Contacts of the helix formed by residues 371 - 380 (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 PRO 371 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108H HIS* 4.1 1.1 - - - +
370H GLY* 1.3 82.2 - - - +
372H LEU* 1.3 57.4 + - - +
375H VAL* 2.8 35.7 + - - +
410H ARG* 4.9 2.7 - - + +
413H ALA* 3.6 7.6 - - + +
414H ARG* 3.6 60.8 - - + +
417H GLN* 3.5 33.8 - - + +
462H PRO 3.6 13.9 - - - +
463H ARG* 4.6 2.2 - - - -
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Residues in contact with LEU 372 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277H THR* 4.5 3.6 - - - +
280H PHE* 3.7 25.8 - - + -
368H GLU* 3.7 18.4 - - - +
369H VAL 6.2 0.2 - - - +
370H GLY 3.3 0.6 - - - -
371H PRO* 1.3 78.3 - - - +
373H ALA* 1.3 58.8 + - - +
375H VAL* 3.8 2.1 - - + -
376H LEU* 2.8 54.6 + - + +
404H LEU* 3.5 36.3 - - + +
405H PHE* 4.6 2.5 - - - -
406H SER 4.6 1.3 - - - +
409H GLY 3.7 15.3 - - - +
410H ARG* 4.2 25.6 + - + +
413H ALA* 3.6 13.7 - - + +
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Residues in contact with ALA 373 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280H PHE* 3.7 22.5 - - + +
281H LEU 3.6 15.9 - - - +
282H THR* 4.7 1.6 - - - -
368H GLU* 3.4 28.2 + - + +
369H VAL* 3.8 1.5 - - - -
370H GLY* 3.0 15.4 + - - +
372H LEU* 1.3 79.8 - - - +
374H SER* 1.3 61.7 + - - +
376H LEU* 3.4 2.0 + - - +
377H VAL* 3.1 30.3 + - - +
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Residues in contact with SER 374 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282H THR* 3.6 20.3 + - - +
298H THR* 6.0 5.5 - - - -
299H PRO* 5.0 2.3 - - - +
370H GLY 2.8 22.6 + - - -
371H PRO 3.6 3.6 - - - -
373H ALA* 1.3 77.6 - - - +
375H VAL* 1.3 59.1 - - - +
377H VAL* 3.4 3.3 + - - +
378H ALA* 3.0 29.9 + - - +
417H GLN* 3.7 14.9 + - - -
460H ASN* 3.1 24.3 + - - -
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Residues in contact with VAL 375 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371H PRO 2.8 25.6 + - - +
372H LEU* 3.9 3.4 - - + +
374H SER* 1.3 70.3 - - - +
376H LEU* 1.3 66.4 + - + +
378H ALA* 4.5 4.9 - - - -
379H TYR* 3.0 28.1 + - - +
386H THR* 3.8 5.6 - - + +
390H VAL* 3.9 26.5 - - + -
404H LEU* 5.7 5.4 - - + -
413H ALA* 3.7 28.5 - - + +
416H ILE* 4.0 26.9 - - + -
417H GLN* 4.1 12.6 - - + +
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Residues in contact with LEU 376 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280H PHE* 4.0 19.1 - - + -
303H ILE* 3.7 14.3 - - + +
308H LEU* 3.6 29.1 - - + +
372H LEU* 2.8 40.0 + - + +
373H ALA* 3.9 4.0 - - - +
375H VAL* 1.3 79.3 - - + +
377H VAL* 1.3 55.8 + - - +
379H TYR* 4.0 3.9 - - + +
380H ALA* 2.9 32.1 + - - +
404H LEU* 4.2 26.7 - - + -
405H PHE* 3.3 36.3 - - + -
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Residues in contact with VAL 377 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280H PHE* 4.9 5.6 - - + +
281H LEU* 5.0 0.2 - - - -
282H THR* 3.5 25.4 - - + +
299H PRO* 3.9 5.8 - - + +
300H GLN 3.7 30.1 - - - +
301H GLY* 3.8 19.7 - - - +
303H ILE* 4.2 20.4 - - + -
311H VAL* 4.1 4.0 - - + -
373H ALA 3.1 15.3 + - - +
374H SER 3.8 1.1 - - - +
376H LEU* 1.3 74.7 - - - +
378H ALA* 1.3 66.3 + - - +
380H ALA* 3.3 3.1 + - - +
381H LYS* 2.9 33.4 + - + +
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Residues in contact with ALA 378 (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* 5.5 3.6 - - + -
299H PRO* 3.4 24.4 - - + +
374H SER 3.0 17.2 + - - +
375H VAL* 4.1 1.8 - - - +
377H VAL* 1.3 76.5 - - - +
379H TYR* 1.3 53.9 + - - +
381H LYS 3.2 2.3 + - - -
382H LYS 2.9 9.9 + - - -
383H HIS* 2.7 39.3 + - + +
386H THR* 3.5 27.4 - - + +
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Residues in contact with TYR 379 (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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308H LEU* 4.2 25.8 - - + -
375H VAL 3.0 19.8 + - - +
376H LEU* 4.0 4.5 - - + +
378H ALA* 1.3 74.6 - - - +
380H ALA* 1.3 61.6 + - - +
382H LYS* 2.9 21.7 + - - +
386H THR* 3.7 11.0 - - + +
387H VAL* 3.8 37.8 - - + +
390H VAL* 3.4 36.7 - - + +
391H ASP* 4.0 16.2 + - - -
394H LEU* 4.7 1.2 - - - +
401H PRO* 4.1 24.2 - - + +
404H LEU* 5.1 5.4 - - + -
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Residues in contact with ALA 380 (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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303H ILE* 4.3 1.3 - - + -
308H LEU* 3.1 36.2 - - + +
311H VAL* 3.3 23.1 - - + +
376H LEU 2.9 20.2 + - - +
377H VAL 3.7 0.2 - - - +
379H TYR* 1.3 78.8 - - - +
381H LYS* 1.3 58.3 - - - +
382H LYS* 3.0 15.2 + - - +
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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