Contacts of the helix formed by residues 415 - 431 (chain B) in PDB entry 3GSB
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 THR 415 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B TYR* 4.3 3.1 + - - +
331B TYR* 3.6 6.7 - - - +
335B ILE* 4.9 0.4 - - - -
413B ALA 3.3 10.4 + - - +
414B HIS* 1.3 75.3 - - - +
416B GLU* 1.3 67.6 + - - +
417B GLU* 3.0 14.0 + - - +
418B ASP* 3.0 37.8 + - - -
419B ILE* 3.0 17.5 + - - +
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Residues in contact with GLU 416 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331B TYR* 3.7 19.7 + - - -
334B GLN* 3.9 23.3 - - - +
335B ILE* 3.7 15.5 - - - +
338B ARG* 2.7 52.9 + - - +
415B THR* 1.3 72.5 - - - +
417B GLU* 1.3 62.6 + - + +
419B ILE* 3.1 3.7 + - - +
420B ASP* 2.9 17.2 + - - +
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Residues in contact with GLU 417 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415B THR* 3.0 11.5 + - - +
416B GLU* 1.3 80.6 - - + +
418B ASP* 1.3 65.2 + - - +
420B ASP* 3.4 12.9 + - - +
421B ALA* 3.1 23.6 + - - +
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Residues in contact with ASP 418 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B ALA* 4.0 11.3 - - - +
51B TYR* 2.7 44.5 + - - -
59B ARG* 5.1 0.7 + - - -
61B ILE* 4.2 23.5 - - + +
63B TYR* 4.3 3.1 - - - +
413B ALA 4.2 1.4 - - - +
414B HIS* 4.1 4.9 - - + -
415B THR* 3.0 31.8 + - - +
417B GLU* 1.3 77.4 - - - +
419B ILE* 1.3 62.8 + - - +
421B ALA* 3.2 5.2 + - - +
422B THR* 3.1 27.6 + - - -
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Residues in contact with ILE 419 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B TYR* 4.4 14.4 - - + +
335B ILE* 3.9 39.0 - - + +
338B ARG* 3.6 33.7 - - + +
339B LEU* 3.7 30.9 - - + +
410B THR* 5.0 4.3 - - - +
414B HIS* 4.6 13.5 - - + -
415B THR 3.0 15.4 + - - +
416B GLU 3.3 7.4 - - - +
418B ASP* 1.3 77.0 - - - +
420B ASP* 1.3 60.2 + - - +
422B THR* 3.6 3.1 + - - -
423B LEU* 3.2 24.7 + - + +
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Residues in contact with ASP 420 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338B ARG* 2.6 42.1 + - - -
416B GLU* 2.9 10.6 + - - +
417B GLU* 3.7 13.0 - - - +
418B ASP 3.2 0.4 - - - -
419B ILE* 1.3 77.8 - - - +
421B ALA* 1.3 56.8 + - - +
423B LEU* 3.3 13.4 + - - +
424B ALA* 3.0 24.3 + - - +
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Residues in contact with ALA 421 (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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61B ILE* 4.8 10.3 - - + -
398B ILE* 4.4 4.2 - - + +
417B GLU 3.1 16.4 + - - +
418B ASP* 3.2 6.3 + - - +
420B ASP* 1.3 75.5 - - - +
422B THR* 1.3 62.0 + - - +
424B ALA* 3.4 10.6 - - + +
425B ALA* 3.2 20.1 + - - +
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Residues in contact with THR 422 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B ILE* 4.5 1.2 - - - +
63B TYR* 2.7 34.1 + - + +
339B LEU* 4.0 18.8 - - + -
343B LEU* 4.9 3.8 - - + -
393B MET* 3.8 21.7 - - + +
398B ILE* 3.7 25.7 - - + +
400B LEU* 5.9 1.8 - - + -
418B ASP 3.1 11.5 + - - -
419B ILE 4.0 4.9 - - - -
420B ASP 3.2 0.4 - - - -
421B ALA* 1.3 72.8 - - - +
423B LEU* 1.3 57.3 + - - +
424B ALA 3.0 1.6 - - - -
425B ALA* 3.1 3.6 + - - +
426B ALA* 2.7 32.4 + - - +
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Residues in contact with LEU 423 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338B ARG* 3.8 25.4 - - + +
339B LEU* 3.6 21.1 - - + +
342B GLY* 3.4 36.6 - - - +
343B LEU* 3.5 11.2 - - + +
346B ILE* 3.2 17.5 - - + +
419B ILE* 3.2 22.8 + - + +
420B ASP* 3.3 14.5 + - - +
422B THR* 1.3 76.0 - - - +
424B ALA* 1.3 60.1 + - - +
426B ALA* 3.3 2.9 - - - +
427B ARG* 3.2 25.7 + - - +
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Residues in contact with ALA 424 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420B ASP 3.0 13.4 + - - +
421B ALA* 3.4 15.9 - - + +
422B THR 3.0 0.6 - - - -
423B LEU* 1.3 74.6 - - - +
425B ALA* 1.3 65.9 + - - +
427B ARG* 3.0 20.5 + - - +
428B THR* 3.1 17.1 + - - -
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Residues in contact with ALA 425 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393B MET* 3.8 7.6 - - - -
396B GLN* 3.3 39.9 - - + +
398B ILE* 3.7 20.6 - - + -
421B ALA 3.2 6.5 + - - +
422B THR 3.1 8.6 + - - +
424B ALA* 1.3 77.7 - - - +
426B ALA* 1.3 64.8 + - - +
427B ARG 2.9 1.7 + - - -
428B THR* 3.2 2.8 + - - +
429B VAL* 2.9 27.5 + - - +
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Residues in contact with ALA 426 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343B LEU* 3.7 23.6 - - + -
346B ILE* 3.5 17.0 - - + +
389B PHE* 5.1 3.1 - - + -
393B MET* 3.7 14.1 - - + -
422B THR 2.7 13.8 + - - +
423B LEU 3.3 12.1 - - - +
425B ALA* 1.3 77.7 - - - +
427B ARG* 1.3 55.3 + - - +
429B VAL* 4.9 0.4 - - - -
430B MET* 3.2 39.6 + - + +
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Residues in contact with ARG 427 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346B ILE* 3.5 34.6 - - + +
349B GLU* 3.3 29.1 + - - -
350B THR* 5.6 2.2 - - + -
423B LEU* 3.2 21.9 + - - +
424B ALA* 3.0 12.7 + - - +
425B ALA 2.9 1.2 + - - -
426B ALA* 1.3 75.8 - - - +
428B THR* 1.3 68.2 + - - +
429B VAL 3.1 2.2 + - - -
430B MET* 3.3 1.2 + - - +
431B SER* 3.0 33.5 + - - +
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Residues in contact with THR 428 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396B GLN* 4.2 27.7 + - - +
424B ALA 3.1 12.4 + - - -
425B ALA* 3.9 5.4 - - - -
427B ARG* 1.3 77.9 - - - +
429B VAL* 1.3 64.0 + - + +
431B SER* 3.7 16.9 + - - +
432B ALA* 5.0 1.2 - - - +
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Residues in contact with VAL 429 (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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389B PHE* 3.8 41.5 - - + +
392B GLY* 3.7 30.5 - - - +
393B MET* 3.8 9.9 - - - +
396B GLN* 4.0 18.2 - - + +
425B ALA 2.9 20.7 + - - +
426B ALA 4.5 1.6 - - - +
428B THR* 1.3 73.8 - - + +
430B MET* 1.3 64.9 + - - +
431B SER 2.8 5.6 + - - -
432B ALA* 3.3 21.5 + - - +
433B LEU* 4.2 6.1 - - + +
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Residues in contact with MET 430 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343B LEU* 3.7 28.3 - - + +
346B ILE* 4.0 17.5 - - + -
347B ALA* 3.8 23.8 - - - +
350B THR* 3.7 14.8 - - - +
352B HIS* 2.8 34.8 - - + -
365B PHE* 3.9 21.1 - - + -
367B PHE* 4.7 11.9 - - - -
389B PHE* 4.2 21.5 - - + -
426B ALA* 3.2 24.5 + - + +
427B ARG 3.3 0.8 + - - +
429B VAL* 1.3 77.7 - - - +
431B SER* 1.3 55.8 + - - +
432B ALA 2.9 7.9 + - - +
433B LEU* 3.7 14.4 - - + -
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Residues in contact with SER 431 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350B THR* 3.7 19.2 - - - +
427B ARG* 3.0 22.0 + - - +
428B THR* 3.8 10.4 - - - +
429B VAL 2.8 2.7 + - - -
430B MET* 1.3 73.4 - - - +
432B ALA* 1.3 60.0 + - - +
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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