Contacts of the helix formed by residues 24 - 35 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21D TYR* 2.8 20.1 + - - -
22D ALA 3.1 0.6 - - - -
23D ASP* 1.3 81.8 - - - +
25D GLU* 1.3 62.1 + - - +
26D ALA 3.5 2.2 - - - -
27D ALA* 4.3 7.9 - - - +
28D ARG* 3.5 22.2 + - - +
89D LYS* 4.1 20.9 - - - -
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Residues in contact with GLU 25 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D TYR 5.4 0.2 - - - -
23D ASP* 2.9 29.3 + - + +
24D GLY* 1.3 79.6 - - - +
26D ALA* 1.3 65.6 + - - +
28D ARG* 2.7 37.1 + - - +
29D VAL* 3.3 24.8 + - - +
236D SER* 2.6 23.5 + - - -
237D LYS 3.2 22.9 + - - +
238D PHE* 3.7 18.9 - - + -
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Residues in contact with ALA 26 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20D GLN 5.1 6.4 + - - +
21D TYR* 3.4 25.7 - - + +
23D ASP* 5.0 0.4 + - - -
24D GLY* 3.5 0.4 - - - -
25D GLU* 1.3 80.2 - - - +
27D ALA* 1.3 51.7 + - - +
29D VAL* 3.6 1.9 - - - +
30D TRP* 2.6 63.0 + - + +
238D PHE* 4.3 24.7 - - + +
240D LEU* 4.8 2.2 - - + -
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Residues in contact with ALA 27 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D TYR* 4.5 3.0 - - + -
24D GLY* 4.3 8.4 + - - +
25D GLU 3.4 0.2 - - - -
26D ALA* 1.3 77.3 - - - +
28D ARG* 1.3 66.3 + - - +
30D TRP* 2.9 19.0 + - - +
31D GLN* 3.2 16.5 + - - +
89D LYS* 4.1 15.0 - - + +
90D MET* 3.8 23.6 - - + -
93D TYR* 3.5 26.5 - - + -
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Residues in contact with ARG 28 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D GLY 3.5 17.7 + - - +
25D GLU* 2.7 36.5 + - - +
26D ALA 3.5 0.4 - - - -
27D ALA* 1.3 78.2 - - - +
29D VAL* 1.3 68.9 + - + +
31D GLN* 2.8 16.4 - - - +
32D LEU* 5.3 0.5 - - - +
93D TYR* 4.1 15.7 + - - +
224D VAL* 5.2 4.2 - - - +
236D SER* 2.8 31.1 + - - +
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Residues in contact with VAL 29 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D GLU 3.3 18.2 - - - +
26D ALA 3.8 2.9 - - - +
28D ARG* 1.3 95.4 - - + +
30D TRP* 1.3 58.0 + - - +
31D GLN* 3.0 6.5 - - - -
32D LEU* 2.6 30.9 + - + +
33D TYR 2.8 9.2 + - - -
222D VAL* 3.4 33.2 - - + -
224D VAL* 3.4 30.5 - - + -
236D SER* 3.7 16.2 - - - +
238D PHE* 4.1 7.2 - - + -
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Residues in contact with TRP 30 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D TYR* 3.1 39.3 - + - -
26D ALA* 2.6 51.6 + - + +
27D ALA* 2.9 15.8 + - - +
29D VAL* 1.3 71.8 - - - +
31D GLN* 1.3 58.9 + - - +
33D TYR* 2.8 25.6 + + - +
34D ILE* 2.6 75.1 + - + +
67D THR* 3.8 21.0 + - + -
90D MET* 3.8 9.1 - - + +
142D HIS* 4.7 0.4 - + - -
194D TYR* 4.4 11.0 - + - -
238D PHE* 4.8 2.2 - + - -
240D LEU* 4.2 14.4 - - + -
242D TYR* 5.7 1.1 - - - -
3293D SAM 3.3 41.1 + - + +
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Residues in contact with GLN 31 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27D ALA 3.2 18.5 + - - +
28D ARG* 2.8 22.0 - - - +
29D VAL 3.9 2.9 - - - -
30D TRP* 1.3 73.5 - - - +
32D LEU* 1.3 73.8 + - + +
34D ILE* 3.8 5.3 + - - +
35D GLY 3.1 29.8 + - - +
37D THR* 6.0 0.5 - - - +
67D THR* 4.3 13.1 - - - +
93D TYR* 4.9 11.7 - - - +
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Residues in contact with LEU 32 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28D ARG 5.3 0.4 - - - +
29D VAL* 2.6 17.9 + - + +
31D GLN* 1.3 90.7 - - + +
33D TYR* 1.3 66.7 + - - +
34D ILE 3.1 0.2 - - - -
35D GLY* 3.0 15.4 + - - +
196D SER* 3.5 14.9 - - - -
198D LEU* 3.3 25.1 - - + +
222D VAL* 3.9 9.2 - - + -
223D GLN 4.1 0.7 - - - +
224D VAL* 3.4 25.4 - - + +
225D PRO* 3.3 35.0 - - + -
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Residues in contact with TYR 33 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29D VAL 2.8 7.0 + - - +
30D TRP* 2.8 39.8 + + - +
32D LEU* 1.3 79.0 - - - +
34D ILE* 1.3 59.9 + - - +
175D LYS* 5.8 1.4 + - - -
194D TYR* 3.2 61.8 - + + +
195D LYS 4.2 0.9 + - - -
196D SER* 4.7 4.7 - - - -
199D THR* 5.4 10.4 + - + -
220D TYR* 3.0 53.5 + + + -
222D VAL* 3.8 15.0 - - + +
238D PHE* 3.3 31.6 - + + -
240D LEU* 5.3 0.4 - - + -
242D TYR* 3.6 7.5 + - - -
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Residues in contact with ILE 34 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30D TRP* 2.6 43.0 + - + +
31D GLN* 4.0 4.7 - - - +
33D TYR* 1.3 73.3 - - - +
35D GLY* 1.3 64.9 + - - +
37D THR* 4.9 8.5 - - + -
40D ARG* 3.5 39.9 - - + +
67D THR* 4.2 0.2 - - - +
69D VAL* 3.8 17.9 - - + -
193D TYR 3.5 9.7 - - - +
194D TYR* 3.7 14.1 - - + -
195D LYS* 3.2 27.1 + - - -
3293D SAM 3.1 28.5 - - - +
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Residues in contact with GLY 35 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31D GLN 3.1 16.4 + - - +
32D LEU* 3.0 17.4 + - - -
34D ILE* 1.3 80.8 - - - +
36D ASP* 1.3 62.0 + - - -
37D THR* 3.2 10.0 + - - +
38D ARG* 4.0 3.1 + - - -
195D LYS 3.7 13.7 - - - -
196D SER* 4.6 2.5 - - - -
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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