Contacts of the helix formed by residues 23 - 34 (chain B) in PDB entry 3NTV
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 23 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A ASP* 5.0 10.9 - - - +
220A ASN* 3.6 16.4 + - - -
24B LEU* 1.3 64.8 + - - +
25B ASN* 3.2 14.7 + - - +
26B LYS* 3.1 35.6 + - + +
27B LYS* 3.3 18.7 + - - +
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Residues in contact with LEU 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184A SER* 3.6 32.3 + - - +
23B ASP* 1.3 75.4 + - - +
25B ASN* 1.3 59.7 + - - +
27B LYS* 3.3 23.8 + - + +
28B TYR* 2.8 29.3 + - - +
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Residues in contact with ASN 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178A LEU* 4.0 26.8 - - + +
181A GLY* 3.3 30.6 + - - +
183A VAL* 3.3 22.6 - - - +
184A SER* 3.6 14.7 + - - -
220A ASN* 5.0 3.6 - - + +
23B ASP* 3.2 9.8 + - - +
24B LEU* 1.3 73.3 - - - +
26B LYS* 1.3 59.9 + - - +
28B TYR* 3.2 6.8 + - - +
29B LEU* 3.0 35.7 + - - +
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Residues in contact with LYS 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220A ASN* 3.8 17.6 - - - +
23B ASP* 3.1 33.2 + - + +
25B ASN* 1.3 75.9 - - - +
27B LYS* 1.4 57.4 + - - +
29B LEU* 3.2 3.1 + - - +
30B ILE* 2.9 56.2 + - + +
56B ASP* 4.5 13.6 + - - -
58B LEU* 4.3 14.8 - - + +
222B ASP* 4.0 22.9 + - - +
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Residues in contact with LYS 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B ASP 3.3 11.3 + - - +
24B LEU* 3.3 26.0 + - + +
26B LYS* 1.4 76.6 - - - +
28B TYR* 1.3 57.8 + - - +
30B ILE* 3.4 10.1 + - + +
31B ASP* 2.9 60.6 + - - +
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Residues in contact with TYR 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A VAL 4.3 0.4 - - - -
178A LEU* 3.9 13.0 - - + -
183A VAL* 4.0 15.7 - - + -
184A SER* 3.9 13.7 - - - +
202A GLN* 3.7 34.5 + - + -
205A ASN* 3.1 38.8 + - - +
206A GLU* 5.1 5.7 + - - -
24B LEU 2.8 17.0 + - - +
25B ASN* 3.2 4.5 + - - +
27B LYS* 1.3 76.7 - - - +
29B LEU* 1.3 75.0 + - + +
31B ASP* 3.3 13.0 + - + +
32B LEU* 3.1 42.4 + - + +
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Residues in contact with LEU 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A VAL* 5.0 4.5 - - + +
178A LEU* 3.8 15.7 - - + -
218A PHE* 3.6 29.4 - - + -
219A LEU* 3.6 34.3 - - - +
220A ASN* 3.6 18.2 - - + +
25B ASN 3.0 17.1 + - - +
26B LYS 3.8 3.6 - - - +
28B TYR* 1.3 90.0 - - + +
30B ILE* 1.3 64.4 + - - +
32B LEU* 3.0 25.8 + - + +
33B HIS* 3.1 17.7 + - - -
58B LEU* 4.0 18.4 - - + -
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Residues in contact with ILE 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B LYS* 2.9 49.7 + - + +
27B LYS* 3.9 7.9 - - + +
29B LEU* 1.3 73.9 - - - +
31B ASP* 1.4 64.7 + - - +
33B HIS* 3.0 15.1 + - - +
34B GLN* 3.0 35.1 + - - +
57B ARG* 4.3 27.1 - - + +
58B LEU* 4.0 22.7 - - + +
222B ASP* 5.8 0.2 - - - +
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Residues in contact with ASP 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B LYS* 2.9 52.5 + - - +
28B TYR* 3.4 13.7 - - + +
30B ILE* 1.4 76.4 - - - +
32B LEU* 1.4 63.9 + - + +
34B GLN* 3.2 30.0 + - - +
35B HIS 4.7 0.5 + - - -
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Residues in contact with LEU 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205A ASN* 3.9 25.6 - - + +
206A GLU* 3.6 26.9 - - - +
209A ILE* 3.8 26.9 - - + +
218A PHE* 4.0 21.8 - - + -
28B TYR* 3.1 45.9 + - + +
29B LEU* 3.0 24.7 + - + +
31B ASP* 1.4 76.7 - - + +
33B HIS* 1.4 52.7 + - - +
34B GLN 3.5 0.5 + - - -
35B HIS* 2.7 33.7 + - - -
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Residues in contact with HIS 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217A ASN* 3.7 9.9 - - + -
218A PHE* 2.9 53.1 + + - +
29B LEU 3.1 16.2 + - - +
30B ILE* 3.0 13.5 + - - +
32B LEU* 1.4 72.3 - - - +
34B GLN* 1.4 57.9 + - - +
35B HIS* 3.1 7.4 - + - -
36B GLN* 2.8 33.0 + - - +
37B ASN* 4.1 0.2 - - - -
57B ARG* 3.0 25.2 + - + +
58B LEU* 3.8 21.0 - - + +
61B ASP* 2.6 44.5 + - + +
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Residues in contact with GLN 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B ILE* 3.0 37.8 + - - +
31B ASP* 3.2 28.9 + - - +
33B HIS* 1.4 76.8 - - - +
35B HIS* 1.4 61.5 + - - +
37B ASN* 2.9 45.2 + - - +
41B GLU* 5.7 0.5 - - - +
57B ARG* 3.7 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