Contacts of the helix formed by residues 20 - 28 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A PRO* 4.3 25.8 - - + -
22A ILE* 4.8 1.1 - - + -
18C LEU 3.4 3.8 - - - +
19C LEU* 1.3 91.8 - - + +
21C PRO* 1.3 73.2 - - + +
22C ILE* 3.6 18.4 - - + -
23C ALA* 3.0 21.2 + - + +
24C HIS* 3.4 9.0 - - - -
154C TYR* 3.7 1.6 - - - +
216C LYS 3.8 2.5 - - - +
217C ALA 3.3 35.0 - - - +
218C GLY* 3.8 2.7 - - - -
219D HIS* 4.3 8.1 - - + +
220D SER* 4.2 4.5 - - - +
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Residues in contact with PRO 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C PRO* 1.3 83.5 - - + +
22C ILE* 1.3 63.4 + - - +
24C HIS* 3.0 7.2 + - + +
25C LEU* 2.9 25.4 + - + +
153C GLN* 3.5 42.8 - - + +
154C TYR* 3.4 37.6 - - + +
214C VAL* 4.7 4.0 - - + -
215C THR 4.1 11.0 - - - +
216C LYS* 3.3 22.9 - - + +
218C GLY* 4.2 4.9 - - - -
220D SER* 4.7 0.4 - - - +
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Residues in contact with ILE 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A LEU 6.1 0.4 - - - +
19A LEU* 4.0 20.1 - - + +
20A PRO* 5.4 2.0 - - + -
20C PRO* 3.6 20.4 - - + -
21C PRO* 1.3 77.2 - - - +
23C ALA* 1.3 57.2 + - - +
25C LEU* 3.8 17.2 - - + +
26C TYR* 2.9 28.5 + - + +
216C LYS* 2.8 31.7 + - + +
217C ALA* 4.0 11.4 - - + -
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Residues in contact with ALA 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A LEU* 4.2 11.4 - - + -
23A ALA* 3.9 27.8 - - + -
19C LEU* 4.1 21.1 - - + -
20C PRO* 3.0 18.8 + - + +
22C ILE* 1.3 79.6 - - - +
24C HIS* 1.3 63.0 + - - +
26C TYR* 3.3 6.0 - - - +
27C GLU* 3.3 26.0 + - - +
126C ARG* 4.1 3.6 - - - +
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Residues in contact with HIS 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A TYR* 5.9 0.2 - + - -
19C LEU* 3.9 20.1 + - + +
20C PRO 3.4 23.8 - - - -
21C PRO 3.0 4.8 + - - +
23C ALA* 1.3 74.4 - - - +
25C LEU* 1.3 59.3 + - - +
26C TYR 3.1 1.3 - - - -
27C GLU* 3.2 1.7 + - - +
28C LEU* 2.8 34.5 + - - +
122C ASN* 3.5 26.5 + - - -
125C LEU* 4.1 9.9 - - + +
126C ARG* 2.9 50.7 + - + +
129C ARG* 4.0 19.3 - - + -
154C TYR* 3.5 32.0 - + + +
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Residues in contact with LEU 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C PRO 2.9 20.7 + - - +
22C ILE* 3.8 18.2 - - + +
24C HIS* 1.3 76.1 - - - +
26C TYR* 1.3 60.9 + - - +
28C LEU 4.2 2.5 - - - +
29C PRO* 3.3 27.5 - - + +
30C ILE* 5.6 0.4 - - + +
129C ARG* 3.2 37.9 - - - +
153C GLN 4.6 5.4 - - - +
154C TYR 4.9 2.2 - - - +
157C ASP* 3.9 9.4 - - - +
216C LYS* 3.9 37.0 - - + -
8D ASP* 6.2 0.2 - - - -
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Residues in contact with TYR 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A LEU* 3.6 28.0 - - + -
120A ASP* 4.7 3.3 + - - -
122A ASN* 3.8 23.2 - - + -
123A PHE* 3.6 38.1 + - - +
126A ARG* 4.2 14.1 - - + +
22C ILE* 2.9 19.3 + - + +
23C ALA 3.3 6.7 - - - +
24C HIS 3.1 0.2 - - - -
25C LEU* 1.3 79.0 - - - +
27C GLU* 1.3 88.2 + - - +
29C PRO* 3.7 8.7 - - - +
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Residues in contact with GLU 27 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A GLU* 3.5 28.9 - - - +
126A ARG* 2.8 35.3 + - - -
23C ALA 3.4 13.5 - - - +
24C HIS 3.2 5.9 + - - +
26C TYR* 1.3 94.9 - - - +
28C LEU* 1.3 70.8 + - + +
29C PRO* 3.2 7.9 - - - +
126C ARG* 3.5 14.8 - - - +
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Residues in contact with LEU 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C HIS 2.8 15.8 + - - +
25C LEU 3.6 3.4 - - - +
27C GLU* 1.3 87.7 - - + +
29C PRO* 1.3 65.8 - - - +
126C ARG* 3.6 29.4 - - - +
129C ARG* 2.9 36.9 + - + +
130C SER* 3.6 41.3 - - - +
133C LEU* 4.1 21.7 - - + +
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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
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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