Contacts of the helix formed by residues 415 - 431 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51A TYR* 5.0 2.6 + - - +
331A TYR* 3.5 6.7 - - - +
335A ILE* 5.1 0.9 - - - -
413A ALA 3.9 7.2 - - - +
414A HIS* 1.3 76.8 - - - +
416A GLU* 1.3 58.6 + - - +
417A GLU* 3.3 29.2 + - - +
418A ASP* 2.7 55.9 + - - +
419A ILE* 3.0 16.5 + - - +
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Residues in contact with GLU 416 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331A TYR* 4.0 13.4 + - - -
334A GLN* 3.3 28.1 - - - +
335A ILE* 4.1 14.6 - - + +
338A ARG* 2.9 37.5 + - - +
415A THR* 1.3 72.3 - - - +
417A GLU* 1.3 59.4 + - + +
419A ILE* 3.3 7.9 + - - +
420A ASP* 3.0 33.9 + - - +
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Residues in contact with GLU 417 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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415A THR* 3.3 26.7 + - - +
416A GLU* 1.3 77.9 - - + +
418A ASP* 1.3 61.8 + - - +
420A ASP* 3.3 9.0 + - - +
421A ALA* 2.9 30.7 + - - +
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Residues in contact with ASP 418 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A ALA* 4.0 6.2 - - - +
51A TYR* 2.8 37.2 + - - -
61A ILE* 3.6 27.4 - - + +
63A TYR* 4.1 1.3 - - - -
413A ALA 3.7 5.5 - - - +
414A HIS* 3.5 15.1 - - + -
415A THR* 2.7 44.4 + - - +
417A GLU* 1.3 75.0 - - - +
419A ILE* 1.3 56.7 + - - +
421A ALA* 3.4 0.8 + - - -
422A THR* 2.7 33.5 + - - -
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Residues in contact with ILE 419 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A TYR* 3.9 16.8 - - + +
335A ILE* 4.1 38.6 - - + +
338A ARG* 3.8 22.2 - - + +
339A LEU* 4.2 30.7 - - + +
410A THR* 5.2 2.5 - - - +
414A HIS* 4.8 6.5 - - + -
415A THR 3.0 18.0 + - - +
416A GLU* 3.3 10.1 - - - +
417A GLU 3.1 0.2 - - - -
418A ASP* 1.3 76.1 - - - +
420A ASP* 1.3 55.8 + - - +
422A THR* 2.8 27.6 + - - -
423A LEU* 2.9 29.9 + - + +
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Residues in contact with ASP 420 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338A ARG* 2.9 27.0 + - - -
416A GLU* 3.0 19.0 + - - +
417A GLU* 3.7 9.7 - - - +
419A ILE* 1.3 78.8 - - - +
421A ALA* 1.3 63.5 + - - +
422A THR 3.1 0.2 + - - -
423A LEU* 3.1 16.6 + - - +
424A ALA* 2.9 25.0 + - - +
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Residues in contact with ALA 421 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A ILE* 4.2 13.9 - - + -
398A ILE* 4.3 4.6 - - + +
417A GLU 2.9 17.0 + - - +
418A ASP* 3.7 5.2 - - - +
420A ASP* 1.3 76.8 - - - +
422A THR* 1.3 60.8 - - - +
424A ALA* 3.7 7.8 - - - +
425A ALA* 3.3 21.1 + - - +
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Residues in contact with THR 422 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A ILE* 4.3 1.6 - - - +
63A TYR* 2.8 39.7 + - + +
339A LEU* 4.3 16.2 - - + -
343A LEU* 5.4 2.9 - - + -
393A MET* 3.9 9.9 - - + +
398A ILE* 3.7 25.6 - - + +
400A LEU* 6.0 0.4 - - + -
418A ASP 2.7 19.4 + - - -
419A ILE* 2.8 11.5 + - - -
421A ALA* 1.3 75.4 - - - +
423A LEU* 1.3 65.5 + - - +
425A ALA* 3.1 5.5 + - - +
426A ALA* 2.9 20.5 + - - +
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Residues in contact with LEU 423 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338A ARG* 4.5 14.1 - - + +
339A LEU* 3.9 23.3 - - + +
342A GLY* 3.9 34.1 - - - +
343A LEU* 3.9 5.4 - - + +
346A ILE* 3.4 12.6 - - + +
419A ILE* 2.9 31.1 + - + +
420A ASP* 3.1 21.5 + - - +
422A THR* 1.3 73.9 - - - +
424A ALA* 1.3 50.6 - - - +
426A ALA* 2.7 26.4 + - - +
427A ARG* 2.8 19.7 + - - +
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Residues in contact with ALA 424 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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420A ASP 2.9 15.8 + - - +
421A ALA* 3.7 9.2 - - - +
423A LEU* 1.3 76.0 - - - +
425A ALA* 1.3 56.7 + - - +
427A ARG* 3.3 12.4 + - - +
428A THR* 3.1 29.7 + - - -
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Residues in contact with ALA 425 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393A MET* 4.1 2.7 - - - -
396A GLN* 3.6 35.2 - - + +
398A ILE* 4.0 16.8 - - + -
421A ALA 3.3 10.8 + - - +
422A THR 3.1 9.0 + - - +
424A ALA* 1.3 76.2 - - - +
426A ALA* 1.3 61.3 + - - +
428A THR* 3.5 4.4 + - - -
429A VAL* 2.8 35.2 + - - +
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Residues in contact with ALA 426 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343A LEU* 3.7 29.6 - - + -
346A ILE* 4.0 10.5 - - + -
389A PHE* 4.9 2.9 - - + -
393A MET* 3.9 15.2 - - + -
422A THR 2.9 12.0 + - - +
423A LEU* 2.7 12.7 + - - +
425A ALA* 1.3 75.3 - - - +
427A ARG* 1.3 63.7 + - - +
429A VAL* 4.6 0.7 - - - +
430A MET* 3.0 36.5 + - + +
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Residues in contact with ARG 427 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346A ILE* 3.6 42.0 - - + +
349A GLU* 2.7 35.0 + - - +
350A THR* 4.6 5.4 - - + +
423A LEU* 2.8 11.9 + - - +
424A ALA* 3.4 14.8 - - - +
426A ALA* 1.3 79.0 - - - +
428A THR* 1.3 64.2 + - - +
430A MET* 3.3 0.9 + - - +
431A SER* 3.1 31.0 + - - +
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Residues in contact with THR 428 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396A GLN* 3.8 27.1 + - - +
424A ALA 3.1 12.1 + - - -
425A ALA* 3.7 11.7 - - - -
427A ARG* 1.3 81.2 - - - +
429A VAL* 1.3 62.8 + - - +
431A SER* 3.5 16.0 + - - -
432A ALA* 4.1 4.2 + - - +
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Residues in contact with VAL 429 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388A ARG 4.5 2.0 - - - +
389A PHE* 3.7 42.8 - - + +
392A GLY* 3.6 35.2 - - - +
393A MET* 3.7 11.7 - - - -
396A GLN* 4.3 10.5 - - + +
425A ALA* 2.8 24.0 + - - +
426A ALA 3.9 2.7 - - - +
428A THR* 1.3 76.8 - - - +
430A MET* 1.3 62.5 + - - +
432A ALA* 3.3 13.3 + - - +
433A LEU* 3.7 13.3 + - + +
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Residues in contact with MET 430 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343A LEU* 3.6 19.7 - - + +
346A ILE* 3.3 33.7 - - + -
347A ALA* 3.8 21.1 - - + +
350A THR* 3.6 19.4 - - + +
352A HIS* 3.3 25.6 - - - +
365A PHE* 4.7 5.4 - - + -
367A PHE* 4.3 19.3 - - - -
389A PHE* 4.2 15.7 - - + -
426A ALA* 3.0 31.2 + - + +
427A ARG 4.1 1.8 - - - +
429A VAL* 1.3 71.6 - - - +
431A SER* 1.3 65.2 + - - +
432A ALA 3.0 7.7 + - - -
433A LEU* 3.8 16.8 - - + +
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Residues in contact with SER 431 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350A THR* 4.1 15.7 - - - +
427A ARG* 3.1 19.9 + - - +
428A THR* 3.6 13.6 - - - -
429A VAL 3.3 0.6 - - - -
430A MET* 1.3 76.1 - - - +
432A ALA* 1.3 60.7 + - - +
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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