Contacts of the helix formed by residues 24 - 35 (chain C) in PDB entry 1NBI
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 GLY 24 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21C TYR* 2.7 19.8 + - - -
22C ALA 3.1 0.6 - - - -
23C ASP* 1.3 80.4 - - - +
25C GLU* 1.3 63.4 + - - +
26C ALA 3.5 1.8 - - - -
27C ALA* 4.3 7.5 - - - +
28C ARG* 3.5 21.8 + - - +
89C LYS* 4.1 21.1 - - - -
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Residues in contact with GLU 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 TYR* 5.4 0.4 - - - +
23C ASP* 2.9 30.2 + - + +
24C GLY* 1.3 78.4 - - - +
26C ALA* 1.3 65.3 + - - +
27C ALA 3.4 0.2 - - - -
28C ARG* 2.7 37.9 + - - +
29C VAL* 3.3 24.8 + - - +
236C SER* 2.6 24.5 + - - -
237C LYS 3.2 22.0 + - - +
238C PHE* 3.7 19.7 - - + -
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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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20C GLN 5.1 5.5 + - - +
21C TYR* 3.4 21.5 - - + +
23C ASP* 5.5 0.2 - - - -
24C GLY* 3.5 0.4 - - - -
25C GLU* 1.3 79.8 - - - +
27C ALA* 1.3 50.8 - - - +
29C VAL* 3.6 1.9 - - - +
30C TRP* 2.6 67.6 + - + +
238C PHE* 4.3 25.1 - - + +
240C LEU* 4.9 2.9 - - + -
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Residues in contact with ALA 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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21C TYR* 4.5 2.9 - - + -
24C GLY* 4.3 8.7 + - - +
26C ALA* 1.3 77.5 - - - +
28C ARG* 1.3 66.0 + - - +
30C TRP* 2.9 20.2 + - - +
31C GLN* 3.1 16.6 + - - +
89C LYS* 4.2 15.0 - - + +
90C MET* 3.9 24.5 - - + -
93C TYR* 3.5 25.7 - - + -
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Residues in contact with ARG 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 GLY 3.5 18.6 + - - +
25C GLU* 2.7 37.3 + - - +
26C ALA 3.5 0.4 - - - -
27C ALA* 1.3 77.8 - - - +
29C VAL* 1.3 69.9 + - + +
31C GLN* 2.9 17.0 - - - +
32C LEU* 5.3 0.9 - - - +
93C TYR* 4.1 15.8 + - - +
224C VAL* 5.2 4.0 - - - +
236C SER* 2.8 31.3 + - - +
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Residues in contact with VAL 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 3.3 18.4 - - - +
26C ALA 3.8 2.7 - - - +
28C ARG* 1.3 94.5 - - + +
30C TRP* 1.3 68.7 + - - +
31C GLN* 3.0 6.7 - - - -
32C LEU* 2.7 18.9 + - + +
33C TYR 2.8 9.7 + - - -
222C VAL* 3.4 32.5 - - + -
224C VAL* 3.5 31.6 - - + -
236C SER* 3.7 16.4 - - - +
238C PHE* 4.1 6.7 - - + -
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Residues in contact with TRP 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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21C TYR* 3.2 38.8 - + - -
26C ALA* 2.6 51.8 + - + +
27C ALA* 2.9 15.1 + - - +
29C VAL* 1.3 72.8 - - - +
31C GLN* 1.3 58.9 + - - +
33C TYR* 2.8 25.0 + + + +
34C ILE* 2.7 74.7 + - + +
67C THR* 3.7 21.2 + - + -
90C MET* 3.8 9.1 - - + +
142C HIS* 4.7 0.4 - + - -
194C TYR* 4.3 10.5 - + - -
238C PHE* 4.8 2.5 - + - -
240C LEU* 4.3 14.6 - - + -
242C TYR* 5.7 0.7 - - - -
2293C SAM 3.4 41.6 + - + +
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Residues in contact with GLN 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 ALA 3.1 19.2 + - - +
28C ARG* 2.9 21.7 - - - +
29C VAL 4.0 2.7 - - - -
30C TRP* 1.3 75.1 - - - +
32C LEU* 1.3 75.4 + - + +
34C ILE* 3.7 5.4 + - - +
35C GLY 3.1 29.5 + - - +
37C THR* 6.0 0.3 - - - +
67C THR* 4.3 13.1 - - - +
93C TYR* 4.9 11.9 - - - +
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Residues in contact with LEU 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 ARG 5.3 0.4 - - - +
29C VAL* 2.7 19.0 + - - +
31C GLN* 1.3 90.5 - - + +
33C TYR* 1.3 65.1 + - - +
35C GLY* 3.0 16.4 + - - +
196C SER* 3.5 14.9 - - - -
198C LEU* 3.3 24.7 - - + +
222C VAL* 3.8 8.5 - - + -
223C GLN 4.2 1.1 - - - +
224C VAL* 3.4 25.1 - - + -
225C PRO* 3.3 35.7 - - + -
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Residues in contact with TYR 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 VAL 2.8 6.8 + - - +
30C TRP* 2.8 38.6 + + - +
32C LEU* 1.3 78.1 - - - +
34C ILE* 1.3 61.7 + - - +
175C LYS* 5.7 2.3 + - - -
194C TYR* 3.1 62.4 - + + +
195C LYS 4.2 0.5 + - - -
196C SER* 4.6 5.0 - - - -
199C THR* 5.4 9.8 + - + -
220C TYR* 3.1 54.8 + + + -
222C VAL* 3.8 15.4 - - + +
238C PHE* 3.3 31.0 - + + -
242C TYR* 3.6 7.4 + - - -
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Residues in contact with ILE 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 TRP* 2.7 42.1 + - + +
31C GLN* 4.0 5.2 - - - +
33C TYR* 1.3 72.9 - - - +
35C GLY* 1.3 65.6 + - - +
37C THR* 4.9 8.3 - - + -
40C ARG* 3.5 39.9 - - + +
67C THR* 4.2 0.2 - - - +
69C VAL* 3.8 17.0 - - + -
193C TYR 3.5 6.3 - - - +
194C TYR* 3.5 17.9 - - + -
195C LYS* 3.2 27.6 + - - -
2293C SAM 3.1 27.8 - - - +
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Residues in contact with GLY 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 GLN 3.1 15.5 + - - +
32C LEU* 3.0 17.0 + - - -
34C ILE* 1.3 80.6 - - - +
36C ASP* 1.3 61.6 + - - -
37C THR* 3.1 10.1 + - - +
38C ARG* 4.0 3.3 + - - -
195C LYS 3.7 13.5 - - - -
196C SER* 4.6 2.9 - - - -
198C LEU* 6.3 0.2 - - - -
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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