Contacts of the helix formed by residues 21 - 31 (chain L) in PDB entry 1NSK
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 VAL 21 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11L ILE* 4.1 15.0 - - + +
16L VAL* 4.1 35.0 - - + -
20L LEU* 1.3 79.1 - - - +
22L GLY* 1.3 63.8 + - - +
24L ILE* 3.3 1.6 + - - +
25L ILE* 3.0 47.8 + - + +
74L VAL* 4.2 20.2 - - + -
25R ILE* 4.1 14.1 - - + -
29R GLU* 3.2 21.3 + - - +
35R LEU* 5.2 8.3 - - + -
38R MET* 4.6 4.3 - - + -
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Residues in contact with GLY 22 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21L VAL* 1.3 76.5 - - - +
23L GLU* 1.3 56.9 + - - +
25L ILE* 4.8 0.4 - - - -
26L LYS* 2.9 33.7 + - - +
22R GLY* 3.3 29.5 - - - -
25R ILE* 4.1 5.5 - - - +
26R LYS* 3.9 10.8 - - - -
29R GLU* 2.9 16.9 + - - -
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Residues in contact with GLU 23 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19L GLY 5.7 1.5 + - - +
20L LEU* 3.6 17.8 + - + +
21L VAL 3.3 0.4 - - - -
22L GLY* 1.3 75.3 - - - +
24L ILE* 1.3 61.2 + - + +
26L LYS* 3.6 16.4 - - - +
27L ARG* 2.9 53.6 + - - +
108L PHE* 4.1 29.0 - - + -
30N GLN* 6.3 0.2 - - - +
26R LYS* 3.0 41.8 + - - +
29R GLU* 4.8 0.4 + - - -
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Residues in contact with ILE 24 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11L ILE* 3.9 34.1 - - + -
20L LEU* 3.0 35.9 + - + +
21L VAL 3.8 2.0 - - - +
23L GLU* 1.3 75.5 - - + +
25L ILE* 1.3 66.2 + - - +
27L ARG* 3.4 7.8 + - - +
28L PHE* 3.1 31.2 + - + -
76L MET* 5.0 3.8 - - + -
104L ILE* 3.5 37.5 - - + -
108L PHE* 5.3 2.5 - - + -
116L ILE* 4.7 10.3 - - + +
117L ILE* 3.5 27.4 - - + -
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Residues in contact with ILE 25 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11L ILE* 4.8 1.8 - - + -
21L VAL* 3.0 31.9 + - + +
22L GLY 4.0 2.7 - - - +
24L ILE* 1.3 75.4 - - - +
26L LYS* 1.3 65.5 + - - +
28L PHE* 2.9 16.6 + - - +
29L GLU* 3.0 26.4 + - - +
35L LEU* 5.5 2.0 - - + -
38L MET* 3.9 22.2 - - - -
76L MET* 4.1 19.5 - - - -
78L TRP* 4.0 20.9 - - + +
21R VAL* 4.1 14.4 - - + -
22R GLY* 4.1 2.7 - - - +
25R ILE* 3.3 32.8 - - + -
38R MET* 4.8 0.2 - - + -
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Residues in contact with LYS 26 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22L GLY 2.9 19.4 + - - +
23L GLU* 3.6 25.4 - - - +
25L ILE* 1.3 76.7 - - - +
27L ARG* 1.3 63.0 + - + +
29L GLU* 3.0 16.5 + - + +
30L GLN* 2.9 43.7 + - + +
22R GLY* 3.9 7.8 - - - -
23R GLU* 3.0 46.5 + - + +
26R LYS* 4.9 4.0 - - + +
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Residues in contact with ARG 27 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23L GLU* 2.9 36.0 + - - +
24L ILE* 3.6 6.1 - - - +
25L ILE 3.2 0.2 - - - -
26L LYS* 1.3 75.3 - - + +
28L PHE* 1.3 62.7 + - + +
30L GLN* 3.2 33.2 - - - +
31L LYS* 3.4 11.4 + - - +
90L MET* 3.6 16.0 - - + +
102L GLY 3.1 17.6 + - - -
104L ILE* 3.5 31.9 - - + +
107L ASP* 3.0 31.1 + - - -
108L PHE* 3.1 31.3 - - - -
30N GLN* 5.6 0.8 + - - -
107O ASP 4.4 0.9 - - - +
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Residues in contact with PHE 28 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9L ILE* 4.0 26.7 - - + -
24L ILE* 3.1 27.6 - - + -
25L ILE* 2.9 8.0 + - - +
27L ARG* 1.3 74.2 - - - +
29L GLU* 1.3 67.7 + - - +
31L LYS* 3.3 10.8 + - - +
33L PHE* 3.4 37.0 + + - +
76L MET* 6.0 0.2 - - + -
78L TRP* 3.7 42.0 - + + -
83L VAL* 5.5 1.8 - - + -
87L GLY* 4.2 14.1 - - - -
90L MET* 3.9 24.2 - - + -
91L LEU* 3.5 24.9 - - + -
104L ILE* 3.8 24.0 - - + -
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Residues in contact with GLU 29 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25L ILE* 3.0 14.7 + - + +
26L LYS* 3.3 11.8 - - + +
28L PHE* 1.3 76.0 - - - +
30L GLN* 1.3 58.0 + - - +
32L GLY* 3.0 23.0 + - - -
33L PHE 4.2 7.2 + - - +
78L TRP* 3.9 15.9 - - + -
18O ARG* 4.8 1.0 + - - -
16R VAL 4.3 2.8 - - - +
19R GLY* 3.3 34.4 - - - +
21R VAL* 3.2 33.5 + - - +
22R GLY* 2.9 28.1 + - - -
23R GLU 4.8 0.3 + - - -
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Residues in contact with GLN 30 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26L LYS* 2.9 31.3 + - + +
27L ARG* 3.2 36.2 - - - +
29L GLU* 1.3 75.7 - - - +
31L LYS* 1.3 56.4 + - - +
18O ARG* 3.2 19.2 + - - +
20O LEU* 5.2 3.6 - - + +
27O ARG* 5.8 0.5 + - - -
107O ASP* 3.6 17.2 - - - +
108O PHE* 3.2 42.9 - - + +
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Residues in contact with LYS 31 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27L ARG 3.4 12.1 + - - +
28L PHE 3.5 10.5 - - - +
29L GLU 3.0 1.0 + - - -
30L GLN* 1.3 79.6 - - - +
32L GLY* 1.3 57.7 + - - +
33L PHE* 3.4 35.7 - - + -
86L THR* 5.0 9.4 - - - +
90L MET* 4.0 13.7 - - + +
150L VAL* 4.7 0.5 - - - +
18O ARG* 3.7 2.6 + - - -
96O PRO 4.1 11.9 + - - -
99O SER 5.2 1.0 + - - -
105O ARG 3.5 5.3 + - - -
106O GLY* 3.1 32.7 + - - +
107O ASP 3.3 11.2 - - - +
108O PHE 3.4 12.4 - - - +
109O CYS* 2.6 32.1 + - - +
110O ILE* 3.3 22.7 - - + +
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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