Contacts of the helix formed by residues 384 - 397 (chain H) in PDB entry 2FRV
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 GLU 384 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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382H LYS 3.3 8.2 + - - +
383H HIS* 1.3 69.5 - - - +
385H PRO* 1.3 62.7 - - + +
387H VAL* 4.2 15.0 - - + +
388H LYS* 2.7 76.0 + - - +
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Residues in contact with PRO 385 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297H TYR* 3.6 22.4 - - + +
383H HIS* 3.1 33.4 - - + +
384H GLU* 1.3 96.9 - - + +
386H THR* 1.3 53.7 + - - +
388H LYS* 3.5 16.3 + - - +
389H ALA* 3.1 27.9 + - - +
420H THR* 3.9 8.9 - - + +
423H GLN* 3.9 19.5 + - - +
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Residues in contact with THR 386 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298H THR* 5.7 0.5 - - - +
375H VAL* 3.8 24.2 - - + +
378H ALA* 3.5 12.9 - - + +
379H TYR* 3.7 32.3 - - + +
383H HIS* 2.7 32.9 - - - -
385H PRO* 1.3 75.6 - - - +
387H VAL* 1.3 61.2 + - - +
389H ALA* 3.1 4.3 + - - +
390H VAL* 2.8 29.6 + - + +
416H ILE* 4.7 3.8 - - + +
420H THR* 4.0 14.6 + - - +
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Residues in contact with VAL 387 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379H TYR* 3.8 32.3 - - + +
382H LYS* 3.8 28.7 - - + -
383H HIS 2.7 22.5 + - - +
384H GLU* 3.7 15.5 - - - +
386H THR* 1.3 71.2 - - - +
388H LYS* 1.3 66.9 + - + +
389H ALA 3.2 0.3 + - - -
391H ASP* 3.1 39.9 + - - +
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Residues in contact with LYS 388 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384H GLU* 2.7 60.2 + - - +
385H PRO* 3.8 16.1 - - - +
387H VAL* 1.3 76.0 - - + +
389H ALA* 1.3 55.4 + - - +
391H ASP* 3.7 6.2 + - - +
392H LEU* 3.4 22.4 + - - +
423H GLN* 5.6 3.2 - - - +
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Residues in contact with ALA 389 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385H PRO 3.1 17.5 + - - +
386H THR* 3.1 5.1 + - - +
388H LYS* 1.3 72.6 - - - +
390H VAL* 1.3 64.9 + - - +
391H ASP 3.2 1.6 - - - -
392H LEU* 3.4 15.1 - - + +
393H VAL* 3.3 22.2 - - - +
416H ILE* 3.8 25.4 - - + -
419H LEU* 4.7 16.2 - - + -
420H THR* 4.5 6.5 - - + -
423H GLN* 6.0 0.2 - - - +
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Residues in contact with VAL 390 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375H VAL* 3.9 28.3 - - + -
379H TYR* 3.4 42.8 - - + -
386H THR* 2.8 21.0 + - + +
387H VAL 4.2 0.2 - - - +
389H ALA* 1.3 71.5 - - - +
391H ASP* 1.3 65.9 + - - +
393H VAL* 3.3 4.3 + - - +
394H LEU* 3.0 49.2 + - + +
404H LEU* 4.4 14.4 - - + -
416H ILE* 3.9 15.3 - - + -
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Residues in contact with ASP 391 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379H TYR* 4.0 11.8 + - - -
387H VAL* 3.1 31.1 + - - +
388H LYS* 3.8 6.5 - - - +
389H ALA 3.2 0.2 - - - -
390H VAL* 1.3 87.3 - - - +
392H LEU* 1.3 63.0 + - - +
394H LEU* 4.1 8.3 - - - +
395H LYS* 2.9 29.4 + - + +
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Residues in contact with LEU 392 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258H ILE* 4.8 12.1 - - + -
262H LEU* 4.7 10.5 - - + -
388H LYS 3.4 12.1 + - - +
389H ALA* 3.4 16.2 - - + +
390H VAL 3.3 0.2 - - - -
391H ASP* 1.3 79.3 - - - +
393H VAL* 1.3 60.4 + - + +
395H LYS* 3.6 20.6 - - + +
396H THR* 2.5 50.6 + - - +
419H LEU* 5.6 8.5 - - + -
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Residues in contact with VAL 393 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258H ILE* 5.5 5.4 - - + -
261H LEU* 6.4 1.8 - - + -
262H LEU* 3.7 31.4 - - + -
389H ALA 3.3 13.7 - - - +
390H VAL* 3.4 9.6 - - - +
392H LEU* 1.3 84.0 - - + +
394H LEU* 1.3 58.4 + - + +
395H LYS 3.0 3.6 - - - -
396H THR* 2.8 5.0 + - - -
397H LEU* 2.7 45.2 + - + +
404H LEU* 5.5 2.9 - - + -
412H ALA* 4.1 22.9 - - + +
416H ILE* 4.1 22.0 - - + -
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Residues in contact with LEU 394 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379H TYR* 4.7 1.3 - - - +
390H VAL* 3.0 37.9 + - + +
391H ASP* 4.1 9.9 - - - +
393H VAL* 1.3 76.3 - - + +
395H LYS* 1.3 55.6 - - - +
397H LEU* 5.9 0.4 - - + -
398H GLY* 2.7 28.0 + - - -
399H VAL* 2.8 37.4 + - + +
400H GLY* 3.5 20.9 - - - +
401H PRO* 3.9 28.5 - - + -
403H ALA* 5.2 0.7 - - + -
404H LEU* 4.1 25.8 - - + -
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Residues in contact with LYS 395 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391H ASP 2.9 19.3 + - - +
392H LEU* 3.7 21.9 - - + +
394H LEU* 1.3 80.5 - - - +
396H THR* 1.3 82.8 + - - +
398H GLY* 3.5 10.4 + - - -
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Residues in contact with THR 396 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262H LEU* 3.5 37.2 - - + +
392H LEU* 2.5 32.8 + - - +
393H VAL 2.8 5.0 + - - -
395H LYS* 1.3 99.1 + - - +
397H LEU* 1.3 59.8 + - + +
398H GLY 3.2 0.7 + - - -
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Residues in contact with LEU 397 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262H LEU* 3.4 37.5 - - + +
265H ALA* 3.9 16.2 - - + +
266H GLY* 3.9 19.7 - - - +
269H LYS* 2.8 41.9 + - + +
393H VAL* 2.7 38.5 + - + +
394H LEU* 5.9 0.2 - - + -
396H THR* 1.3 75.4 - - + +
398H GLY* 1.3 58.8 + - - +
399H VAL* 3.4 25.3 + - + +
408H LEU* 4.9 11.4 - - + -
412H ALA* 5.2 7.2 - - + -
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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