Contacts of the helix formed by residues 371 - 380 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108D HIS* 4.1 0.9 - - - +
370D GLY* 1.3 82.8 - - - +
372D LEU* 1.3 57.8 + - - +
375D VAL* 2.8 35.9 + - - +
410D ARG* 4.9 2.7 - - + +
413D ALA* 3.6 7.9 - - + +
414D ARG* 3.6 61.2 - - + +
417D GLN* 3.5 32.7 - - + +
462D PRO 3.6 14.1 - - - +
463D ARG* 4.6 2.5 - - - -
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Residues in contact with LEU 372 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277D THR* 4.6 3.8 - - - +
280D PHE* 3.7 25.8 - - + -
368D GLU* 3.7 20.2 - - - +
370D GLY* 3.3 1.0 - - - -
371D PRO* 1.3 79.2 - - - +
373D ALA* 1.3 59.7 + - - +
375D VAL* 3.8 1.7 - - + -
376D LEU* 2.8 53.9 + - + +
404D LEU* 3.5 35.0 - - + +
405D PHE* 4.6 2.5 - - - -
406D SER 4.6 1.8 - - - +
409D GLY 3.7 15.9 - - - +
410D ARG* 4.2 25.2 + - + +
413D ALA* 3.6 13.5 - - + +
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Residues in contact with ALA 373 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280D PHE* 3.7 23.4 - - + +
281D LEU 3.6 15.0 - - - +
282D THR* 4.7 1.3 - - - -
368D GLU* 3.4 27.3 + - + +
369D VAL* 3.8 2.0 - - - -
370D GLY 3.0 15.0 + - - +
372D LEU* 1.3 79.7 - - - +
374D SER* 1.3 63.2 + - - +
376D LEU* 3.4 1.8 + - - +
377D VAL* 3.1 30.6 + - - +
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Residues in contact with SER 374 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282D THR* 3.6 19.6 + - - +
298D THR* 6.0 4.9 - - - -
299D PRO 5.0 2.4 - - - +
370D GLY 2.8 22.1 + - - -
371D PRO 3.6 3.6 - - - -
373D ALA* 1.3 77.6 - - - +
375D VAL* 1.3 58.7 - - - +
377D VAL* 3.4 3.3 + - - +
378D ALA* 3.0 29.3 + - - +
417D GLN* 3.7 14.7 + - - -
460D ASN* 3.1 24.7 + - - -
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Residues in contact with VAL 375 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371D PRO 2.8 24.1 + - - +
372D LEU* 3.9 2.9 - - + +
374D SER* 1.3 70.7 - - - +
376D LEU* 1.3 66.8 + - + +
378D ALA* 4.5 4.9 - - - -
379D TYR* 3.0 28.5 + - + +
386D THR* 3.8 6.2 - - + +
390D VAL* 3.9 26.0 - - + -
404D LEU* 5.7 4.7 - - + -
413D ALA* 3.7 27.8 - - + +
416D ILE* 4.0 27.6 - - + -
417D GLN* 4.1 12.8 - - + +
420D THR* 6.1 0.2 - - - +
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Residues in contact with LEU 376 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280D PHE* 4.0 19.3 - - + -
303D ILE* 3.7 14.0 - - + +
308D LEU* 3.6 29.7 - - + +
372D LEU* 2.8 39.6 + - + +
373D ALA* 3.9 4.3 - - - +
375D VAL* 1.3 77.9 - - + +
377D VAL* 1.3 56.7 + - - +
379D TYR* 4.0 3.3 - - + +
380D ALA* 2.9 32.4 + - - +
404D LEU* 4.2 25.4 - - + -
405D PHE* 3.3 35.9 - - + -
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Residues in contact with VAL 377 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280D PHE 4.9 5.6 - - - +
281D LEU* 5.0 0.2 - - - -
282D THR* 3.5 24.0 - - + +
299D PRO* 3.9 5.8 - - + +
300D GLN 3.7 30.3 - - - +
301D GLY* 3.8 18.8 - - - +
302D VAL 4.5 0.2 - - - +
303D ILE* 4.2 20.0 - - + -
311D VAL* 4.1 3.4 - - + -
373D ALA 3.1 17.0 + - - +
374D SER 3.8 1.3 - - - +
375D VAL 3.3 0.4 - - - -
376D LEU* 1.3 72.9 - - - +
378D ALA* 1.3 67.3 + - - +
380D ALA* 3.3 3.5 + - - +
381D LYS* 2.9 33.8 + - + +
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Residues in contact with ALA 378 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298D THR* 5.5 3.4 - - + -
299D PRO* 3.4 25.3 - - + +
374D SER 3.0 18.0 + - - +
375D VAL* 4.1 1.3 - - - +
377D VAL* 1.3 75.8 - - - +
379D TYR* 1.3 54.9 + - - +
381D LYS 3.2 2.8 + - - -
382D LYS 2.9 10.0 + - - -
383D HIS* 2.7 40.3 + - + +
386D THR* 3.5 26.5 - - + +
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Residues in contact with TYR 379 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308D LEU* 4.2 25.8 - - + -
375D VAL* 3.0 20.5 + - + +
376D LEU* 4.0 4.5 - - + +
378D ALA* 1.3 74.8 - - - +
380D ALA* 1.3 62.3 + - - +
382D LYS* 2.9 22.3 + - - +
386D THR* 3.7 11.0 - - + +
387D VAL* 3.8 37.3 - - + +
390D VAL* 3.4 36.0 - - + +
391D ASP* 4.0 16.2 + - - -
394D LEU* 4.7 1.4 - - - +
401D PRO* 4.1 23.8 - - + +
404D LEU* 5.1 5.6 - - + -
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Residues in contact with ALA 380 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303D ILE* 4.3 1.6 - - + -
308D LEU* 3.1 36.5 - - + +
311D VAL* 3.3 23.4 - - + +
376D LEU 2.9 19.3 + - - +
377D VAL 3.7 0.2 - - - +
379D TYR* 1.3 79.8 - - - +
381D LYS* 1.3 58.0 + - - +
382D LYS* 3.0 15.7 + - - +
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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