Contacts of the helix formed by residues 19 - 29 (chain C) in PDB entry 3K9S
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 ASP 19 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15C GLU* 3.6 10.3 - - - +
17C HIS 4.1 2.0 + - - -
18C PHE* 1.3 75.3 - - - +
20C LYS* 1.3 64.9 + - - +
21C GLN* 4.0 8.6 + - + +
22C THR* 2.8 45.2 + - - +
23C MET* 3.0 21.9 + - - +
172C ALA 5.1 2.6 - - - +
173C TYR* 5.5 1.2 - - - -
175C LEU* 4.0 9.7 - - - +
176C LYS* 3.5 38.0 + - + +
177C PHE* 4.9 3.3 - - - -
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Residues in contact with LYS 20 (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 ALA* 6.1 0.4 - - - -
11C TYR* 3.2 47.1 - - + +
12C ASP* 3.3 23.8 - - + +
15C GLU* 3.0 18.0 + - - +
18C PHE 3.7 0.8 + - - -
19C ASP* 1.3 69.3 - - - +
21C GLN* 1.3 65.8 + - - +
23C MET* 3.4 1.9 + - - +
24C GLU* 3.1 39.8 + - - +
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Residues in contact with GLN 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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19C ASP* 3.3 7.5 + - + +
20C LYS* 1.3 79.0 - - - +
22C THR* 1.3 63.5 + - - +
24C GLU* 3.3 7.7 + - - +
25C ILE* 3.1 38.2 + - + +
175C LEU* 3.8 30.0 - - + +
178D GLN* 5.0 6.9 - - - +
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Residues in contact with THR 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C PHE* 6.3 1.8 - - + -
19C ASP* 2.8 36.1 + - - +
20C LYS 3.2 0.4 - - - -
21C GLN* 1.3 75.1 - - - +
23C MET* 1.3 71.0 + - - +
24C GLU 3.1 0.2 + - - -
25C ILE* 4.6 2.9 - - - +
26C HIS* 2.8 37.0 + - + +
171C HIS 3.8 16.3 + - - +
172C ALA* 3.6 28.4 + - - +
173C TYR* 5.5 0.3 - - - -
175C LEU* 3.3 26.7 + - + +
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Residues in contact with MET 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C LEU* 4.8 3.7 - - + +
9C TYR* 4.8 7.4 - - + +
11C TYR* 3.4 40.7 - - + +
14C LEU* 1.8 57.2 - - + -
18C PHE* 3.7 24.7 - - + +
19C ASP 3.0 17.1 + - - +
20C LYS 3.7 2.7 - - - +
22C THR* 1.3 79.2 - - - +
24C GLU* 1.3 63.6 + - - +
26C HIS* 3.8 5.5 - - - +
27C HIS* 3.1 27.2 + - - +
84C PHE* 5.9 1.3 - - - -
85C TRP* 4.3 20.5 - - - -
88C LEU* 4.2 4.0 - - + -
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Residues in contact with GLU 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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11C TYR* 3.6 35.2 - - + -
20C LYS* 3.1 29.7 + - - +
21C GLN* 3.6 11.1 - - - +
22C THR 3.1 1.0 - - - -
23C MET* 1.3 77.9 - - - +
25C ILE* 1.3 55.9 + - + +
27C HIS* 3.9 0.2 - - - -
28C THR* 2.8 49.5 + - + +
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Residues in contact with ILE 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 GLN* 3.1 27.5 + - + +
22C THR* 3.9 3.1 - - - +
24C GLU* 1.3 74.8 - - + +
26C HIS* 1.3 61.5 + - - +
28C THR* 4.0 4.7 - - - -
29C LYS* 2.8 36.4 + - + +
30C HIS* 3.3 8.7 + - + -
175C LEU* 3.9 17.0 - - + -
174D TYR* 3.4 23.1 - - + +
178D GLN* 3.8 28.0 - - + +
179D ASN* 4.1 17.3 - - - +
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Residues in contact with HIS 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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22C THR* 2.8 30.9 + - + +
23C MET* 3.8 3.6 - - - +
25C ILE* 1.3 72.7 - - - +
27C HIS* 1.3 57.1 + - - +
30C HIS* 3.4 13.4 - - + +
31C HIS* 3.0 27.5 + - - +
81C HIS* 3.0 15.8 + + - -
84C PHE* 4.2 10.1 - + - -
85C TRP* 3.6 20.7 - + + -
167C ASP* 2.8 19.7 - - - -
171C HIS* 2.9 21.0 + + - +
172C ALA* 3.7 17.8 - - + +
206C MN 2.1 30.0 + - - -
174D TYR* 5.3 0.4 + - - -
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Residues in contact with HIS 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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4C LEU* 3.6 29.3 - - + +
5C PRO 2.8 29.4 + - - -
6C SER* 4.7 1.8 - - - -
7C LEU* 3.3 37.2 - - + +
11C TYR* 2.8 31.1 + - + -
23C MET 3.1 17.4 + - - +
26C HIS* 1.3 78.7 - - - +
28C THR* 1.3 63.6 + - + +
31C HIS* 3.4 6.5 - - - +
32C GLN 3.3 19.8 + - - -
85C TRP* 3.6 26.0 - - + -
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Residues in contact with THR 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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4C LEU* 4.8 5.2 - - + -
11C TYR* 3.5 24.2 - - + +
24C GLU* 2.8 38.8 + - + +
25C ILE* 4.0 0.7 - - - -
27C HIS* 1.3 75.5 - - + +
29C LYS* 1.3 78.7 + - - +
32C GLN* 3.3 20.7 - - - +
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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 ILE* 2.8 29.9 + - + +
28C THR* 1.3 91.1 - - - +
30C HIS* 1.3 65.3 + - - +
31C HIS 3.6 0.2 - - - -
32C GLN* 3.6 1.6 + - - +
33C THR* 2.9 31.8 + - - -
179D ASN* 3.8 38.4 - - - +
180D ARG* 6.3 0.9 - - - +
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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