Contacts of the helix formed by residues 328 - 340 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114A ARG* 5.7 8.7 - - - +
129A ASP* 3.9 28.9 - - + +
244A THR* 4.9 10.5 - - + -
246A GLY* 4.9 2.9 - - - -
247A CYS* 4.8 17.5 - - - +
250A GLU* 4.7 22.2 - - + +
323A LYS 3.2 7.8 + - - +
324A LEU* 3.5 9.2 + - - +
327A ARG* 1.3 95.4 - - + +
329A PRO* 1.4 67.6 - - - +
330A PHE 3.6 1.6 - - - -
331A ILE* 3.8 12.9 + - + -
332A CYS* 3.2 21.7 + - - +
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Residues in contact with PRO 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A ASP* 4.5 8.1 - - - +
325A HIS 3.8 14.3 - - - +
326A GLU 3.4 17.7 - - - +
327A ARG 2.8 22.0 - - - +
328A LEU* 1.4 76.2 - - + +
330A PHE* 1.3 70.2 + - - +
332A CYS* 3.0 4.0 + - + +
333A GLU* 2.8 34.9 + - + +
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Residues in contact with PHE 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A ALA* 6.5 0.4 - - - -
49A GLU* 3.3 27.4 - - + +
129A ASP* 4.1 22.8 + - - +
130A LYS* 5.3 11.7 - - + -
328A LEU 3.6 0.4 - - - -
329A PRO* 1.3 77.8 - - - +
331A ILE* 1.3 51.5 + - - +
333A GLU* 2.5 40.3 + - + +
334A LEU* 2.5 38.1 + - + +
59B MET* 3.5 30.7 - - + -
60B ALA* 3.7 12.1 - - + -
61B ILE* 3.8 22.7 - - + -
216B LYS* 3.1 28.5 - - - -
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Residues in contact with ILE 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A GLU* 4.0 12.1 - - - +
129A ASP* 4.2 12.2 + - - +
242A LEU 4.2 11.2 - - - +
243A MET* 4.3 26.2 - - - -
244A THR* 4.4 19.1 - - + +
247A CYS* 4.4 18.6 - - - -
316A LEU* 5.1 4.3 - - + -
328A LEU* 3.8 16.5 + - + +
329A PRO 3.4 0.4 - - - -
330A PHE* 1.3 76.6 - - - +
332A CYS* 1.3 59.3 + - + +
334A LEU* 2.6 28.8 + - + -
335A ALA* 2.6 33.1 + - + -
343A PRO* 5.2 1.6 - - + -
348A ILE* 4.7 11.0 - - + -
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Residues in contact with CYS 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324A LEU* 3.6 16.6 - - - +
325A HIS* 3.4 34.5 - - + -
328A LEU 3.2 16.6 + - - +
329A PRO* 3.0 5.9 + - + +
331A ILE* 1.3 81.2 - - - +
333A GLU* 1.3 51.4 + - + +
335A ALA* 4.1 0.3 - - - +
336A LYS* 2.6 43.2 + - + +
343A PRO* 3.6 38.6 - - - -
344A VAL* 4.5 2.7 - - - -
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Residues in contact with GLU 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329A PRO* 2.8 23.7 + - + +
330A PHE* 2.5 30.4 + - + +
332A CYS* 1.3 71.2 - - + +
334A LEU* 1.3 64.9 + - - +
336A LYS* 3.3 7.4 + - + +
337A ALA* 2.8 28.2 + - - +
78B LYS* 5.0 13.8 + - - +
215B PRO 4.9 5.7 - - - +
216B LYS* 5.0 4.9 + - - -
217B HIS* 4.4 24.4 + - - -
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Residues in contact with LEU 334 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A GLU* 3.9 9.2 - - - +
236A LEU* 5.0 1.6 - - - -
241A ILE* 4.2 4.3 - - + -
242A LEU 4.2 8.1 - - - +
243A MET* 4.3 9.0 - - + -
330A PHE* 2.5 33.9 + - + +
331A ILE* 2.6 30.8 + - + +
333A GLU* 1.3 71.5 - - - +
335A ALA* 1.3 57.9 + - - +
337A ALA* 3.6 1.8 - - - +
338A TYR* 2.9 64.7 + - + +
59B MET* 3.6 44.4 - - + +
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Residues in contact with ALA 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236A LEU* 4.9 0.2 - - - -
243A MET* 4.5 7.1 - - - +
331A ILE* 2.6 18.7 + - + +
334A LEU* 1.3 70.1 - - - +
336A LYS* 1.3 66.1 + - - +
339A VAL* 2.8 34.8 + - + +
340A GLY 3.2 3.6 + - - -
341A VAL* 3.3 6.3 + - + +
343A PRO* 3.7 27.1 - - + -
348A ILE* 4.1 21.5 - - + -
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Residues in contact with LYS 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325A HIS* 4.7 13.9 + - + +
332A CYS 2.6 26.8 + - - +
333A GLU* 3.3 8.7 + - + +
335A ALA* 1.3 77.9 - - - +
337A ALA* 1.3 58.6 + - - +
340A GLY* 2.8 27.0 - - - -
341A VAL 3.3 18.8 - - - +
342A ASP* 3.4 31.1 + - - +
343A PRO* 4.3 5.6 - - + -
82B ARG* 5.6 1.6 + - - -
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Residues in contact with ALA 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333A GLU 2.8 22.2 + - - +
334A LEU* 3.7 2.7 - - - +
336A LYS* 1.3 75.7 - - - +
338A TYR* 1.3 71.1 + - + +
339A VAL 3.6 0.4 + - - -
340A GLY* 4.4 1.7 + - - -
78B LYS* 5.0 18.2 - - + +
80B PHE* 3.5 34.4 - - + -
82B ARG* 4.2 11.3 + - - +
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Residues in contact with TYR 338 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236A LEU* 3.9 15.0 - - + -
237A PRO 5.7 0.2 - - - +
239A SER* 5.0 8.5 + - - +
241A ILE* 3.3 29.2 - - + -
308A ARG* 2.8 14.3 + - - -
334A LEU* 2.9 49.4 + - + +
337A ALA* 1.3 81.1 - - + +
339A VAL* 1.3 60.9 + - - +
340A GLY 3.6 0.4 - - - -
33B THR* 4.9 8.1 - - - -
35B SER* 5.5 2.0 - - - -
58B ARG 3.6 9.7 + - - -
59B MET* 3.3 23.4 - - - -
60B ALA* 3.7 5.5 + - + +
77B CYS* 2.8 31.5 + - - -
78B LYS* 4.4 3.6 - - + +
80B PHE* 3.9 21.1 - + - -
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Residues in contact with VAL 339 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A LEU* 3.8 37.0 - - + -
237A PRO* 4.4 7.2 - - + +
239A SER* 5.8 0.2 - - - +
308A ARG* 2.9 36.4 + - - +
335A ALA* 2.8 32.3 - - + +
338A TYR* 1.3 81.6 - - - +
340A GLY* 1.3 70.0 + - - +
341A VAL* 3.5 15.2 - - + +
348A ILE* 4.7 0.9 - - + -
349A PRO* 4.1 23.8 - - + -
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Residues in contact with GLY 340 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335A ALA 3.2 0.6 + - - -
336A LYS 2.8 21.4 + - - -
337A ALA 4.3 2.5 + - - -
338A TYR 3.6 0.8 - - - -
339A VAL* 1.3 83.7 - - - +
341A VAL* 1.3 63.9 + - - +
346A GLU* 4.9 1.6 - - - +
82B ARG* 6.1 2.0 - - - -
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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