Contacts of the helix formed by residues 388 - 399 (chain A) in PDB entry 4LZ6
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 PRO 388 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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243A LEU* 3.4 15.9 - - + +
244A VAL* 3.4 30.3 - - + +
246A LEU* 5.6 0.2 - - - +
247A PRO* 3.3 28.6 - - + +
382A TYR 3.6 11.9 - - - +
383A GLN* 4.6 6.7 - - + -
386A GLY* 3.4 10.3 - - - +
387A LYS* 1.4 83.1 - - - +
389A LYS* 1.3 73.1 + - + +
390A GLN 3.5 0.7 - - - -
391A ALA* 3.9 5.8 - - + -
392A LEU* 3.1 27.1 + - - +
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Residues in contact with LYS 389 (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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243A LEU* 4.5 24.7 - - - +
386A GLY 5.2 2.5 - - - -
387A LYS* 2.7 14.0 + - + +
388A PRO* 1.3 98.4 - - + +
390A GLN* 1.3 61.1 + - + +
391A ALA 3.5 0.2 - - - -
392A LEU* 3.5 12.8 - - + +
393A ILE* 3.2 31.0 + - - +
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Residues in contact with GLN 390 (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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382A TYR* 3.3 45.9 + - + -
387A LYS* 3.6 26.0 + - + +
389A LYS* 1.3 78.9 - - + +
391A ALA* 1.3 58.4 + - - +
392A LEU 3.4 0.2 - - - -
393A ILE* 3.6 14.9 + - + +
394A LEU* 3.1 24.1 + - - +
437A LEU* 3.9 21.2 - - + +
440A ARG* 5.0 4.2 - - - +
441A ASP* 3.4 23.4 + - - +
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Residues in contact with ALA 391 (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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247A PRO* 4.3 2.9 - - + -
251A GLN* 4.9 4.0 + - - +
379A GLY* 4.6 4.9 - - - +
382A TYR* 3.6 27.2 - - + +
383A GLN* 4.1 26.5 - - + +
388A PRO* 4.2 6.7 - - + -
389A LYS 3.5 2.0 - - - +
390A GLN* 1.3 76.8 - - - +
392A LEU* 1.3 55.9 + - - +
394A LEU* 2.6 30.7 + - + +
395A SER* 2.6 19.8 + - - -
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Residues in contact with LEU 392 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A LEU* 4.3 18.4 - - + +
247A PRO* 3.6 36.7 - - + +
250A VAL* 5.0 8.3 - - + -
388A PRO 3.1 17.2 + - - +
389A LYS* 3.5 16.2 - - + +
391A ALA* 1.3 79.7 - - - +
393A ILE* 1.3 67.1 + - + +
394A LEU 3.0 0.2 + - - -
395A SER* 3.1 8.7 + - - -
396A LEU* 3.4 35.7 + - + +
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Residues in contact with ILE 393 (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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389A LYS* 3.2 18.6 + - + +
390A GLN* 3.6 16.8 - - + +
391A ALA 3.2 0.6 - - - -
392A LEU* 1.3 83.8 - - + +
394A LEU* 1.3 61.8 + - - +
396A LEU* 4.4 5.3 - - - +
397A SER* 3.6 19.6 + - - -
433A LEU* 4.9 6.2 - - + +
437A LEU* 5.0 15.0 - - + -
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Residues in contact with LEU 394 (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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375A GLN* 5.1 7.2 - - + +
378A ALA* 4.3 3.4 - - + -
379A GLY* 4.3 27.1 - - - +
382A TYR* 4.5 13.5 - - + -
390A GLN 3.1 14.1 + - - +
391A ALA* 2.6 19.2 + - + +
393A ILE* 1.3 71.1 - - - +
395A SER* 1.3 60.4 + - - -
397A SER* 2.3 26.1 + - - +
398A ARG* 3.3 9.3 + - + +
430A SER* 4.4 4.0 - - - +
433A LEU* 3.8 9.9 - - + -
434A THR* 3.2 33.4 - - - +
437A LEU* 3.2 25.6 - - + -
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Residues in contact with SER 395 (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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247A PRO 5.1 0.2 - - - -
250A VAL* 3.4 15.5 - - - +
251A GLN* 3.2 41.7 - - - +
254A SER* 4.3 3.3 + - - -
391A ALA 2.6 16.5 + - - -
392A LEU* 3.1 5.6 + - - -
394A LEU* 1.3 70.9 - - - +
396A LEU* 1.3 53.4 + - - +
397A SER 2.9 6.3 + - - -
398A ARG* 3.0 7.7 + - - +
399A GLN* 2.8 38.2 + - - +
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Residues in contact with LEU 396 (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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250A VAL* 3.6 36.1 - - + -
254A SER* 4.5 3.8 - - - +
392A LEU* 3.4 37.0 - - + +
393A ILE* 4.4 4.7 - - - +
395A SER* 1.3 73.4 + - - +
397A SER* 1.3 56.6 + - - +
399A GLN* 4.9 0.9 - - - -
400A ILE* 3.8 33.2 - - + -
401A ILE* 2.9 43.4 + - + +
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Residues in contact with SER 397 (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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393A ILE 3.6 13.3 + - - -
394A LEU* 2.3 34.0 + - - +
395A SER 2.9 2.0 - - - -
396A LEU* 1.3 79.8 - - - +
398A ARG* 1.3 67.2 + - - +
399A GLN 3.2 0.7 + - - -
400A ILE 4.0 0.5 + - - -
401A ILE* 3.8 4.0 - - - -
402A PHE* 3.2 57.8 + - - +
430A SER* 4.7 5.6 - - - -
433A LEU* 3.9 15.9 - - - +
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Residues in contact with ARG 398 (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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251A GLN* 5.9 0.6 + - - -
285A MET* 6.2 1.6 - - - +
375A GLN* 4.5 14.2 - - + +
376A ILE* 6.1 4.2 - - - +
394A LEU* 4.0 7.0 - - + +
395A SER* 3.0 9.7 + - - +
397A SER* 1.3 83.0 + - - +
399A GLN* 1.3 82.1 + - - +
402A PHE* 5.4 0.2 - - - +
403A LEU* 4.0 16.3 + - - +
426A ALA* 5.3 4.2 - - - +
427A ASP* 4.0 19.9 + - - +
430A SER* 3.2 30.4 + - - +
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Residues in contact with GLN 399 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A GLN* 2.9 23.7 - - - +
254A SER* 3.0 35.9 - - - +
255A ALA* 3.0 31.4 - - - +
258A MET* 5.1 9.6 - - + +
395A SER* 2.8 22.4 + - - +
398A ARG* 1.3 95.3 + - + +
400A ILE* 1.3 64.9 + - + +
403A LEU* 3.3 30.3 - - - +
404A ILE* 4.8 0.9 + - - +
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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