Contacts of the helix formed by residues 385 - 397 (chain A) in PDB entry 3F2B
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 SER 385 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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349A THR* 2.7 41.8 + - - -
350A PRO* 5.0 1.4 - - - +
351A MET* 3.5 11.6 - - - +
360A VAL* 4.1 11.9 - - - +
377A VAL* 4.2 9.9 - - - -
379A ASP* 3.7 8.2 + - - -
383A VAL 3.0 1.8 + - - -
384A GLN* 1.3 75.1 - - - +
386A PHE* 1.3 55.4 + - - +
387A PRO* 3.4 1.8 - - - -
388A GLU* 3.2 11.0 + - - +
389A ALA* 2.7 34.4 + - - +
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Residues in contact with PHE 386 (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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377A VAL* 4.1 17.9 - - + -
382A VAL 5.4 0.2 - - - -
383A VAL* 3.3 37.9 - - + +
385A SER* 1.3 77.0 - - - +
387A PRO* 1.3 60.3 - - + +
389A ALA* 3.1 5.1 + - - +
390A TYR* 2.8 36.7 + - - +
402A TYR* 3.4 47.0 - + + -
403A GLY 3.2 35.0 - - - -
631A LEU* 3.9 22.7 - - + -
634A LEU* 4.1 5.8 - - + -
635A PHE* 4.1 9.6 - + - -
816A PRO* 4.3 9.4 - - + -
817A ILE* 6.1 0.2 - - + -
1085A PHE* 4.1 6.5 - - + -
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Residues in contact with PRO 387 (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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384A GLN 3.6 11.7 - - - +
385A SER 3.4 4.0 - - - -
386A PHE* 1.3 96.8 - - + +
388A GLU* 1.3 60.2 + - - +
390A TYR* 3.5 3.9 + - + +
391A SER* 3.2 24.5 + - - -
817A ILE* 4.0 24.5 - - + -
1085A PHE* 3.9 21.1 - - + -
1089A SER* 3.6 36.8 - - - +
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Residues in contact with GLU 388 (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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359A SER* 4.0 12.5 - - - -
360A VAL* 3.5 14.3 + - + +
361A THR* 2.5 38.1 + - - +
384A GLN 5.3 0.6 + - - +
385A SER* 3.2 11.9 + - - +
387A PRO* 1.3 77.2 - - - +
389A ALA* 1.3 67.2 + - - +
391A SER* 3.3 8.0 + - - -
392A ALA* 3.0 21.3 + - - +
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Residues in contact with ALA 389 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360A VAL* 3.9 20.6 - - + +
364A ILE* 3.9 17.5 - - + +
377A VAL* 4.3 4.7 - - + -
385A SER 2.7 18.9 + - - +
386A PHE* 3.4 6.3 - - - +
388A GLU* 1.3 75.8 - - - +
390A TYR* 1.3 52.0 + - - +
392A ALA* 3.1 2.9 + - - +
393A ALA* 2.6 36.8 + - - +
400A VAL* 4.3 7.9 - - + -
402A TYR* 4.0 16.4 - - + -
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Residues in contact with TYR 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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386A PHE 2.8 18.8 + - - +
387A PRO* 3.5 7.0 - - + +
389A ALA* 1.3 72.6 - - - +
391A SER* 1.3 63.6 + - - +
393A ALA* 3.0 7.1 + - + +
394A LYS* 2.8 65.5 + - + +
402A TYR* 3.3 21.4 + - - +
813A ASP* 6.1 0.2 - - - -
814A VAL 4.9 2.2 - - - -
815A LYS* 3.4 42.2 - - + +
816A PRO* 3.7 20.9 - - + -
817A ILE* 3.7 34.7 + - + -
819A ASP* 5.0 8.4 + - - -
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Residues in contact with SER 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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387A PRO 3.2 12.2 + - - -
388A GLU* 3.6 11.9 - - - -
390A TYR* 1.3 79.8 - - - +
392A ALA* 1.3 58.2 + - - +
394A LYS* 3.2 15.8 + - - +
395A LYS* 2.8 30.2 + - - +
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Residues in contact with ALA 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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361A THR* 3.9 37.7 - - + +
364A ILE* 4.2 16.6 - - + +
388A GLU 3.0 16.6 + - - +
389A ALA 3.7 2.2 - - - +
391A SER* 1.3 74.6 - - - +
393A ALA* 1.3 68.4 + - - +
395A LYS* 4.4 5.6 - - - +
396A HIS* 2.9 33.1 + - + +
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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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364A ILE* 4.5 1.6 - - - +
389A ALA 2.6 18.5 + - - +
390A TYR* 3.3 15.0 - - + +
392A ALA* 1.3 72.8 - - - +
394A LYS* 1.3 56.6 + - + +
397A GLY* 3.0 24.3 + - - -
398A MET* 3.1 32.2 + - - +
400A VAL* 3.6 23.3 - - + +
402A TYR* 4.3 3.1 - - - +
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Residues in contact with LYS 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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390A TYR* 2.8 67.3 + - + +
391A SER* 3.6 13.8 + - - +
392A ALA 3.1 0.2 - - - -
393A ALA* 1.3 72.3 - - - +
395A LYS* 1.3 66.8 + - - +
396A HIS 3.2 0.2 + - - -
397A GLY* 3.5 8.0 + - - -
819A ASP* 5.5 4.4 + - - -
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Residues in contact with LYS 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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361A THR* 6.1 2.0 - - - +
365A GLU* 5.7 0.4 + - - -
391A SER 2.8 20.2 + - - +
392A ALA* 4.2 1.6 - - - +
394A LYS* 1.3 74.7 - - - +
396A HIS* 1.3 86.1 + - + +
397A GLY 3.7 0.2 + - - -
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Residues in contact with HIS 396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361A THR* 5.0 4.1 - - + +
364A ILE* 4.6 9.6 - - + -
365A GLU* 2.8 50.9 + - + +
368A LYS* 2.8 41.8 + - + +
392A ALA* 2.9 27.7 + - + +
395A LYS* 1.3 110.8 + - + +
397A GLY* 1.3 60.7 + - - +
398A MET* 4.5 5.4 - - + +
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Residues in contact with GLY 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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368A LYS* 3.9 12.3 - - - +
393A ALA 3.0 9.7 + - - -
394A LYS 3.5 4.8 + - - -
395A LYS 3.5 3.0 + - - -
396A HIS* 1.3 78.9 - - - +
398A MET* 1.3 59.3 + - - +
399A LYS 4.3 0.2 + - - -
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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