Contacts of the helix formed by residues 17 - 26 (chain B) in PDB entry 2NUF
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 17 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15B PHE* 3.9 6.8 - - - -
16B LYS* 1.3 78.3 - - + +
18B LYS* 1.3 57.5 + - - +
19B SER* 3.0 28.4 + - - -
20B LEU* 2.9 35.9 + - + +
21B LEU 3.6 1.9 + - - -
119B ASP* 3.3 11.2 + - - +
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Residues in contact with LYS 18 (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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2B LYS* 6.1 2.7 - - - +
4B LEU* 4.5 21.4 - - + +
5B GLU* 5.6 8.1 - - + -
8B GLU* 2.9 37.8 + - - +
14B THR* 4.1 7.1 - - - +
15B PHE* 3.2 23.8 + - + +
16B LYS 3.8 3.9 + - - +
17B ASP* 1.3 71.8 - - - +
19B SER* 1.3 59.0 + - - +
20B LEU 3.1 0.2 - - - -
21B LEU* 3.3 12.3 + - + +
22B GLU* 3.0 33.9 + - - +
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Residues in contact with SER 19 (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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17B ASP* 3.0 14.7 + - - -
18B LYS* 1.3 77.2 - - - +
20B LEU* 1.3 62.0 + - - +
22B GLU* 3.3 16.8 + - - +
23B LYS* 3.1 22.3 + - - +
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Residues in contact with LEU 20 (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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15B PHE* 4.1 1.1 - - + -
17B ASP* 2.9 24.6 + - + +
19B SER* 1.3 78.5 - - - +
21B LEU* 1.3 63.8 + - - +
23B LYS* 3.2 22.2 + - + +
24B ALA* 3.2 12.5 + - - +
39B LEU* 4.3 20.1 - - + +
115B ALA* 3.1 32.5 - - + +
118B ILE* 4.2 17.0 - - + -
119B ASP* 3.4 32.5 - - + +
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Residues in contact with LEU 21 (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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4B LEU* 4.5 23.1 - - + +
7B LEU* 4.6 11.7 - - + -
8B GLU* 4.0 22.9 - - + +
11B LEU* 6.4 0.4 - - + -
15B PHE* 3.8 45.2 - - + -
17B ASP 3.6 0.8 + - - -
18B LYS* 3.3 11.3 + - + +
20B LEU* 1.3 79.2 - - - +
22B GLU* 1.3 60.8 + - - +
24B ALA* 3.4 9.3 + - - +
25B LEU* 3.2 36.8 + - + +
112B LEU* 3.5 30.7 - - + -
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Residues in contact with GLU 22 (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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2B LYS* 4.3 10.0 - - - -
4B LEU* 3.7 28.9 - - + +
18B LYS* 3.0 22.9 + - - +
19B SER* 3.5 17.8 + - - +
20B LEU 3.2 0.2 - - - -
21B LEU* 1.3 75.6 - - - +
23B LYS* 1.3 60.9 + - - +
25B LEU* 3.2 11.1 + - - +
26B THR* 2.7 32.4 + - - -
94B ARG* 4.2 29.2 + - - +
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Residues in contact with LYS 23 (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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19B SER 3.1 13.1 + - - +
20B LEU* 3.2 18.6 + - + +
22B GLU* 1.3 76.4 - - - +
24B ALA* 1.3 65.1 + - - +
26B THR* 3.0 15.2 + - - +
33B LYS 5.4 0.9 - - - -
34B GLU* 3.3 38.4 + - + +
35B HIS 3.5 28.2 - - - +
36B TYR 3.3 18.9 + - - -
38B THR* 5.8 7.2 - - - -
39B LEU* 4.0 21.2 - - + +
94B ARG* 5.8 0.2 - - - +
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Residues in contact with ALA 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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20B LEU 3.2 2.9 + - - +
21B LEU 3.5 10.8 - - - +
22B GLU 3.3 0.2 - - - -
23B LYS* 1.3 80.0 - - - +
25B LEU* 1.3 57.0 + - - +
36B TYR* 3.4 20.7 - - - +
39B LEU* 3.9 7.3 - - + +
108B VAL* 3.4 20.5 - - - +
111B ALA* 3.8 29.0 - - - +
112B LEU* 4.0 13.2 - - + -
115B ALA* 3.9 17.7 - - + -
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Residues in contact with LEU 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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4B LEU* 3.8 28.7 - - + -
7B LEU* 4.0 20.6 - - + -
21B LEU* 3.2 26.9 - - + +
22B GLU* 3.2 8.9 + - - +
23B LYS 3.0 0.6 - - - -
24B ALA* 1.3 78.7 - - + +
26B THR* 1.3 58.7 + - - +
36B TYR* 4.5 2.2 - - - -
89B LEU* 4.4 3.1 - - + -
92B PHE* 4.0 33.2 - - + +
93B ILE* 3.5 14.3 - - - +
94B ARG* 2.9 27.7 + - + +
108B VAL* 3.9 23.2 - - + +
112B LEU* 4.3 7.4 - - + -
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Residues in contact with THR 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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22B GLU 2.7 19.9 + - - -
23B LYS 3.0 5.7 + - - -
25B LEU* 1.3 77.2 - - - +
27B HIS* 1.3 73.5 + - - +
30B TYR* 4.0 14.8 - - + -
31B SER* 3.7 17.0 - - - -
34B GLU 3.4 23.7 + - - +
35B HIS* 3.1 2.8 - - - +
36B TYR* 3.0 34.2 + - - -
94B ARG* 3.0 29.2 + - - +
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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