Contacts of the helix formed by residues 21 - 33 (chain B) in PDB entry 4F5G
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 ASP 21 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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290A ARG* 5.2 11.8 + - - +
19B PRO 3.5 3.1 + - - +
20B ALA* 1.3 72.5 - - - +
22B PRO* 1.3 70.0 - - - +
23B ILE* 2.8 27.7 + - - +
24B LEU* 3.1 30.8 + - + +
25B GLY* 3.0 18.5 + - - -
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Residues in contact with PRO 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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20B ALA* 3.1 12.7 - - + +
21B ASP* 1.3 86.7 - - - +
23B ILE* 1.3 66.1 + - + +
25B GLY* 3.4 2.7 + - - +
26B LEU* 3.0 36.6 + - + +
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Residues in contact with ILE 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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21B ASP* 2.8 17.5 + - - +
22B PRO* 1.3 83.5 - - + +
24B LEU* 1.3 66.5 + - - +
26B LEU* 3.2 9.6 + - + +
27B ALA* 2.9 23.6 + - + +
42B GLY 5.6 4.7 - - - +
380B VAL* 3.8 30.5 - - + -
384B ARG* 5.7 2.9 - - - +
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Residues in contact with LEU 24 (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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286A LYS* 5.7 7.0 - - - +
21B ASP* 3.1 29.7 + - + +
23B ILE* 1.3 80.4 - - - +
25B GLY* 1.3 58.8 + - - +
27B ALA* 3.2 8.7 + - - +
28B ASP* 2.9 58.7 + - - +
31B ARG* 5.0 5.8 - - - +
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Residues in contact with GLY 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 ASP 3.0 13.2 + - - -
22B PRO* 3.8 4.3 - - - -
24B LEU* 1.3 82.9 - - - +
26B LEU* 1.3 59.7 + - - +
28B ASP* 3.4 6.9 + - - +
29B LEU* 3.1 31.7 + - - +
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Residues in contact with LEU 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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22B PRO* 3.0 20.5 + - + +
23B ILE* 3.2 10.5 + - + +
25B GLY* 1.3 75.3 - - - +
27B ALA* 1.3 58.3 + - - +
29B LEU* 3.2 11.7 + - + +
30B PHE* 2.8 31.9 + - - +
42B GLY* 6.4 0.2 - - - -
372B ARG* 3.8 33.0 - - - +
378B TYR* 4.0 13.2 - - + -
379B ALA 3.7 22.7 - - - +
380B VAL* 4.3 19.3 - - + -
381B ALA* 5.0 3.4 - - + +
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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 ILE* 2.9 15.7 + - + +
24B LEU* 3.4 12.6 - - - +
26B LEU* 1.3 76.7 - - - +
28B ASP* 1.3 61.0 + - - +
30B PHE* 3.5 7.4 + - - +
31B ARG* 3.0 47.7 + - - +
40B ASP* 5.4 6.1 - - - +
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Residues in contact with ASP 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 LEU* 2.9 36.8 + - - +
25B GLY* 3.7 9.9 - - - +
26B LEU 3.2 0.2 - - - -
27B ALA* 1.3 73.8 - - - +
29B LEU* 1.3 66.1 + - - +
31B ARG* 2.7 43.3 + - - +
32B ALA* 3.0 24.6 + - - +
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Residues in contact with LEU 29 (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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25B GLY 3.1 18.5 + - - +
26B LEU* 3.2 15.2 + - + +
28B ASP* 1.3 79.1 - - + +
30B PHE* 1.3 57.1 + - - +
32B ALA* 3.3 7.6 + - + +
33B ASP* 2.9 28.2 + - - +
372B ARG* 3.8 34.3 - - - +
378B TYR* 3.6 11.9 + - + +
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Residues in contact with PHE 30 (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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26B LEU 2.8 17.3 + - - +
27B ALA* 3.7 8.1 - - - +
29B LEU* 1.3 78.0 - - - +
31B ARG* 1.3 59.1 + - + +
33B ASP* 3.0 8.8 + - - +
38B LYS* 2.6 71.2 + - + -
39B VAL* 3.8 4.7 - - - -
40B ASP* 3.6 46.2 - - + +
47B LYS* 6.3 1.3 - - - -
378B TYR* 3.6 37.6 - + + -
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Residues in contact with ARG 31 (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 LEU* 4.4 7.3 + - - +
27B ALA* 3.0 39.6 + - - +
28B ASP* 2.7 38.4 + - - +
30B PHE* 1.3 82.7 - - + +
32B ALA* 1.3 58.7 + - + +
33B ASP 3.7 0.7 + - - +
38B LYS* 3.8 10.9 + - - +
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Residues in contact with ALA 32 (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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28B ASP 3.0 17.0 + - - +
29B LEU* 3.6 7.0 - - + +
31B ARG* 1.3 76.0 - - + +
33B ASP* 1.3 62.8 + - - +
34B GLU* 3.3 17.1 + - - +
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Residues in contact with ASP 33 (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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29B LEU 2.9 5.8 + - - +
30B PHE 3.0 13.6 + - - +
31B ARG 4.4 0.7 - - - +
32B ALA* 1.3 76.7 - - - +
34B GLU* 1.3 59.3 + - - +
35B ARG* 2.9 53.8 + - - +
38B LYS* 2.7 43.6 + - + +
378B TYR* 2.5 32.9 + - - +
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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