Contacts of the helix formed by residues 13 - 17 (chain B) in PDB entry 1NUE
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 13 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B LYS* 1.4 87.4 - - + +
14B ASP* 1.3 57.8 + - - +
16B VAL* 3.4 2.8 + - - +
17B GLN* 2.9 32.8 + - + +
67B TYR* 3.6 23.6 - - + +
68B MET* 3.6 29.4 - - - +
71B GLY* 3.6 27.8 - - - +
72B PRO* 3.6 12.9 - - - +
73B VAL* 4.0 5.4 - - + -
149C TRP* 3.8 19.5 - - + -
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Residues in contact with ASP 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B LYS* 3.3 11.3 - - - +
13B PRO* 1.3 71.6 - - - +
15B GLY* 1.3 59.3 + - - +
18B ARG* 2.9 36.2 + - - +
67B TYR* 2.5 32.6 + - + -
114B ARG* 3.1 18.3 - - - +
116B ILE* 2.9 30.6 + - + +
149C TRP* 3.1 44.5 - - + +
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Residues in contact with GLY 15 (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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11B ILE* 3.8 16.6 - - - -
12B LYS 2.9 10.0 + - - -
14B ASP* 1.3 82.4 + - - +
16B VAL* 1.3 60.5 + - - +
18B ARG 3.6 0.3 + - - -
19B GLY 3.3 3.1 + - - -
20B LEU* 3.0 38.4 + - - +
21B VAL* 4.1 0.9 + - - -
24B ILE* 5.3 0.4 - - - -
116B ILE* 4.0 17.8 - - - +
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Residues in contact with VAL 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B ILE* 4.3 5.6 - - + +
12B LYS 3.4 8.0 + - - +
13B PRO 3.4 6.9 + - - +
14B ASP 3.3 0.2 - - - -
15B GLY* 1.3 76.2 - - - +
17B GLN* 1.3 62.1 + - + +
19B GLY* 3.0 14.7 + - - -
21B VAL* 4.0 14.8 - - + -
40B PHE* 4.0 16.6 - - + -
72B PRO* 3.6 28.7 - - + +
74B VAL* 4.1 26.2 - - + -
29E GLU* 4.5 1.9 - - - +
35E LEU* 5.8 2.7 - - + -
142E TYR* 4.0 25.1 - - + +
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Residues in contact with GLN 17 (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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13B PRO* 2.9 22.3 + - + +
14B ASP 3.9 1.3 - - - +
16B VAL* 1.3 77.9 - - + +
18B ARG* 1.3 61.0 + - - +
19B GLY 3.5 0.9 + - - -
70B SER 5.7 0.6 + - - -
71B GLY* 5.5 2.2 - - - -
72B PRO* 5.3 4.3 - - + +
149C TRP* 3.4 56.3 - - + -
142E TYR* 3.7 22.0 - - - +
143E LYS 3.0 21.2 + - - -
144E SER* 3.4 8.2 - - - -
145E CYS* 2.9 43.3 + - - -
146E ALA* 5.9 1.2 - - - +
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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