Contacts of the helix formed by residues 384 - 397 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382B LYS 3.3 6.4 + - - -
383B HIS* 1.3 68.9 - - - +
385B PRO* 1.3 62.3 - - + +
387B VAL* 4.2 14.0 - - + +
388B LYS* 2.7 76.3 + - - +
104E LYS 5.5 0.2 - - - +
139E GLY 4.8 7.2 - - - +
141E LYS* 3.2 49.1 + - + +
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Residues in contact with PRO 385 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297B TYR* 3.6 22.0 - - + +
383B HIS* 3.1 33.7 - - + +
384B GLU* 1.3 96.2 - - + +
386B THR* 1.3 54.3 + - - +
388B LYS* 3.5 15.3 + - - +
389B ALA* 3.1 28.4 + - - +
420B THR* 3.9 8.5 - - + +
423B GLN* 3.9 20.1 + - - +
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Residues in contact with THR 386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298B THR* 5.7 0.9 - - - +
375B VAL* 3.8 23.1 - - + +
378B ALA* 3.5 12.1 - - + +
379B TYR* 3.7 32.1 - - + +
383B HIS* 2.7 32.7 + - - -
385B PRO* 1.3 75.1 - - - +
387B VAL* 1.3 61.0 + - - +
389B ALA* 3.1 3.9 + - - +
390B VAL* 2.8 30.5 + - + +
416B ILE* 4.7 4.2 - - + +
420B THR* 4.0 15.5 + - - +
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Residues in contact with VAL 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379B TYR* 3.8 33.4 - - + +
382B LYS* 3.8 28.7 - - + -
383B HIS 2.7 22.5 + - - +
384B GLU* 3.7 17.0 - - + +
386B THR* 1.3 71.0 - - - +
388B LYS* 1.3 66.6 + - - +
389B ALA 3.2 0.2 + - - -
391B ASP* 3.1 39.4 + - - +
141E LYS* 5.9 0.9 - - - +
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Residues in contact with LYS 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384B GLU* 2.7 59.5 + - - +
385B PRO* 3.8 16.7 - - - +
387B VAL* 1.3 74.9 - - + +
389B ALA* 1.3 56.6 + - - +
391B ASP* 3.7 6.7 + - - +
392B LEU* 3.4 23.0 + - - +
423B GLN* 5.6 3.0 - - - +
104E LYS* 3.8 24.5 - - + +
105E ALA* 6.0 0.9 - - - +
167E MET* 5.4 16.6 - - - +
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Residues in contact with ALA 389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385B PRO 3.1 17.8 + - - +
386B THR* 3.1 4.2 + - - +
388B LYS* 1.3 73.9 - - - +
390B VAL* 1.3 64.0 + - - +
391B ASP 3.2 1.1 - - - -
392B LEU* 3.4 14.9 - - + +
393B VAL* 3.3 22.5 - - - +
416B ILE* 3.8 25.1 - - + -
419B LEU* 4.7 15.7 - - + -
420B THR* 4.5 6.7 - - + -
423B GLN* 6.0 0.2 - - - +
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Residues in contact with VAL 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375B VAL* 3.9 28.5 - - + -
379B TYR* 3.4 42.6 - - + -
386B THR* 2.8 21.9 + - + +
387B VAL 4.2 0.2 - - - +
389B ALA* 1.3 71.4 - - - +
391B ASP* 1.3 66.2 + - - +
393B VAL* 3.3 4.6 + - - +
394B LEU* 3.0 49.7 + - + +
404B LEU* 4.4 13.7 - - + -
416B ILE* 3.9 15.3 - - + -
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Residues in contact with ASP 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379B TYR* 4.0 12.0 + - - -
387B VAL* 3.1 31.3 + - - +
388B LYS* 3.8 5.8 - - - +
389B ALA 3.2 0.2 - - - -
390B VAL* 1.3 87.2 - - - +
392B LEU* 1.3 63.1 + - - +
394B LEU* 4.1 8.3 - - - +
395B LYS* 2.9 27.7 + - - +
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Residues in contact with LEU 392 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258B ILE* 4.8 11.7 - - + -
262B LEU* 4.7 9.4 - - + -
388B LYS 3.4 11.7 + - - +
389B ALA* 3.4 15.3 - - + +
391B ASP* 1.3 77.9 - - - +
393B VAL* 1.3 61.2 + - + +
395B LYS* 3.6 21.4 - - + +
396B THR* 2.5 50.7 + - - +
419B LEU* 5.6 9.0 - - + -
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Residues in contact with VAL 393 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258B ILE* 5.5 5.2 - - + -
261B LEU* 6.4 1.6 - - + -
262B LEU* 3.7 31.0 - - + -
389B ALA 3.3 14.1 - - - +
390B VAL* 3.4 9.2 - - - +
392B LEU* 1.3 84.6 - - + +
394B LEU* 1.3 59.2 + - + +
395B LYS 3.0 3.4 - - - -
396B THR* 2.8 5.2 + - - -
397B LEU* 2.7 44.0 + - + +
404B LEU* 5.5 2.5 - - + -
412B ALA* 4.1 22.4 - - + +
416B ILE* 4.1 21.5 - - + -
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Residues in contact with LEU 394 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379B TYR* 4.7 1.6 - - - +
390B VAL* 3.0 38.1 + - + +
391B ASP* 4.1 9.4 - - - +
393B VAL* 1.3 76.6 - - + +
395B LYS* 1.3 55.8 + - - +
397B LEU* 5.9 0.4 - - + -
398B GLY* 2.7 27.4 + - - -
399B VAL* 2.8 36.9 + - + +
400B GLY* 3.5 20.6 - - - +
401B PRO* 3.9 27.1 - - + -
403B ALA* 5.2 0.4 - - + -
404B LEU* 4.1 26.2 - - + -
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Residues in contact with LYS 395 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391B ASP 2.9 17.9 + - - +
392B LEU* 3.7 22.0 - - + +
394B LEU* 1.3 81.8 - - - +
396B THR* 1.3 82.1 + - - +
398B GLY* 3.5 9.8 + - - -
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Residues in contact with THR 396 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262B LEU* 3.5 37.8 - - + +
392B LEU* 2.5 31.7 + - - +
393B VAL 2.8 5.3 + - - -
395B LYS* 1.3 99.9 + - - +
397B LEU* 1.3 59.3 + - + +
398B GLY 3.3 0.8 + - - -
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Residues in contact with LEU 397 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262B LEU* 3.4 37.0 - - + +
265B ALA* 3.9 16.2 - - + +
266B GLY* 3.9 18.8 - - - +
269B LYS* 2.8 40.6 + - + +
393B VAL* 2.7 37.1 + - + +
394B LEU* 5.9 0.2 - - + -
396B THR* 1.3 74.9 - - + +
398B GLY* 1.3 59.6 + - - +
399B VAL* 3.4 25.1 + - + +
408B LEU* 4.9 12.1 - - + -
412B ALA* 5.2 6.7 - - + -
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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