Contacts of the helix formed by residues 17 - 28 (chain B) in PDB entry 2YZ5
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 HIS 17 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54A GLU* 4.8 0.2 + - - -
57A PRO* 3.6 33.2 - - + +
61A LEU* 3.9 13.8 - - + +
16B GLY* 1.3 73.2 - - - -
18B PRO* 1.3 84.4 - - + +
19B GLU* 2.9 60.0 + - + +
20B ALA* 2.8 30.1 + - + +
21B TYR* 3.3 5.0 - - - -
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Residues in contact with PRO 18 (chain B).
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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57A PRO* 4.0 8.5 - - + -
58A PHE* 3.9 35.7 - - + -
61A LEU* 3.6 23.6 - - + -
8B THR* 6.3 0.4 - - + -
16B GLY 3.5 1.9 - - - +
17B HIS* 1.3 95.3 - - + +
19B GLU* 1.3 55.1 + - - +
21B TYR* 3.1 32.4 + - + +
22B LEU* 3.3 11.6 + - - +
35B PHE* 3.7 19.8 - - + -
63B LEU* 4.5 2.9 - - + -
66B VAL* 3.9 15.0 - - + -
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Residues in contact with GLU 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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61A LEU* 5.0 2.1 - - - +
17B HIS* 2.9 31.3 + - + +
18B PRO* 1.3 74.5 - - - +
20B ALA* 1.3 59.8 + - - +
22B LEU* 3.3 14.1 + - + +
23B GLU* 2.9 24.4 + - - +
26B ARG* 4.7 2.5 + - - +
66B VAL* 4.1 25.3 - - + +
69B ARG* 2.9 54.0 + - - +
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Residues in contact with ALA 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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16B GLY* 5.1 0.2 - - - -
17B HIS* 2.8 26.7 + - + +
19B GLU* 1.3 75.9 - - - +
21B TYR* 1.3 63.5 + - - +
23B GLU* 3.2 12.3 + - - +
24B GLU* 3.1 19.1 + - - +
228B PRO* 3.6 27.1 - - + +
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Residues in contact with TYR 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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6B VAL* 4.5 9.2 - - + -
7B HIS 3.5 26.4 + - - -
8B THR* 4.6 1.5 - - + -
9B PRO* 4.9 2.0 - - + -
14B ALA* 4.1 3.8 - - - +
15B GLU 2.8 32.1 + - - -
16B GLY 3.5 14.1 - - - -
17B HIS 3.3 18.4 - - - -
18B PRO* 3.1 13.6 + - + +
20B ALA* 1.3 80.3 - - - +
22B LEU* 1.3 57.7 + - + +
24B GLU 3.5 1.0 + - - -
25B ALA* 3.1 24.8 + - - +
33B VAL* 4.8 2.4 - - + +
35B PHE* 4.2 14.8 - + + -
225B ALA* 4.0 13.2 - - + -
226B HIS* 3.2 18.0 + - - -
227B ARG 3.8 13.0 - - - -
228B PRO* 3.6 19.1 - - + -
231B VAL* 3.6 31.9 - - + +
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Residues in contact with LEU 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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18B PRO 3.3 10.3 + - - +
19B GLU* 3.6 12.3 - - + +
20B ALA 3.2 0.6 - - - -
21B TYR* 1.3 75.1 - - - +
23B GLU* 1.3 65.4 + - - +
25B ALA* 3.3 5.5 + - - +
26B ARG* 3.0 41.2 + - - +
33B VAL* 3.8 31.0 - - + -
35B PHE* 4.2 14.1 - - + -
66B VAL* 3.4 28.9 - - + -
70B ALA* 3.7 26.7 - - + -
73B LEU* 4.2 9.1 - - + +
75B VAL* 4.2 12.6 - - + -
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Residues in contact with GLU 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 GLU 2.9 13.9 + - - +
20B ALA* 3.2 15.4 + - - +
22B LEU* 1.3 77.2 - - - +
24B GLU* 1.3 63.4 + - - +
26B ARG* 3.1 16.2 + - + +
27B ALA* 3.0 22.3 + - + +
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Residues in contact with GLU 24 (chain B).
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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20B ALA 3.1 8.4 + - - +
21B TYR 3.8 5.6 - - - +
23B GLU* 1.3 79.8 - - - +
25B ALA* 1.3 62.7 + - - +
27B ALA* 3.2 12.1 + - - +
28B LYS* 2.8 65.8 + - - +
228B PRO* 3.0 29.8 - - + +
229B GLU* 3.5 24.3 - - - +
231B VAL* 3.9 6.5 - - + -
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Residues in contact with ALA 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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21B TYR 3.1 15.6 + - - +
22B LEU* 3.4 11.0 - - - +
24B GLU* 1.3 76.8 - - - +
26B ARG* 1.3 61.1 + - - +
28B LYS 3.2 2.3 + - - -
29B GLY 3.1 4.3 + - - -
30B LEU* 2.8 40.4 + - + +
32B GLY 5.0 0.2 - - - +
33B VAL* 3.7 26.9 - - + -
73B LEU* 4.9 7.6 - - + -
231B VAL* 3.9 12.5 - - + +
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Residues in contact with ARG 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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19B GLU* 4.7 3.0 + - - +
22B LEU* 3.0 45.7 + - - +
23B GLU* 3.1 13.9 + - + +
25B ALA* 1.3 73.2 - - - +
27B ALA* 1.3 60.9 + - - +
29B GLY* 2.8 20.0 + - - -
30B LEU 4.7 5.6 - - - +
69B ARG 5.1 1.2 + - - -
70B ALA* 3.6 22.6 - - - +
72B ASP* 2.7 41.7 + - - +
73B LEU* 3.7 18.4 - - + +
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Residues in contact with ALA 27 (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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23B GLU* 3.0 13.9 + - + +
24B GLU* 3.6 20.0 - - - +
26B ARG* 1.3 77.9 - - - +
28B LYS* 1.3 59.9 + - - +
29B GLY 3.2 1.1 + - - -
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Residues in contact with LYS 28 (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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24B GLU* 2.8 44.2 + - - +
25B ALA* 3.8 4.9 - - - +
26B ARG 3.1 0.4 - - - -
27B ALA* 1.3 77.2 - - - +
29B GLY* 1.3 62.1 + - - +
30B LEU* 3.3 19.8 + - + +
229B GLU 3.2 13.1 + - - -
231B VAL 2.7 30.4 + - - +
232B GLY* 4.0 15.0 - - - +
233B PHE* 4.4 9.3 - - - +
234B ALA 5.6 1.3 - - - +
236B PRO* 5.9 4.7 - - + -
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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