Contacts of the helix formed by residues 428 - 443 (chain B) in PDB entry 2FGY
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 ASN 428 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199B TYR* 3.5 17.2 - - - -
205B ASP* 4.9 10.0 + - - +
421B HIS 3.5 13.3 - - - +
422B LEU* 3.6 34.4 - - + +
423B ASP 4.5 2.4 - - - +
424B THR 3.5 10.8 + - - +
425B VAL 3.1 5.6 + - - -
427B GLU* 1.3 101.3 + - - +
429B ALA* 1.3 62.5 + - - +
430B ILE* 3.2 4.7 - - - -
431B ASP* 3.1 29.1 + - - +
432B VAL* 3.4 11.7 + - - +
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Residues in contact with ALA 429 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425B VAL* 2.8 23.8 + - + +
426B GLU* 4.1 8.5 + - - +
427B GLU 3.7 1.6 - - - -
428B ASN* 1.3 72.0 - - - +
430B ILE* 1.3 59.2 + - - +
432B VAL* 3.2 4.0 + - - +
433B ASP* 2.8 34.6 + - - +
483B ARG* 3.5 35.2 - - - +
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Residues in contact with ILE 430 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200B ALA* 4.4 10.5 - - + -
255B ALA* 6.1 2.2 - - + -
428B ASN* 4.9 1.8 - - - -
429B ALA* 1.3 78.3 - - - +
431B ASP* 1.3 79.7 + - - +
433B ASP* 3.3 10.1 + - + +
434B VAL* 3.0 41.5 + - + +
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Residues in contact with ASP 431 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B TYR* 3.4 16.6 - - - +
200B ALA* 2.8 33.3 + - - +
418B TYR* 2.6 37.4 + - - +
420B ALA* 3.8 22.4 - - + -
421B HIS 5.7 0.4 - - - -
422B LEU* 5.0 0.4 - - + -
428B ASN* 3.1 33.8 + - + +
430B ILE* 1.3 88.1 - - - +
432B VAL* 1.3 61.3 + - - +
435B GLY 3.4 2.4 + - - -
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Residues in contact with VAL 432 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402B ILE* 5.2 5.9 - - + +
404B VAL* 4.8 9.4 - - + -
418B TYR* 5.4 0.7 - - - -
420B ALA* 5.6 0.4 - - - -
422B LEU* 3.8 27.8 - - + -
425B VAL* 4.5 21.1 - - + -
428B ASN 3.4 7.6 + - - +
429B ALA* 3.2 8.6 + - - +
431B ASP* 1.3 76.2 - - - +
433B ASP* 1.3 65.1 + - - +
435B GLY* 3.2 4.2 + - - -
436B ILE* 3.0 25.8 + - + +
480B ILE* 4.5 21.8 - - + -
483B ARG* 5.0 4.0 - - - -
484B PHE* 3.9 24.2 - - + -
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Residues in contact with ASP 433 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429B ALA 2.8 19.1 + - - +
430B ILE* 3.3 10.8 + - + +
432B VAL* 1.3 75.7 - - - +
434B VAL* 1.3 56.4 + - + +
436B ILE* 3.3 2.6 + - - +
437B THR* 2.9 33.7 + - - +
483B ARG* 2.7 43.8 + - - -
484B PHE* 3.2 21.2 - - + -
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Residues in contact with VAL 434 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200B ALA* 4.2 11.9 - - + -
254B ALA* 6.2 4.0 - - + -
255B ALA* 5.8 8.5 - - + +
418B TYR* 3.5 28.7 - - + +
430B ILE* 3.0 38.5 + - + +
432B VAL 3.3 0.2 - - - -
433B ASP* 1.3 72.1 - - + +
435B GLY* 1.3 60.0 + - - +
437B THR* 3.4 7.7 + - - -
438B ILE* 2.9 38.0 + - + +
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Residues in contact with GLY 435 (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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402B ILE* 3.7 11.2 - - - -
418B TYR* 3.6 32.8 - - - -
431B ASP 3.4 5.7 + - - -
432B VAL 3.2 6.7 + - - -
434B VAL* 1.3 77.2 - - - +
436B ILE* 1.3 57.4 + - - +
438B ILE* 3.4 3.0 + - - +
439B PHE* 2.9 34.8 + - - -
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Residues in contact with ILE 436 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402B ILE* 4.0 17.7 - - + +
432B VAL* 3.0 19.6 + - + +
433B ASP 3.7 6.1 - - - +
435B GLY* 1.3 74.3 - - - +
437B THR* 1.3 63.3 + - - +
439B PHE* 3.1 1.8 + - - +
440B THR* 2.8 35.0 + - - +
450B ILE* 4.1 17.7 - - + +
452B ILE* 4.4 8.1 - - + -
480B ILE* 5.2 0.7 - - + -
484B PHE* 3.6 44.9 - - + -
487B LEU* 4.1 19.3 - - + -
493B LEU* 4.4 16.2 - - + -
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Residues in contact with THR 437 (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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433B ASP* 2.9 17.1 + - - +
434B VAL* 3.5 11.4 - - - -
436B ILE* 1.3 75.1 - - - +
438B ILE* 1.3 65.1 + - + +
440B THR* 3.2 22.9 + - - -
441B LYS* 3.5 30.0 + - - +
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Residues in contact with ILE 438 (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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397B HIS* 3.4 39.0 - - + +
399B GLU* 3.8 13.5 - - - +
418B TYR* 3.8 26.9 - - + -
434B VAL* 2.9 29.6 + - + +
435B GLY* 3.6 4.5 - - - +
437B THR* 1.3 77.8 - - + +
439B PHE* 1.3 65.1 + - + +
441B LYS* 3.3 12.8 + - + +
442B LEU* 3.1 51.7 + - + +
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Residues in contact with PHE 439 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399B GLU* 3.5 35.4 - - + -
400B ARG 3.6 15.3 - - - -
401B TYR* 3.4 32.8 - - - -
402B ILE* 3.5 19.7 - - + -
418B TYR* 4.3 7.4 - - + -
435B GLY* 2.9 25.8 + - - +
436B ILE 3.1 0.8 + - - -
438B ILE* 1.3 77.8 - - + +
440B THR* 1.3 60.3 + - - +
442B LEU* 3.8 8.1 - - + -
443B ASN* 2.8 49.6 + - - +
444B LEU* 3.1 9.7 + - - +
450B ILE* 3.7 34.7 - - + +
451B PRO* 4.2 4.3 - - + -
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Residues in contact with THR 440 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436B ILE* 2.8 28.2 + - - +
437B THR* 3.2 12.5 + - - -
439B PHE* 1.3 77.3 - - - +
441B LYS* 1.3 61.8 + - + +
444B LEU* 3.7 28.5 - - + +
445B SER* 3.0 30.0 + - - -
450B ILE* 4.5 0.2 - - - +
487B LEU* 5.3 0.3 - - - +
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Residues in contact with LYS 441 (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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437B THR* 3.7 32.6 - - - +
438B ILE* 3.3 10.5 + - + +
439B PHE 3.3 0.2 - - - -
440B THR* 1.3 78.8 - - + +
442B LEU* 1.3 65.7 + - + +
445B SER* 2.6 29.5 + - - -
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Residues in contact with LEU 442 (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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397B HIS* 3.9 21.8 - - + +
398B ALA* 4.2 3.4 - - - -
399B GLU* 3.5 51.1 - - + +
438B ILE* 3.1 31.7 + - + +
439B PHE* 4.1 9.9 - - + -
441B LYS* 1.3 90.6 - - + +
443B ASN* 1.3 62.5 + - - +
445B SER* 4.4 0.6 + - - -
446B ARG* 2.7 38.7 + - - +
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Residues in contact with ASN 443 (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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127B PHE* 3.8 12.9 - - - -
399B GLU 4.8 2.3 - - - +
400B ARG 4.8 2.0 + - - -
439B PHE* 2.8 34.0 + - + +
442B LEU* 1.3 81.4 - - - +
444B LEU* 1.3 65.5 + - - +
445B SER 3.2 2.0 - - - -
446B ARG* 3.0 39.2 + - - +
448B LEU* 3.0 33.0 + - + +
449B PRO 2.9 22.6 + - - +
450B ILE* 4.7 1.3 - - + -
451B PRO* 3.7 16.2 - - - +
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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
------------------------------------------------------------
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