Contacts of the helix formed by residues 24 - 35 (chain D) in PDB entry 2IBS
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 24 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22D GLU* 3.5 13.2 - - - +
23D THR* 1.3 88.0 - - + +
25D PRO* 1.4 75.9 - - + +
26D GLU* 4.0 11.4 - - + +
27D VAL* 3.0 27.9 + - + +
28D VAL* 3.1 10.2 + - - +
195D VAL 3.7 22.4 - - - +
196D PHE* 3.4 27.6 - - + -
197D PRO* 4.5 9.9 - - + -
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Residues in contact with PRO 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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22D GLU* 4.5 8.5 - - - +
23D THR 3.5 4.4 - - - +
24D PRO* 1.4 83.6 - - + +
26D GLU* 1.3 72.3 + - - +
28D VAL* 3.8 8.0 - - + +
29D ASP* 3.0 41.0 + - - +
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Residues in contact with GLU 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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81A PRO* 5.3 15.2 - - + +
24D PRO* 3.1 7.9 - - + +
25D PRO* 1.3 97.7 - - - +
27D VAL* 1.3 63.4 + - + +
29D ASP 3.9 0.2 + - - -
30D PHE* 3.4 18.5 + - - +
223D SER 6.1 0.2 - - - +
224D GLU 5.9 0.2 - - - +
225D SER* 3.8 23.3 - - - +
226D GLY* 3.5 17.9 - - - +
227D PHE* 3.7 17.8 - - + -
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Residues in contact with VAL 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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23D THR* 3.8 16.8 - - + -
24D PRO* 3.0 29.3 + - + +
26D GLU* 1.3 77.2 - - + +
28D VAL* 1.3 58.6 + - - +
30D PHE* 3.3 5.1 + - + +
31D MET* 3.0 44.6 + - + +
163D VAL* 4.2 9.2 - - + -
192D LEU* 3.9 20.2 - - + -
195D VAL* 4.0 25.8 - - + -
196D PHE* 4.9 0.9 - - + -
205D VAL* 4.8 0.2 - - + -
227D PHE* 4.1 15.3 - - + -
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Residues in contact with VAL 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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23D THR* 3.8 29.2 - - + +
24D PRO 3.1 14.3 + - - +
25D PRO* 3.8 9.0 - - + +
26D GLU 3.5 0.2 - - - -
27D VAL* 1.3 76.1 - - - +
29D ASP* 1.3 59.2 + - - +
31D MET* 3.2 2.8 + - - +
32D VAL* 2.9 34.1 + - + +
52D PRO* 4.3 14.1 - - + +
53D PHE* 3.9 31.9 - - + -
56D ALA* 3.8 28.5 - - + -
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Residues in contact with ASP 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 PRO* 3.0 23.2 + - - +
26D GLU 4.0 0.7 - - - +
28D VAL* 1.3 80.3 - - - +
30D PHE* 1.3 61.8 + - - +
32D VAL* 3.5 8.1 + - - +
33D SER* 3.2 22.7 + - - -
56D ALA* 5.4 3.8 - - - +
225D SER* 3.3 34.1 - - - +
226D GLY* 4.8 0.9 - - - -
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Residues in contact with PHE 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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26D GLU 3.4 15.9 + - - +
27D VAL 3.3 5.1 + - - +
28D VAL 3.2 0.4 - - - -
29D ASP* 1.3 79.3 - - - +
31D MET* 1.3 62.1 + - - +
33D SER* 2.7 26.9 + - - -
34D LEU* 3.4 34.0 + - + +
190D TYR* 3.8 25.1 - + + -
192D LEU* 4.2 18.6 - - + -
205D VAL* 3.9 25.6 - - + -
220D THR* 3.9 10.5 - - + -
226D GLY* 4.9 1.0 - - - -
227D PHE* 3.3 39.0 - + + +
229D PRO* 3.7 24.7 - - + -
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Residues in contact with MET 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 VAL* 3.0 26.0 + - - +
28D VAL 3.2 4.0 + - - +
30D PHE* 1.3 74.2 - - + +
32D VAL* 1.3 60.0 + - - +
34D LEU* 3.2 8.2 + - - +
35D ALA* 2.9 26.9 + - - +
53D PHE* 3.6 31.0 - - + -
103D LEU* 5.2 3.1 - - + +
104D GLY 3.5 10.3 - - - +
161D VAL* 3.4 38.0 - - + +
162D PHE 3.6 2.7 - - - -
163D VAL* 3.5 42.8 - - - +
205D VAL* 4.0 23.8 - - + -
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Residues in contact with VAL 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 VAL* 2.9 23.9 + - + +
29D ASP* 3.8 7.2 - - - +
30D PHE 3.3 0.2 - - - -
31D MET* 1.3 76.1 - - - +
33D SER* 1.3 58.8 + - - +
35D ALA* 3.1 19.9 + - - +
53D PHE* 4.7 6.1 - - + +
56D ALA* 3.9 31.2 - - + +
57D PHE* 4.0 12.3 - - + +
60D ALA* 3.9 19.3 - - + -
61D HIS* 3.2 38.0 - - + +
103D LEU* 4.9 6.7 - - + -
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Residues in contact with SER 33 (chain D).
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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29D ASP 3.2 12.6 + - - -
30D PHE* 2.7 31.2 + - - -
32D VAL* 1.3 76.7 - - - +
34D LEU* 1.3 62.6 + - - +
35D ALA 4.5 2.0 - - - +
61D HIS* 5.1 3.5 + - - -
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Residues in contact with LEU 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 PHE* 3.4 42.6 - - + +
31D MET* 3.2 8.4 + - - +
32D VAL 3.1 0.6 - - - -
33D SER* 1.3 81.7 + - - +
35D ALA* 1.3 64.1 + - - +
36D GLU* 3.7 6.6 + - - +
159D VAL* 4.7 0.2 - - - +
161D VAL* 4.2 11.4 - - + +
190D TYR* 3.5 39.9 - - + +
205D VAL* 3.8 25.8 - - + -
207D ARG* 3.5 28.4 + - + +
229D PRO* 5.0 4.9 - - + -
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Residues in contact with ALA 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 MET 2.9 12.3 + - - +
32D VAL* 3.1 18.5 + - - +
33D SER 4.5 2.1 - - - +
34D LEU* 1.3 80.6 - - - +
36D GLU* 1.3 61.8 + - - +
57D PHE* 3.9 19.1 - - + -
61D HIS* 3.8 13.5 + - - -
101D LEU* 3.9 7.6 - - + -
103D LEU* 3.9 21.1 - - + -
161D VAL* 3.9 11.9 - - + +
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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