Contacts of the helix formed by residues 26 - 34 (chain C) in PDB entry 1P8N
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 LYS 26 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22C GLY 5.6 0.2 - - - -
23C GLY* 3.0 13.9 + - - +
25C GLU* 1.3 99.0 + - + +
27C GLY* 1.3 66.2 + - - +
28C PRO* 3.8 0.2 - - - -
29C ALA* 3.0 14.2 + - + +
30C ALA* 2.9 18.9 + - - +
280C PRO* 4.0 14.4 - - + -
281C THR* 3.8 31.6 - - + +
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Residues in contact with GLY 27 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24C VAL 3.0 9.7 + - - -
26C LYS* 1.3 76.4 - - - +
28C PRO* 1.3 71.8 - - - +
30C ALA* 2.6 22.0 + - - +
31C LEU* 2.8 16.7 + - - +
98C GLY 3.9 4.7 - - - -
278C VAL* 3.4 26.8 + - - -
280C PRO* 3.9 1.6 - - - +
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Residues in contact with PRO 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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13C ALA 3.9 11.4 - - - +
14C PRO* 4.0 9.2 - - + -
25C GLU 3.5 13.0 - - - +
27C GLY* 1.3 82.4 - - - +
29C ALA* 1.3 63.4 + - - +
31C LEU* 3.0 4.6 + - + +
32C ARG* 2.9 31.3 + - - +
52C ASP* 3.7 26.0 - - - +
97C LEU* 3.5 36.5 - - + +
98C GLY 2.9 22.6 - - - +
99C GLY 3.9 1.6 - - - +
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Residues in contact with ALA 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 GLU 5.0 0.8 + - - +
26C LYS* 3.0 14.6 + - + +
28C PRO* 1.3 78.7 - - - +
30C ALA* 1.3 53.7 + - - +
32C ARG* 3.9 8.6 - - - +
33C LYS* 2.7 38.1 + - - +
52C ASP* 4.8 3.7 + - - +
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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 LYS 2.9 5.0 + - - +
27C GLY* 2.6 17.9 + - - +
29C ALA* 1.3 73.2 - - - +
31C LEU* 1.3 59.0 + - + -
33C LYS* 3.6 7.1 - - - +
34C ALA* 3.5 14.9 + - - +
278C VAL* 5.1 1.8 - - + -
280C PRO* 3.5 31.9 - - + -
289C VAL* 5.8 1.1 - - + -
293C VAL* 3.5 29.2 - - + +
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Residues in contact with LEU 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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27C GLY 2.8 17.5 + - - +
28C PRO 3.5 6.1 - - - +
30C ALA* 1.3 75.3 - - + +
32C ARG* 1.3 64.0 + - - +
34C ALA* 3.6 8.3 + - - +
35C GLY 3.7 0.2 + - - -
36C LEU* 3.1 38.7 + - + +
97C LEU* 4.0 29.4 - - + -
98C GLY 5.3 2.0 - - - +
275C ILE* 3.9 26.2 - - + +
278C VAL* 4.8 14.6 - - + -
293C VAL* 4.0 19.7 - - + +
296C ALA* 3.7 28.9 - - + -
297C VAL* 4.4 8.0 - - + +
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Residues in contact with ARG 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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10C ILE* 4.0 5.3 - - - +
12C GLY* 3.8 9.9 - - - +
28C PRO* 2.9 24.9 + - - +
29C ALA* 3.9 5.9 - - - +
31C LEU* 1.3 74.0 - - - +
33C LYS* 1.3 59.0 + - - +
34C ALA 3.1 1.8 - - - -
35C GLY* 2.6 27.0 + - - -
36C LEU* 4.3 6.1 - - + +
37C VAL* 4.3 13.2 - - + +
38C GLU* 4.3 4.7 - - - +
49C ASP* 2.7 41.9 + - - -
51C GLY* 3.7 14.2 - - - -
52C ASP* 3.0 39.3 + - - -
97C LEU* 4.4 13.8 - - + +
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Residues in contact with LYS 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 ALA 2.7 23.1 + - - +
30C ALA* 3.6 9.4 - - - +
32C ARG* 1.3 73.7 - - - +
34C ALA* 1.3 58.1 + - - +
35C GLY* 3.1 4.7 + - - -
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Residues in contact with ALA 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 3.5 3.2 + - - +
31C LEU 3.9 4.5 - - - +
32C ARG 3.1 1.0 - - - -
33C LYS* 1.3 77.2 - - - +
35C GLY* 1.3 61.7 + - - +
36C LEU 3.5 1.1 - - - -
39C LYS* 3.8 17.3 - - - -
293C VAL* 3.6 31.2 - - + -
294C ASN* 4.8 9.2 - - - +
297C VAL* 4.5 8.6 - - + +
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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