.9 + - - +
126D ARG* 3.9 3.9 + - - +
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Residues in contact with HIS 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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26B TYR* 6.0 0.2 - + - -
19D LEU* 4.0 18.9 + - + +
20D PRO 3.5 9.4 - - - -
21D PRO 3.0 5.1 + - - +
23D ALA* 1.3 76.3 - - - +
25D LEU* 1.3 58.8 + - + +
27D GLU* 3.3 1.9 + - - +
28D LEU* 2.9 33.3 + - - +
122D ASN* 3.5 28.0 + - - -
125D LEU* 3.9 9.7 - - + +
126D ARG* 3.0 49.6 + - - +
129D ARG* 4.0 18.7 - - + -
154D TYR* 3.4 41.2 - + + +
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Residues in contact with LEU 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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21D PRO* 2.9 24.2 + - + +
22D ILE* 3.9 10.3 - - + +
24D HIS* 1.3 76.9 - - - +
26D TYR* 1.3 61.5 + - - +
28D LEU 4.0 3.1 - - - -
29D PRO* 3.2 29.9 - - + +
30D ILE* 5.4 0.7 - - + +
129D ARG* 3.2 36.1 - - - +
153D GLN 4.6 3.4 - - - +
154D TYR 5.2 2.7 - - - +
157D ASP* 3.9 9.4 - - - +
216D LYS* 4.1 34.3 - - + -
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Residues in contact with TYR 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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19B LEU* 3.7 24.0 - - + -
120B ASP* 5.1 4.5 - - - -
122B ASN* 4.0 26.1 + - + -
123B PHE* 3.4 41.7 - + + -
126B ARG* 3.6 31.4 - - + +
22D ILE 3.0 17.0 + - - +
23D ALA 3.8 4.5 - - - +
24D HIS 3.2 0.2 - - - -
25D LEU* 1.3 76.6 - - - +
27D GLU* 1.3 78.5 + - - +
29D PRO* 3.5 12.4 - - - +
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Residues in contact with GLU 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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27B GLU* 3.5 17.4 - - - +
126B ARG* 2.6 41.4 + - - -
23D ALA 3.4 14.2 + - - +
24D HIS 3.3 6.8 + - - +
26D TYR* 1.3 83.6 - - - +
28D LEU* 1.3 72.9 + - + +
29D PRO* 3.6 4.7 - - - +
126D ARG* 3.7 27.6 - - - +
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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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24D HIS 2.9 9.0 + - - +
25D LEU 3.5 3.5 - - - +
27D GLU* 1.3 88.9 - - + +
29D PRO* 1.3 66.0 - - - +
126D ARG* 3.5 32.8 - - - +
129D ARG* 2.8 36.1 + - + +
130D SER* 3.6 40.8 - - - +
133D LEU* 4.0 23.9 - - + +
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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