Contacts of the helix formed by residues 337 - 346 (chain F) in PDB entry 3J0S
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 TYR 337 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18F LYS* 5.1 6.3 - - + +
25F ASP 5.0 0.2 - - - -
26F ALA* 3.7 17.9 - - + -
27F PRO* 3.4 26.7 - - + -
30F VAL* 5.4 7.9 - - + -
305F MET* 5.8 3.9 - - + +
334F GLU* 3.2 8.4 + - + +
336F LYS* 1.3 105.2 + - + +
338F SER* 1.3 53.7 + - - +
339F VAL 3.3 2.9 - - - -
340F TRP* 3.2 6.1 + - - +
341F ILE* 2.7 58.0 + - + +
92U LYS* 5.8 2.8 - - - -
93U GLU* 2.8 36.4 + - + -
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Residues in contact with SER 338 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140F LEU* 4.9 0.7 - - - +
141F SER* 4.3 12.2 + - - -
144F ALA* 4.9 14.1 - - - +
300F SER* 3.9 17.9 + - - -
332F PRO* 4.1 10.0 - - - +
334F GLU* 2.7 23.6 + - - +
335F ARG* 3.0 22.4 + - - -
337F TYR* 1.3 77.1 - - - +
339F VAL* 1.3 62.8 + - - +
341F ILE* 3.8 7.5 - - - +
342F GLY* 3.0 21.5 + - - -
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Residues in contact with VAL 339 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11F ASP* 3.6 16.6 - - - +
18F LYS* 4.9 6.1 - - - +
106F THR* 5.3 2.0 - - + -
137F GLN* 3.3 49.4 - - + +
140F LEU* 3.8 14.0 - - + +
141F SER* 3.5 20.4 - - - +
154F ASP* 3.6 20.4 - - - +
155F SER 5.7 0.2 - - - +
156F GLY* 6.4 0.9 - - - -
301F GLY* 4.8 13.9 - - - +
335F ARG 4.7 0.4 + - - -
336F LYS 4.8 2.0 + - - +
337F TYR 3.3 1.0 - - - -
338F SER* 1.3 79.4 - - - +
340F TRP* 1.3 62.6 + - - +
342F GLY 3.7 3.8 + - - -
343F GLY 3.8 6.6 + - - -
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Residues in contact with TRP 340 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9F VAL* 3.6 41.4 + - + +
11F ASP* 4.2 21.1 - - + -
18F LYS* 3.8 22.3 - - + +
19F ALA 3.8 0.6 - - - -
20F GLY* 3.3 31.8 - - - +
21F PHE 3.2 26.0 - - - -
24F ASP* 3.8 8.5 - - + -
26F ALA* 3.3 29.2 - - - -
27F PRO* 3.3 34.9 - - + +
337F TYR 3.2 7.1 + - - +
339F VAL* 1.3 77.8 - - - +
341F ILE* 1.3 69.7 + - - +
343F GLY* 3.2 3.8 + - - -
344F SER* 3.1 39.1 + - - -
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Residues in contact with ILE 341 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25F ASP* 3.0 35.0 - - - +
26F ALA* 4.3 2.2 - - - +
144F ALA* 6.0 0.4 - - + -
334F GLU* 3.4 34.1 - - + +
337F TYR* 2.7 41.7 + - + +
338F SER* 3.8 5.8 - - - +
340F TRP* 1.3 75.9 - - - +
342F GLY* 1.3 66.1 + - - +
343F GLY 3.3 0.5 + - - -
344F SER* 3.4 9.6 + - - -
345F ILE* 3.5 20.6 + - + +
111S LEU* 5.5 5.4 - - + -
115S MET* 3.1 35.6 - - + +
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Residues in contact with GLY 342 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140F LEU* 4.2 17.7 - - - -
144F ALA* 5.2 3.6 - - - +
338F SER 3.0 16.2 + - - -
340F TRP 3.3 0.4 - - - -
341F ILE* 1.3 78.4 - - - +
343F GLY* 1.3 60.5 + - - +
345F ILE* 4.2 5.0 + - - +
346F LEU 4.2 3.1 + - - -
1S MET* 3.1 33.4 - - - +
115S MET* 4.8 9.5 - - - +
119S SER* 4.9 1.0 + - - -
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Residues in contact with GLY 343 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9F VAL* 4.4 9.0 - - - +
104F LEU* 4.0 22.8 - - - +
135F ALA* 5.8 0.4 - - - -
140F LEU* 3.9 14.8 - - - +
339F VAL 3.8 6.2 + - - -
340F TRP* 3.2 8.2 + - - -
342F GLY* 1.3 79.6 - - - +
344F SER* 1.3 60.8 + - - +
346F LEU* 4.0 5.0 + - - +
347F ALA* 3.9 15.6 + - - +
1S MET* 5.1 4.7 - - - +
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Residues in contact with SER 344 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9F VAL* 4.2 12.6 - - - +
21F PHE 3.0 24.6 + - - -
22F ALA* 3.2 28.7 - - - +
23F GLY 3.6 4.2 + - - -
24F ASP 3.8 3.3 + - - -
340F TRP* 3.1 41.8 + - - -
341F ILE 3.4 4.9 + - - -
343F GLY* 1.3 77.7 - - - +
345F ILE* 1.3 66.2 + - - +
347F ALA* 3.7 5.5 + - - +
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Residues in contact with ILE 345 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22F ALA* 5.2 1.0 - - - +
23F GLY* 4.7 13.9 + - - +
24F ASP 3.2 27.1 - - - +
25F ASP* 5.3 2.2 - - - +
341F ILE* 3.5 12.9 + - + +
342F GLY 4.2 1.8 + - - +
343F GLY 3.5 0.4 - - - -
344F SER* 1.3 82.2 - - - +
346F LEU* 1.3 60.0 + - + +
347F ALA 3.1 5.8 + - - -
348F SER* 4.1 6.9 + - - -
349F LEU* 4.7 6.4 + - - +
111S LEU* 6.5 0.2 - - + -
112S LYS* 5.8 1.6 - - + +
115S MET* 3.4 44.9 - - + +
116S ILE* 3.3 34.5 - - + +
119S SER* 5.5 1.3 - - - +
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Residues in contact with LEU 346 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104F LEU* 6.2 0.2 - - - -
342F GLY 4.2 2.4 + - - +
343F GLY 4.0 5.1 + - - -
344F SER 3.6 0.8 - - - -
345F ILE* 1.3 77.4 - - + +
347F ALA* 1.3 57.2 + - - +
348F SER 3.7 0.9 - - - -
349F LEU* 3.7 28.9 - - + -
352F PHE* 3.0 48.0 - - + -
1S MET* 3.8 31.3 - - + +
2S ALA 5.5 1.3 - - - +
3S SER 4.9 0.7 - - - -
4S GLY* 3.5 33.4 - - - +
116S ILE* 4.9 6.3 - - + +
119S SER* 3.4 32.5 - - - +
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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