Contacts of the helix formed by residues 336 - 348 (chain B) in PDB entry 5JLH
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 336 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B MET* 5.1 5.5 - - + +
17B LYS* 3.5 27.6 - - + +
26B PRO* 4.9 16.8 - - + -
29B VAL* 4.5 22.7 - - + +
333B GLU* 3.2 24.5 + - + +
334B ARG 3.1 0.8 - - - -
335B LYS* 1.4 110.2 + - + +
337B SER* 1.3 64.9 + - - +
338B VAL 3.2 2.2 - - - -
339B TRP* 2.8 17.6 + - + -
340B ILE* 3.0 25.4 + - + -
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Residues in contact with SER 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B SER* 3.7 27.3 - - - -
143B ALA* 3.3 19.2 - - - +
144B SER* 5.3 1.9 + - - -
298B LEU 5.0 0.7 + - - -
299B SER* 4.4 6.0 - - - -
331B PRO* 4.7 7.3 - - - +
333B GLU 3.5 4.0 + - - -
334B ARG* 2.9 34.1 + - - +
335B LYS 3.3 0.8 - - - -
336B TYR* 1.3 75.8 - - - +
338B VAL* 1.3 64.9 + - - +
340B ILE* 3.2 5.3 + - - +
341B GLY* 2.9 20.1 + - - -
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Residues in contact with VAL 338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B ASP* 3.2 29.4 - - + +
17B LYS* 5.1 3.4 - - - +
105B THR* 3.4 28.7 - - + +
136B GLN* 3.8 25.8 - - + +
139B LEU* 3.6 19.3 - - + +
140B SER* 4.3 3.6 - - - +
153B ASP* 5.3 1.3 - - - +
299B SER* 4.6 16.8 - - - +
300B GLY* 5.4 3.4 - - - +
335B LYS 4.8 1.3 + - - +
336B TYR 3.2 0.8 - - - -
337B SER* 1.3 76.0 - - - +
339B TRP* 1.3 64.0 + - - +
341B GLY* 3.2 2.8 + - - -
342B GLY 2.9 17.7 + - - -
401B ADP 5.3 0.2 - - - +
402B MG 4.2 13.9 - - - -
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Residues in contact with TRP 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B VAL* 3.1 39.5 + - + +
10B ASP* 4.3 7.9 + - + -
17B LYS* 3.1 41.5 - - + +
18B ALA 3.5 0.2 - - - -
19B GLY* 3.3 36.1 - - - +
20B PHE 3.5 19.7 - - - -
23B ASP* 3.6 18.4 - - + -
24B ASP 4.1 1.6 - - - -
25B ALA* 3.3 15.5 - - - -
26B PRO* 3.2 43.5 - - + -
336B TYR* 2.8 9.3 + - - +
338B VAL* 1.3 80.9 - - - +
340B ILE* 1.3 71.5 + - + +
342B GLY* 3.0 4.0 + - - +
343B SER* 2.9 25.1 + - - -
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Residues in contact with ILE 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B ASP* 3.8 22.2 - - - +
25B ALA* 5.5 0.2 - - - -
26B PRO* 5.4 0.9 - - + -
143B ALA* 3.8 20.2 - - + +
333B GLU* 3.6 35.0 - - + +
336B TYR* 3.0 25.2 + - + +
337B SER* 3.7 9.9 - - - +
339B TRP* 1.3 83.6 - - + +
341B GLY* 1.3 63.0 + - - +
343B SER* 2.5 30.7 + - - +
344B ILE* 2.9 9.1 + - + +
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Residues in contact with GLY 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B LEU* 3.1 33.7 - - - -
142B TYR* 4.3 0.2 - - - -
143B ALA* 3.7 3.7 - - - +
337B SER 2.9 10.7 + - - -
338B VAL 3.6 3.1 - - - -
340B ILE* 1.3 76.7 - - - +
342B GLY* 1.3 55.5 + - - +
344B ILE* 2.9 28.1 - - - +
345B LEU* 2.9 17.8 + - - +
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Residues in contact with GLY 342 (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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8B VAL* 3.8 9.3 - - - +
103B LEU* 3.3 32.2 - - - +
139B LEU* 3.6 10.2 - - - +
338B VAL 2.9 11.7 + - - -
339B TRP 3.0 4.2 + - - -
341B GLY* 1.3 76.8 - - - +
343B SER* 1.3 56.3 + - - +
345B LEU* 3.2 1.0 + - - -
346B ALA* 2.9 29.1 + - - +
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Residues in contact with SER 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B VAL* 4.1 2.6 - - - +
21B ALA* 4.1 11.8 - - - +
22B GLY 3.7 10.3 + - - -
23B ASP 3.3 25.9 + - - -
24B ASP* 5.2 0.2 - - - -
339B TRP* 2.9 24.6 + - - -
340B ILE* 2.5 26.4 + - - +
342B GLY* 1.3 77.3 - - - +
344B ILE* 1.3 62.3 + - - +
346B ALA* 3.4 0.9 + - - -
347B SER* 2.6 33.6 + - - -
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Residues in contact with ILE 344 (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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142B TYR* 3.8 38.1 - - + +
143B ALA* 5.0 2.0 - - - -
340B ILE* 2.9 7.6 + - + +
341B GLY* 2.9 34.5 - - - +
343B SER* 1.3 82.1 + - - +
345B LEU* 1.3 63.1 + - - +
347B SER* 3.2 9.1 + - - -
348B LEU* 3.0 42.1 + - + +
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Residues in contact with LEU 345 (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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44A VAL* 4.6 11.4 - - + -
103B LEU* 4.6 5.8 - - + -
132B TYR* 5.1 2.2 - - + -
134B ALA* 5.1 8.3 - - + -
138B VAL* 5.8 1.6 - - + -
139B LEU* 4.4 18.2 - - + -
142B TYR* 3.2 54.5 - - + +
341B GLY 2.9 15.8 + - - +
342B GLY* 3.2 6.3 + - - +
344B ILE* 1.3 78.1 - - - +
346B ALA* 1.3 63.3 + - - +
348B LEU* 3.1 17.1 + - + +
351B PHE* 3.2 48.9 - - + +
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Residues in contact with ALA 346 (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 ALA* 3.8 17.6 - - + +
8B VAL* 4.4 5.6 - - + -
21B ALA* 3.5 27.8 - - + -
103B LEU* 5.0 2.7 - - + +
342B GLY 2.9 13.6 + - - +
345B LEU* 1.3 78.6 - - - +
347B SER* 1.3 59.6 + - - +
348B LEU 3.5 5.5 + - - +
351B PHE* 3.8 10.3 - - + -
352B GLN* 4.2 17.0 + - - +
355B TRP* 4.0 16.8 - - + -
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Residues in contact with SER 347 (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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3B GLU* 5.4 5.7 - - - +
21B ALA* 5.3 0.4 - - - -
22B GLY* 3.2 27.6 + - - -
343B SER 2.6 22.9 + - - -
344B ILE* 3.5 10.0 - - - -
346B ALA* 1.3 75.3 - - - +
348B LEU* 1.3 66.0 + - - +
349B SER* 3.5 5.0 + - - -
352B GLN* 5.6 2.6 + - - -
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Residues in contact with LEU 348 (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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44A VAL* 3.8 39.5 - - + +
45A GLY* 4.9 2.7 - - - +
142B TYR* 4.7 11.9 - - + -
344B ILE* 3.0 43.5 + - + +
345B LEU* 3.1 15.6 + - + +
346B ALA 3.8 1.2 - - - +
347B SER* 1.3 79.9 - - - +
349B SER* 1.3 65.2 + - - +
350B THR* 4.7 0.9 - - - +
351B PHE* 3.5 20.2 + - + +
352B GLN* 3.7 11.3 + - - +
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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