Contacts of the helix formed by residues 394 - 406 (chain A) in PDB entry 4F5G
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 ASN 394 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A LYS 5.7 0.4 + - - -
39A VAL* 3.9 30.5 - - + +
389A GLY 3.0 25.4 + - - -
390A MET* 3.5 5.6 - - - +
391A THR* 2.9 41.9 + - - +
393A ASP* 1.3 75.9 - - + +
395A MET* 1.3 68.7 + - - +
396A ALA 3.4 2.0 - - - -
397A PRO* 3.3 10.0 - - + +
398A LEU* 3.0 25.8 + - - +
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Residues in contact with MET 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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331A MET* 3.7 30.1 - - - +
334A LEU* 3.9 22.9 - - + -
335A PHE* 3.7 33.0 - - - +
338A THR* 3.6 25.6 - - - +
390A MET* 3.6 29.8 - - + +
391A THR 3.0 14.3 + - - +
392A PRO 4.0 7.4 - - - +
393A ASP 3.4 1.8 - - - -
394A ASN* 1.3 82.8 + - - +
396A ALA* 1.3 58.3 + - - +
398A LEU* 3.4 6.5 + - - +
399A CYS* 2.9 39.3 + - - -
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Residues in contact with ALA 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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338A THR* 4.1 12.7 - - + +
342A LYS* 4.2 11.5 - - - +
392A PRO 4.7 2.7 + - - +
393A ASP 4.8 1.1 + - - +
395A MET* 1.3 77.9 - - - +
397A PRO* 1.3 65.6 - - + +
399A CYS* 3.2 2.6 + - - +
400A GLU* 2.8 45.1 + - - +
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Residues in contact with PRO 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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37A GLY 6.1 0.7 - - - +
393A ASP 4.0 8.7 - - - +
394A ASN* 3.3 24.5 - - + +
396A ALA* 1.3 96.6 - - + +
398A LEU* 1.3 60.0 + - - +
400A GLU* 3.3 13.3 + - + +
401A ALA* 3.0 24.6 + - - +
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Residues in contact with LEU 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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39A VAL* 4.4 14.5 - - + +
41A LEU* 3.8 21.1 - - + -
335A PHE* 4.1 8.1 - - + -
377A VAL* 3.5 39.9 - - + -
390A MET* 3.8 37.7 - - + -
394A ASN* 3.0 20.5 + - - +
395A MET* 3.5 10.8 - - - +
397A PRO* 1.3 76.6 - - - +
399A CYS* 1.3 59.6 + - - +
401A ALA* 3.3 3.8 + - - +
402A ILE* 3.1 37.0 + - + +
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Residues in contact with CYS 399 (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 PHE* 3.7 31.0 - - - -
338A THR* 3.7 33.7 - - + -
339A LEU* 3.7 25.1 - - + +
342A LYS* 4.3 4.9 - - + -
395A MET* 2.9 25.5 + - - +
396A ALA 3.9 0.7 - - - +
398A LEU* 1.3 73.8 - - - +
400A GLU* 1.3 60.9 + - - +
402A ILE* 3.4 2.8 + - - +
403A VAL* 2.9 35.6 + - - +
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Residues in contact with GLU 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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342A LYS* 3.1 42.3 + - + -
375A PHE* 5.7 0.4 - - - -
396A ALA* 2.8 27.3 + - - +
397A PRO* 3.6 9.8 - - + +
399A CYS* 1.3 77.1 - - - +
401A ALA* 1.3 62.8 + - - +
403A VAL* 3.4 6.6 + - - +
404A ALA* 3.0 24.1 + - - +
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Residues in contact with ALA 401 (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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371A LEU* 3.8 9.2 - - + -
375A PHE* 3.5 46.2 - - + -
377A VAL* 4.1 7.9 - - + -
397A PRO 3.0 13.6 + - - +
398A LEU 3.5 8.5 - - - +
400A GLU* 1.3 74.9 - - - +
402A ILE* 1.3 64.9 + - - +
404A ALA* 3.1 11.6 + - - +
405A VAL* 3.2 19.4 + - - +
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Residues in contact with ILE 402 (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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41A LEU* 5.3 4.0 - - + -
335A PHE* 3.7 34.1 - - + -
339A LEU* 3.8 15.3 - - + -
348A PHE* 4.7 8.1 - - + -
361A SER* 6.3 0.4 - - - -
363A LEU* 4.4 22.7 - - + -
371A LEU* 4.1 20.2 - - + -
377A VAL* 5.5 0.2 - - + -
398A LEU* 3.1 32.0 + - + +
399A CYS* 3.7 5.4 - - - +
400A GLU 3.4 0.2 - - - -
401A ALA* 1.3 75.4 - - - +
403A VAL* 1.3 63.8 + - - +
405A VAL* 3.0 24.6 + - - +
406A LEU* 3.2 25.4 + - + +
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Residues in contact with VAL 403 (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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339A LEU* 4.2 5.4 - - + -
342A LYS* 3.5 39.5 - - + +
343A GLY 4.2 11.4 - - - +
344A ALA* 3.9 22.9 - - + +
345A ASN 5.5 0.4 - - - +
399A CYS 2.9 21.8 + - - +
400A GLU* 3.7 6.3 - - - +
401A ALA 3.3 0.2 - - - -
402A ILE* 1.3 75.6 - - - +
404A ALA* 1.3 62.3 + - - +
405A VAL 3.2 0.9 + - - -
406A LEU* 3.2 24.5 + - - +
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Residues in contact with ALA 404 (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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370A ARG* 3.4 19.3 + - - +
375A PHE* 3.7 23.1 - - + -
400A GLU 3.0 17.9 + - - +
401A ALA 3.1 6.2 + - - +
403A VAL* 1.3 78.4 - - - +
405A VAL* 1.3 58.8 + - - +
406A LEU* 4.6 2.9 - - - +
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Residues in contact with VAL 405 (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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363A LEU* 4.6 4.9 - - + -
367A GLN* 3.1 43.1 + - + +
370A ARG* 3.7 34.0 + - + +
371A LEU* 3.7 20.4 - - + +
375A PHE* 3.6 22.0 - - + -
401A ALA 3.3 12.3 - - - +
402A ILE* 3.0 22.5 + - - +
404A ALA* 1.3 77.8 - - - +
406A LEU* 1.3 64.8 + - - +
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Residues in contact with LEU 406 (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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344A ALA* 3.9 28.3 - - + -
345A ASN* 3.5 45.1 + - - +
346A ARG* 3.7 28.3 + - + +
348A PHE* 4.2 16.6 - - + -
363A LEU* 3.9 25.6 - - + -
367A GLN* 3.7 13.5 + - - +
402A ILE* 3.2 17.5 + - + +
403A VAL* 3.2 17.6 + - - +
404A ALA 4.6 2.6 - - - +
405A VAL* 1.3 83.3 - - - +
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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