Contacts of the helix formed by residues 389 - 400 (chain A) in PDB entry 4M8J
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 GLY 389 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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384A LEU 3.3 8.9 + - - +
385A ILE* 3.1 27.4 + - - -
387A GLN 3.7 0.4 - - - -
388A TYR* 1.3 82.0 - - - +
390A VAL* 1.3 65.6 + - - +
391A PRO* 3.6 4.0 - - - -
392A ARG* 3.7 9.2 + - - +
393A ALA 3.7 1.9 + - - -
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Residues in contact with VAL 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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106A PHE* 3.7 24.2 - - + -
110A ILE* 4.1 28.5 - - + -
114A TYR* 3.9 18.8 - - - +
385A ILE* 4.3 17.3 - - + -
389A GLY* 1.3 70.3 - - - -
391A PRO* 1.4 67.3 - - + +
393A ALA* 2.8 24.1 + - - +
394A ILE* 3.1 13.0 + - + -
468A GLY* 6.3 1.3 - - - -
469A LEU* 4.1 24.2 - - + +
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Residues in contact with PRO 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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106A PHE* 4.0 19.3 - - + -
213A PRO* 3.5 50.0 - - + +
214A LEU* 4.1 7.0 - - + +
217A GLU* 3.8 6.9 - - + +
227A HIS* 6.1 0.2 - - - +
388A TYR 5.1 2.2 - - - +
389A GLY* 3.7 3.6 - - - -
390A VAL* 1.4 93.4 - - + +
392A ARG* 1.3 60.3 + - - +
394A ILE* 3.8 8.4 - - + +
395A ILE* 3.1 30.5 + - - +
469A LEU* 6.2 0.2 - - + -
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Residues in contact with ARG 392 (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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217A GLU* 3.3 30.6 - - - +
220A GLN* 4.1 11.9 + - - -
221A TYR* 5.8 4.9 - - - -
384A LEU* 4.9 7.1 - - + +
388A TYR* 3.5 64.2 + - + +
389A GLY 3.7 6.3 - - - +
390A VAL 2.9 0.6 + - - -
391A PRO* 1.3 77.1 - - - +
393A ALA* 1.3 66.5 + - - +
395A ILE* 3.1 13.0 + - - +
396A GLU* 2.7 65.3 + - + +
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Residues in contact with ALA 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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110A ILE* 4.6 5.4 - - + -
379A LEU* 4.6 0.2 - - - +
381A ILE* 4.0 18.3 - - + +
384A LEU* 3.8 27.1 - - + +
385A ILE* 3.8 27.6 - - + -
389A GLY 3.7 1.6 + - - +
390A VAL 2.8 14.8 + - - +
392A ARG* 1.3 75.3 - - - +
394A ILE* 1.3 59.7 + - - +
396A GLU* 3.4 9.0 + - - +
397A THR* 3.1 19.6 + - - +
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Residues in contact with ILE 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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105A LEU 4.1 1.3 - - - +
106A PHE* 3.2 57.4 - - + +
109A SER* 3.6 16.4 - - - +
110A ILE* 3.9 25.6 - - + -
214A LEU* 4.2 6.5 - - + -
390A VAL* 3.1 13.2 + - + +
391A PRO* 3.8 7.2 - - + +
393A ALA* 1.3 74.5 - - - +
395A ILE* 1.3 64.2 + - - +
397A THR* 2.7 32.7 + - - -
398A TRP* 3.4 33.3 + - + -
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Residues in contact with ILE 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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214A LEU* 3.7 27.4 - - + +
217A GLU* 3.6 26.9 - - + +
218A CYS* 4.0 14.6 - - - +
221A TYR* 5.0 13.2 - - + -
391A PRO 3.1 22.2 + - - +
392A ARG* 3.1 16.4 + - - +
394A ILE* 1.3 79.4 - - - +
396A GLU* 1.3 65.9 + - + +
398A TRP* 3.2 37.9 + - + +
399A ALA* 3.0 23.4 + - - +
408A MET* 3.8 10.8 - - - +
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Residues in contact with GLU 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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221A TYR* 6.5 0.2 - - + -
379A LEU* 3.4 28.0 - - + +
384A LEU* 3.3 29.1 - - + +
392A ARG* 2.7 54.8 + - - +
393A ALA 3.8 2.7 - - - +
394A ILE 3.2 0.4 - - - -
395A ILE* 1.3 76.6 - - + +
397A THR* 1.3 60.1 + - - +
398A TRP 3.3 0.2 - - - -
399A ALA* 3.6 11.7 - - + +
400A ALA* 3.0 27.7 + - - +
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Residues in contact with THR 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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109A SER* 4.6 5.2 - - - +
110A ILE* 5.7 2.0 - - + -
369A ASN* 4.2 5.6 + - - -
370A THR* 3.9 29.4 + - + +
373A LEU* 3.5 31.1 - - + +
379A LEU* 4.7 1.6 - - + -
381A ILE* 4.6 10.8 - - + -
393A ALA 3.1 18.4 - - - +
394A ILE* 2.7 20.7 + - - +
396A GLU* 1.3 77.0 - - - +
398A TRP* 1.3 77.2 + - - +
400A ALA* 3.5 6.2 + - - +
401A LEU* 3.2 15.5 - - - +
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Residues in contact with TRP 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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105A LEU* 3.9 32.3 - - + -
109A SER* 3.5 15.4 + - - -
214A LEU* 4.3 9.0 - - + -
218A CYS* 4.0 8.5 - - - -
273A VAL* 5.9 0.7 - - + -
366A LEU* 4.8 7.7 - - + +
369A ASN* 5.2 4.9 - - - -
394A ILE* 3.6 27.1 + - + -
395A ILE* 3.2 32.7 + - + +
397A THR* 1.3 101.0 + - - +
399A ALA* 1.3 62.2 + - - +
401A LEU* 3.3 27.6 + - + +
404A SER* 4.8 0.3 - - - -
407A THR* 4.1 7.6 - - - +
408A MET* 3.4 22.7 - - + +
411A PHE* 3.5 64.2 - + + -
415A CYS* 5.1 6.1 - - + -
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Residues in contact with ALA 399 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A TYR* 3.9 26.3 + - + +
395A ILE* 3.0 17.1 + - + +
396A GLU* 3.7 13.5 - - + +
397A THR 3.3 0.4 - - - -
398A TRP* 1.3 72.0 - - - +
400A ALA* 1.3 56.7 + - - +
401A LEU 3.0 12.2 + - - +
404A SER* 3.5 18.4 - - - -
408A MET* 3.3 14.6 - - + +
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Residues in contact with ALA 400 (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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373A LEU* 4.1 20.1 - - + +
378A ILE* 4.4 11.9 - - + +
379A LEU* 3.6 21.1 - - + -
396A GLU 3.0 16.6 + - - +
397A THR 3.9 7.2 - - - +
398A TRP 3.2 1.2 - - - -
399A ALA* 1.3 76.0 - - - +
401A LEU* 1.3 61.5 + - - +
402A PRO* 4.6 1.7 - - - +
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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