Contacts of the helix formed by residues 328 - 338 (chain M) in PDB entry 1L0V
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 LEU 328 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129M ASP* 4.3 0.2 - - - -
244M THR* 6.0 0.9 - - + -
246M GLY 5.0 0.9 - - - -
247M CYS* 4.0 30.7 - - + +
250M GLU* 3.8 30.5 - - + -
316M LEU* 4.1 26.5 - - + -
319M LEU* 5.4 2.9 - - + -
323M LYS 3.3 6.8 + - - +
324M LEU* 3.3 27.0 + - + +
327M ARG* 1.3 104.0 - - + +
329M PRO* 1.4 62.8 - - - +
330M PHE 3.6 1.8 - - - -
331M ILE* 3.3 26.4 - - + +
332M CYS* 3.1 18.2 + - - +
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Residues in contact with PRO 329 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129M ASP* 3.9 10.8 - - - +
324M LEU 3.7 3.6 - - - +
325M HIS* 4.2 9.6 - - - +
326M GLU* 4.1 20.0 - - - +
327M ARG 3.4 9.4 - - - +
328M LEU* 1.4 86.7 - - - +
330M PHE* 1.3 68.7 + - - +
332M CYS* 2.8 8.1 + - + +
333M GLU* 2.7 24.7 + - - +
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Residues in contact with PHE 330 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47M ALA* 6.4 0.4 - - - -
49M GLU* 4.5 13.5 - - + +
129M ASP* 3.7 32.9 + - + +
130M LYS* 5.1 9.9 - - + -
328M LEU 3.6 0.4 - - - -
329M PRO* 1.3 80.8 - - - +
331M ILE* 1.3 58.1 + - + +
333M GLU* 2.8 18.9 + - + +
334M LEU* 2.5 61.5 + - + +
59N MET* 3.6 44.2 - - + -
60N ALA* 4.3 7.9 - - + -
61N ILE* 3.8 26.9 - - + -
216N LYS* 4.3 7.9 - - - -
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Residues in contact with ILE 331 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49M GLU* 4.8 4.0 - - - +
129M ASP* 3.6 23.3 - - + +
243M MET* 4.3 21.3 - - + +
244M THR* 3.7 33.2 - - + +
247M CYS* 3.8 10.1 - - - -
316M LEU* 4.3 24.2 - - + -
328M LEU* 3.3 27.1 - - + +
330M PHE* 1.3 80.2 - - + +
332M CYS* 1.3 57.2 + - - +
334M LEU* 3.5 12.0 - - + +
335M ALA* 2.8 31.4 + - - +
343M PRO* 4.9 2.2 - - + -
348M ILE* 4.4 4.9 - - + -
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Residues in contact with CYS 332 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324M LEU* 3.1 36.1 - - - -
325M HIS* 3.9 25.1 - - + +
328M LEU 3.1 9.9 + - - +
329M PRO* 2.8 13.9 + - + +
331M ILE* 1.3 69.8 - - - +
333M GLU* 1.3 70.2 + - - +
335M ALA* 3.3 0.7 + - - +
336M LYS* 3.0 26.7 + - - +
342M ASP* 4.7 3.4 - - - -
343M PRO* 3.4 26.2 - - + +
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Residues in contact with GLU 333 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329M PRO 2.7 15.1 + - - +
330M PHE* 3.1 24.7 + - + +
332M CYS* 1.3 75.9 - - - +
334M LEU* 1.3 63.3 + - - +
336M LYS* 4.0 3.6 - - - +
337M ALA* 3.1 26.3 + - + +
60N ALA* 6.4 0.2 - - - -
78N LYS* 2.9 37.4 + - - -
215N PRO 4.0 6.6 - - - +
216N LYS* 5.3 5.4 + - - +
217N HIS* 4.1 16.6 - - - -
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Residues in contact with LEU 334 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49M GLU* 4.2 14.8 - - - +
236M LEU* 4.2 2.4 - - - +
241M ILE* 3.8 22.0 - - + -
242M LEU 5.2 0.9 - - - +
243M MET* 3.6 23.1 - - + -
330M PHE* 2.5 54.1 + - + +
331M ILE* 3.5 11.7 - - + +
333M GLU* 1.3 73.1 - - - +
335M ALA* 1.3 56.9 + - - +
338M TYR* 3.0 67.8 + - + +
59N MET* 4.0 10.8 - - + +
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Residues in contact with ALA 335 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236M LEU* 5.0 3.6 - - - -
243M MET* 4.6 1.7 - - + +
331M ILE 2.8 22.8 + - - +
332M CYS 3.3 1.1 + - - +
334M LEU* 1.3 70.6 - - - +
336M LYS* 1.3 60.4 + - - +
339M VAL* 2.6 34.8 + - - +
340M GLY 2.9 8.0 + - - -
341M VAL 3.0 15.1 + - - +
343M PRO* 3.6 17.7 - - + -
348M ILE* 4.1 22.2 - - + -
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Residues in contact with LYS 336 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332M CYS 3.0 16.4 + - - +
333M GLU* 4.0 4.3 - - - +
335M ALA* 1.3 73.6 - - - +
337M ALA* 1.3 60.3 + - - +
340M GLY* 2.9 24.3 + - - -
341M VAL 3.0 23.5 + - - +
342M ASP* 4.3 25.1 + - + +
343M PRO* 5.3 0.4 - - + -
82N ARG* 4.6 6.5 + - - -
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Residues in contact with ALA 337 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333M GLU* 3.1 17.7 + - + +
334M LEU 3.9 1.6 - - - +
336M LYS* 1.3 81.1 - - - +
338M TYR* 1.3 72.9 + - + +
339M VAL 3.6 0.2 + - - -
340M GLY 4.2 0.9 + - - -
78N LYS* 5.3 8.1 - - + -
80N PHE* 3.6 28.4 - - + -
82N ARG* 2.6 33.3 + - - +
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Residues in contact with TYR 338 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236M LEU* 3.9 13.7 - - + -
239M SER* 4.1 16.1 + - - +
241M ILE* 3.6 18.8 - - + -
334M LEU* 3.0 53.9 + - + +
337M ALA* 1.3 83.1 - - + +
339M VAL* 1.3 60.9 + - - +
33N THR* 3.5 27.2 - - - +
35N SER* 5.4 2.9 - - - -
58N ARG 3.9 7.2 - - - -
59N MET* 3.3 29.0 - - - -
60N ALA* 3.5 10.3 + - + +
77N CYS 3.1 29.0 + - - -
78N LYS* 4.4 4.3 - - + +
80N PHE* 4.0 17.9 - + - -
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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