Contacts of the helix formed by residues 25 - 37 (chain C) in PDB entry 5PRC
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 25 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6C PRO* 3.1 36.1 - - + +
7C ALA 4.7 0.2 - - - -
8C THR* 3.5 21.8 - - - +
23C LEU 3.5 4.9 - - - +
24C HIS* 1.3 88.9 - - + +
26C ALA* 1.3 63.3 + - - +
28C VAL* 3.2 10.1 + - + +
29C LYS* 3.0 22.0 + - - +
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Residues in contact with ALA 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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24C HIS* 3.2 21.0 - - + +
25C PRO* 1.3 78.8 - - - +
27C THR* 1.3 62.6 + - - +
29C LYS* 3.2 14.6 + - - +
30C ALA* 3.0 23.4 + - - +
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Residues in contact with THR 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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3C GLU* 4.4 1.6 + - - -
24C HIS* 3.1 28.3 + - - +
26C ALA* 1.3 74.9 - - - +
28C VAL* 1.3 68.4 + - + +
30C ALA* 3.1 7.7 + - + +
31C LYS* 3.0 51.8 + - + +
257L ARG* 4.4 19.1 + - - +
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Residues in contact with VAL 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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8C THR* 6.0 0.2 - - - +
23C LEU* 3.8 33.9 - - + -
24C HIS 3.3 11.9 + - - +
25C PRO* 3.2 10.7 + - + +
27C THR* 1.3 77.0 - - + +
29C LYS* 1.3 59.4 + - - +
31C LYS* 3.1 14.5 + - - +
32C LYS* 2.8 39.6 + - + +
317C PHE* 3.9 20.3 - - + -
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Residues in contact with LYS 29 (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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25C PRO 3.0 12.2 + - - +
26C ALA* 3.4 15.8 + - - +
27C THR 3.1 0.2 - - - -
28C VAL* 1.3 79.7 - - - +
30C ALA* 1.3 64.1 + - - +
32C LYS* 3.1 14.8 + - + +
33C GLU* 3.0 61.7 + - - +
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Residues in contact with ALA 30 (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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26C ALA 3.0 15.3 + - - +
27C THR* 3.1 7.8 + - + +
29C LYS* 1.3 85.6 - - - +
31C LYS* 1.3 60.6 + - + +
33C GLU* 3.4 9.2 + - - +
34C ARG* 3.2 21.7 + - - +
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Residues in contact with LYS 31 (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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23C LEU* 6.2 1.6 - - - +
27C THR* 3.0 40.7 + - + +
28C VAL* 3.7 13.6 - - - +
30C ALA* 1.3 76.5 - - + +
32C LYS* 1.3 68.5 + - - +
33C GLU 3.1 0.2 + - - -
34C ARG* 3.2 19.4 + - - +
35C ASP* 2.9 28.1 + - - +
241C GLY* 5.0 7.6 + - - -
310C GLN 4.3 7.0 - - - +
311C GLY* 3.3 33.0 + - - +
312C VAL* 3.8 11.4 - - + -
317C PHE* 3.6 15.0 - - + -
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Residues in contact with LYS 32 (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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28C VAL* 2.8 23.1 + - + +
29C LYS* 3.1 18.1 + - + +
31C LYS* 1.3 77.2 - - - +
33C GLU* 1.3 57.5 + - + +
35C ASP* 3.3 2.4 + - - +
36C ALA* 3.0 28.4 + - - +
317C PHE* 3.5 45.1 - - + +
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Residues in contact with GLU 33 (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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29C LYS* 3.0 48.3 + - - +
30C ALA* 3.8 8.0 - - - +
31C LYS 3.1 0.4 - - - -
32C LYS* 1.3 76.0 - - + +
34C ARG* 1.3 65.9 + - - +
36C ALA* 3.2 21.2 + - + +
37C GLN* 3.8 9.7 - - - +
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Residues in contact with ARG 34 (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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30C ALA 3.2 11.6 + - - +
31C LYS* 3.7 21.1 - - - +
33C GLU* 1.3 77.2 - - - +
35C ASP* 1.3 94.2 + - - +
36C ALA 3.2 1.0 + - - -
37C GLN* 3.3 35.3 + - - +
133C TYR* 4.5 3.1 + - - -
137C ARG* 3.8 10.6 + - - +
144C TYR* 4.8 10.5 + - - -
309C HIS 4.3 0.8 + - - -
310C GLN* 2.7 49.4 + - - +
312C VAL* 3.8 8.7 - - - +
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Residues in contact with ASP 35 (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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31C LYS 2.9 17.9 + - - +
32C LYS 3.8 3.6 - - - +
34C ARG* 1.3 108.9 + - - +
36C ALA* 1.3 59.2 + - - +
37C GLN 3.0 10.1 + - - -
38C TYR* 3.2 14.4 + - - +
137C ARG* 2.9 11.2 + - - +
312C VAL* 3.6 2.9 - - - +
316C LEU* 3.2 47.5 + - + +
317C PHE* 3.0 28.4 - - + -
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Residues in contact with ALA 36 (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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32C LYS 3.0 13.9 + - - +
33C GLU* 3.3 19.3 - - + +
34C ARG 3.1 0.4 - - - -
35C ASP* 1.3 77.7 - - - +
37C GLN* 1.3 59.4 + - - +
38C TYR* 3.1 10.4 + - - +
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Residues in contact with GLN 37 (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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33C GLU 3.8 9.9 - - - +
34C ARG* 3.4 29.5 + - - +
35C ASP 3.0 0.8 + - - -
36C ALA* 1.3 76.6 - - - +
38C TYR* 1.3 65.1 + - - +
39C PRO* 2.8 14.0 - - - +
133C TYR* 3.4 14.4 + - - +
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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