Contacts of the helix formed by residues 24 - 35 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A TYR* 3.0 8.0 + - - -
22A ALA 2.9 8.1 + - - -
23A ASP* 1.3 74.9 + - - +
25A GLU* 1.3 58.2 + - - +
26A ALA 3.3 2.5 - - - -
27A ALA* 3.8 8.1 - - - +
28A ARG* 3.0 25.5 + - - +
89A LYS* 3.0 32.4 - - - +
93A TYR* 4.9 2.6 + - - -
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Residues in contact with GLU 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A ASP* 2.3 39.3 + - + +
24A GLY* 1.3 68.8 - - - -
26A ALA* 1.3 66.2 + - - +
28A ARG* 3.0 43.3 + - - +
29A VAL* 3.4 10.6 + - - +
236A SER* 2.8 33.3 + - - -
237A LYS 4.1 17.7 + - - +
238A PHE* 4.4 4.3 - - + -
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Residues in contact with ALA 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A GLN 5.5 2.7 - - - +
21A TYR* 4.2 15.5 - - + -
23A ASP* 4.1 4.4 + - - +
24A GLY* 4.3 0.2 - - - -
25A GLU* 1.3 80.9 - - - +
27A ALA* 1.3 57.2 + - - +
29A VAL* 3.1 5.5 + - - +
30A TRP* 2.8 45.9 + - + -
238A PHE* 3.7 41.1 - - + -
240A LEU* 4.8 6.1 - - + -
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Residues in contact with ALA 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A TYR* 4.6 1.9 - - + -
24A GLY* 3.6 18.9 + - - +
25A GLU 3.3 0.2 - - - -
26A ALA* 1.3 79.1 - - - +
28A ARG* 1.3 57.2 + - - +
30A TRP* 3.7 5.3 + - - +
31A GLN* 2.8 19.8 + - - +
67A THR* 4.7 1.1 - - - +
89A LYS* 4.0 8.1 - - + +
90A MET* 3.5 38.4 - - + -
93A TYR* 3.7 29.4 - - + -
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Residues in contact with ARG 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A GLY 3.0 15.2 + - - +
25A GLU* 3.0 41.7 + - - +
27A ALA* 1.3 73.3 - - - +
29A VAL* 1.3 57.6 + - - +
31A GLN* 2.7 26.6 + - - +
93A TYR* 3.9 14.7 + - - +
224A VAL* 3.5 32.7 - - - +
236A SER* 3.8 15.2 - - - -
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Residues in contact with VAL 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A GLU 3.6 6.1 - - - +
26A ALA 3.4 10.1 - - - +
28A ARG* 1.3 83.0 - - - +
30A TRP* 1.3 50.4 + - - +
31A GLN* 2.9 8.1 - - - +
32A LEU* 2.5 33.9 + - + +
33A TYR* 2.6 14.7 + - + -
222A VAL* 3.6 20.6 - - + -
224A VAL* 3.6 30.7 - - + -
236A SER* 3.6 18.8 - - - +
238A PHE* 3.4 31.0 - - + -
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Residues in contact with TRP 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A TYR* 3.1 33.4 - + - -
26A ALA* 2.8 33.2 + - + +
27A ALA* 3.8 8.1 - - - +
29A VAL* 1.3 72.6 - - - +
31A GLN* 1.3 65.8 + - - +
33A TYR* 3.3 45.5 - + + -
34A ILE* 2.6 64.3 + - + +
67A THR* 3.8 22.7 - - + -
90A MET* 4.1 10.5 - - + -
194A TYR* 3.7 5.4 - + - -
238A PHE* 4.7 2.5 - + - -
240A LEU* 4.0 14.8 - - + -
242A TYR* 5.5 0.7 - - - -
293A SAM 3.3 52.8 + - + +
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Residues in contact with GLN 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A ALA 2.8 14.5 + - - +
28A ARG 2.7 24.9 + - - +
29A VAL 4.0 0.7 - - - -
30A TRP* 1.3 94.3 - - - +
32A LEU* 1.3 73.6 + - + +
34A ILE* 4.1 6.7 - - - +
35A GLY 3.3 22.3 + - - +
37A THR* 5.8 1.8 - - - +
67A THR* 5.2 4.8 - - - +
93A TYR* 3.9 22.2 - - - -
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Residues in contact with LEU 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A VAL* 2.5 19.6 + - + +
31A GLN* 1.3 89.3 - - + +
33A TYR* 1.3 59.9 + - - +
34A ILE 3.2 0.4 - - - -
35A GLY* 2.9 7.8 + - - -
196A SER* 2.6 30.0 + - - -
198A LEU* 3.4 21.5 - - + -
222A VAL* 4.4 6.1 - - + -
223A GLN 4.1 2.7 - - - +
224A VAL* 3.9 23.6 - - + -
225A PRO* 3.5 31.2 - - + -
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Residues in contact with TYR 33 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29A VAL* 2.6 21.6 + - + +
30A TRP* 3.3 57.4 - + + +
32A LEU* 1.3 74.3 - - - +
34A ILE* 1.3 61.9 + - - +
194A TYR* 3.5 40.2 - + + +
195A LYS 4.0 6.4 + - - -
196A SER* 3.7 12.0 + - - -
199A THR* 4.3 15.7 + - + -
202A ILE* 6.1 0.4 - - + -
220A TYR* 3.4 44.1 + + - -
222A VAL* 4.5 21.3 - - + -
238A PHE* 4.5 6.1 - + - -
240A LEU* 5.2 0.7 - - + -
242A TYR* 4.2 5.5 + - - -
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Residues in contact with ILE 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A TRP* 2.6 46.7 + - + +
31A GLN* 4.1 6.1 - - - +
33A TYR* 1.3 73.7 - - - +
35A GLY* 1.3 67.8 + - - +
36A ASP 4.0 2.1 + - - +
37A THR* 4.1 17.5 - - + -
40A ARG* 3.9 28.8 - - + +
67A THR* 4.4 4.9 - - - +
69A VAL* 4.3 15.9 - - + -
193A TYR 3.8 1.6 - - - +
194A TYR* 3.7 17.8 - - + -
195A LYS* 3.1 22.7 + - - +
293A SAM 3.3 24.0 - - - +
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Residues in contact with GLY 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A GLN 3.3 13.9 - - - +
32A LEU* 2.9 17.9 + - - -
34A ILE* 1.3 81.2 - - - +
36A ASP* 1.3 62.5 + - - -
37A THR* 3.6 4.0 + - - +
195A LYS 3.0 16.4 - - - -
196A SER* 4.0 4.3 - - - -
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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