Contacts of the helix formed by residues 371 - 380 (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 PRO 371 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B HIS* 4.1 1.3 - - - +
370B GLY* 1.3 82.1 - - - +
372B LEU* 1.3 57.5 + - - +
374B SER* 4.2 0.2 - - - -
375B VAL* 2.8 36.2 + - - +
410B ARG* 4.9 2.2 - - + +
413B ALA* 3.6 8.3 - - - +
414B ARG* 3.6 60.8 - - + +
417B GLN* 3.5 32.7 - - + +
462B PRO 3.6 15.5 - - - +
463B ARG* 4.6 2.0 - - - -
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Residues in contact with LEU 372 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B THR* 4.5 4.0 - - - +
280B PHE* 3.7 25.8 - - + -
368B GLU* 3.7 18.6 - - - +
370B GLY* 3.3 0.8 - - - -
371B PRO* 1.3 78.5 - - - +
373B ALA* 1.3 57.8 + - - +
375B VAL* 3.8 2.1 - - + -
376B LEU* 2.8 53.6 + - + +
404B LEU* 3.5 36.6 - - + +
405B PHE* 4.6 2.7 - - - -
406B SER 4.6 1.6 - - - +
409B GLY 3.7 15.9 - - - +
410B ARG* 4.2 25.5 + - + +
413B ALA* 3.6 13.9 - - + +
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Residues in contact with ALA 373 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B PHE* 3.7 23.8 - - + +
281B LEU 3.6 14.8 - - - +
282B THR* 4.7 1.1 - - - -
368B GLU* 3.4 27.8 + - + +
369B VAL* 3.8 1.5 - - - -
370B GLY 3.0 15.7 + - - +
372B LEU* 1.3 79.3 - - - +
374B SER* 1.3 62.4 + - - +
376B LEU* 3.4 1.6 + - - +
377B VAL* 3.1 30.9 + - - +
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Residues in contact with SER 374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B THR* 3.6 20.8 + - - +
298B THR* 6.0 4.7 - - - -
299B PRO 5.0 1.9 - - - +
370B GLY 2.8 22.3 + - - -
371B PRO 3.6 3.6 - - - -
373B ALA* 1.3 77.7 - - - +
375B VAL* 1.3 59.3 + - - +
377B VAL* 3.4 3.3 + - - +
378B ALA* 3.0 29.4 + - - +
417B GLN* 3.7 14.7 + - - -
460B ASN* 3.1 25.5 + - - -
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Residues in contact with VAL 375 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371B PRO 2.8 24.4 + - - +
372B LEU* 3.9 3.4 - - + +
374B SER* 1.3 72.0 - - - +
376B LEU* 1.3 67.0 + - + +
378B ALA* 4.5 5.2 - - - -
379B TYR* 3.0 29.0 + - + +
386B THR* 3.8 5.5 - - + +
390B VAL* 3.9 26.5 - - + -
404B LEU* 5.7 4.9 - - + -
413B ALA* 3.7 28.3 - - + +
416B ILE* 4.0 27.1 - - + -
417B GLN* 4.1 12.6 - - + +
420B THR* 6.1 0.2 - - - +
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Residues in contact with LEU 376 (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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280B PHE* 4.0 19.3 - - + -
303B ILE* 3.7 13.2 - - + +
308B LEU* 3.6 29.2 - - + +
372B LEU* 2.8 40.2 + - + +
373B ALA* 3.9 4.5 - - - +
375B VAL* 1.3 78.9 - - + +
377B VAL* 1.3 56.3 + - - +
379B TYR* 4.0 4.3 - - + +
380B ALA* 2.9 32.1 + - - +
404B LEU* 4.2 25.8 - - + -
405B PHE* 3.3 35.7 - - + -
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Residues in contact with VAL 377 (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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280B PHE* 4.9 6.1 - - + +
282B THR* 3.5 24.5 - - + +
299B PRO* 3.9 6.1 - - + +
300B GLN 3.7 30.3 - - - +
301B GLY* 3.8 19.3 - - - +
303B ILE* 4.2 20.6 - - + -
311B VAL* 4.1 3.4 - - + -
373B ALA 3.1 16.7 + - - +
374B SER 3.8 1.1 - - - +
375B VAL 3.3 0.2 - - - -
376B LEU* 1.3 73.1 - - - +
378B ALA* 1.3 65.9 + - - +
380B ALA* 3.3 2.9 + - - +
381B LYS* 2.9 34.6 + - + +
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Residues in contact with ALA 378 (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* 5.5 3.8 - - + -
299B PRO* 3.4 25.5 - - + +
374B SER 3.0 16.6 + - - +
375B VAL* 4.5 1.3 - - - -
377B VAL* 1.3 75.7 - - - +
379B TYR* 1.3 55.6 + - - +
381B LYS* 3.2 3.1 + - - +
382B LYS 2.9 9.5 + - - -
383B HIS* 2.7 40.6 + - + +
386B THR* 3.5 25.6 - - + +
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Residues in contact with TYR 379 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308B LEU* 4.2 25.6 - - + -
375B VAL 3.0 20.3 + - - +
376B LEU* 4.0 3.8 - - + +
378B ALA* 1.3 74.6 - - - +
380B ALA* 1.3 60.8 - - - +
382B LYS* 2.9 22.0 + - - +
386B THR* 3.7 11.0 - - + +
387B VAL* 3.8 37.7 - - + +
390B VAL* 3.4 37.1 - - + +
391B ASP* 4.0 15.6 + - - -
394B LEU* 4.7 1.0 - - - +
401B PRO* 4.1 25.0 - - + +
404B LEU* 5.1 5.2 - - + -
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Residues in contact with ALA 380 (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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303B ILE* 4.3 1.8 - - + -
308B LEU* 3.1 37.0 - - + +
311B VAL* 3.3 23.4 - - + +
376B LEU 2.9 19.7 + - - +
377B VAL 3.7 0.2 - - - +
379B TYR* 1.3 79.6 - - - +
381B LYS* 1.3 57.6 + - - +
382B LYS* 3.0 15.5 + - - +
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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