Contacts of the helix formed by residues 419 - 428 (chain A) in PDB entry 3G0H
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 ASP 419 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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391A ASN* 5.0 3.5 + - - -
411A PRO* 2.7 29.7 + - - +
412A VAL 3.8 14.6 - - - +
413A ASP* 4.0 14.0 - - + +
417A ASN 3.1 2.1 + - - -
418A PRO* 1.3 67.7 - - - +
420A ASN* 1.3 62.9 + - - +
421A GLU* 3.4 14.1 - - - +
422A THR* 2.6 38.8 + - - +
423A TYR* 3.1 21.7 + - - +
455A ILE* 5.3 1.5 - - - +
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Residues in contact with ASN 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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418A PRO* 3.3 13.4 + - - +
419A ASP* 1.3 72.4 - - - +
421A GLU* 1.3 72.8 + - - +
423A TYR* 3.4 4.6 + - - +
424A LEU 3.3 10.2 + - - -
454A ARG 4.5 1.4 + - - +
455A ILE* 3.5 36.0 + - - +
458A HIS* 3.0 53.5 + - + +
459A PHE* 3.2 23.9 - - + -
477A GOL 4.8 0.2 - - - -
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Residues in contact with GLU 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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245A ASP* 4.5 5.8 - - - +
276A THR* 3.8 35.2 - - - +
278A GLU* 3.6 27.1 - - + +
395A ARG* 4.7 4.7 - - - +
419A ASP* 3.4 13.0 - - - +
420A ASN* 1.3 82.1 + - - +
422A THR* 1.3 64.3 + - - +
424A LEU* 3.2 5.2 + - - +
425A HIS* 3.0 30.5 + - + -
458A HIS* 4.7 2.1 + - - -
477A GOL 2.7 31.5 + - - +
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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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391A ASN* 3.2 37.9 + - - +
394A ALA* 4.1 7.4 - - + -
395A ARG* 4.3 10.3 + - - +
411A PRO* 4.0 5.6 - - + -
419A ASP* 2.6 34.9 + - - -
421A GLU* 1.3 77.3 - - - +
423A TYR* 1.3 52.9 + - - +
425A HIS* 3.2 8.9 + - - +
426A ARG* 2.7 47.1 + - + +
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Residues in contact with TYR 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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309A GLN* 2.5 34.1 + - - +
407A ASN* 3.6 14.6 - - - -
411A PRO* 3.6 21.7 - - + +
419A ASP 3.1 13.9 + - - +
420A ASN* 3.5 11.2 - - - +
421A GLU 3.2 0.2 - - - -
422A THR* 1.3 77.5 - - - +
424A LEU* 1.3 59.9 + - - +
426A ARG* 3.3 3.5 + - - +
427A ILE* 3.0 49.2 + - + +
439A ALA* 5.4 0.2 - - - +
441A ASN* 3.2 39.3 + - - -
452A LEU* 4.4 8.5 - - + -
455A ILE* 3.8 31.2 - - + -
459A PHE* 4.1 11.7 - + - -
463A ILE* 3.4 8.8 - - + +
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Residues in contact with LEU 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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139A GLN* 5.7 0.4 - - - -
140A SER* 3.4 20.4 + - - +
275A ALA* 4.1 23.6 - - + +
276A THR* 3.9 18.8 - - + -
302A GLU* 3.4 35.7 - - + +
303A THR* 5.4 2.7 - - + -
420A ASN 3.3 1.4 + - - +
421A GLU 3.2 8.8 + - - +
423A TYR* 1.3 79.2 - - - +
425A HIS* 1.3 62.1 + - - +
427A ILE* 3.5 14.2 - - + +
428A GLY 3.1 20.4 + - - -
459A PHE* 3.6 34.8 - - + -
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Residues in contact with HIS 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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1A ANP 4.4 4.2 + - - -
140A SER* 4.9 1.5 + - - -
243A GLU* 3.4 26.8 + - - -
274A SER* 3.9 0.7 - - - -
275A ALA* 3.5 35.7 - - + +
276A THR* 2.7 27.3 + - + +
394A ALA 3.1 16.4 - - - +
395A ARG* 3.3 36.8 + - + +
421A GLU 3.0 23.9 + - - -
422A THR* 3.7 6.3 - - - +
424A LEU* 1.3 75.3 - - - +
426A ARG* 1.3 65.2 + - - +
428A GLY* 3.0 7.1 + - - -
429A ARG* 2.5 28.4 + - - +
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Residues in contact with ARG 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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339A PHE* 3.4 40.3 - - + +
340A CYS 3.6 24.0 + - - -
341A HIS* 4.6 4.8 - - - +
391A ASN* 2.8 31.9 + - - +
394A ALA* 3.4 18.4 + - + -
405A VAL* 3.5 13.6 - - - +
407A ASN* 3.3 24.5 + - - +
409A ASP 2.9 26.9 + - - -
410A LEU 5.0 0.2 - - - -
411A PRO* 3.7 28.7 - - - +
422A THR* 2.7 27.6 + - - +
423A TYR 3.5 4.3 - - - +
425A HIS* 1.3 71.9 - - - +
427A ILE* 1.3 62.8 + - + +
429A ARG* 3.1 20.1 + - - +
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Residues in contact with ILE 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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303A THR* 5.8 5.2 - - + -
307A ILE* 3.0 29.5 - - + +
309A GLN* 3.7 32.1 - - + +
405A VAL* 4.2 9.2 - - + -
407A ASN* 4.3 9.9 - - - +
423A TYR* 3.0 47.5 + - + +
424A LEU* 3.5 16.6 - - + +
426A ARG* 1.3 74.9 - - - +
428A GLY* 1.3 57.6 + - - +
429A ARG 3.2 1.1 - - - -
430A THR* 3.1 17.4 - - - +
439A ALA* 3.5 26.7 - - + -
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Residues in contact with GLY 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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140A SER* 3.4 30.9 - - - -
307A ILE* 3.9 7.0 - - - -
424A LEU 3.1 6.4 + - - -
425A HIS 3.0 9.8 + - - -
426A ARG 3.0 1.8 - - - -
427A ILE* 1.3 74.0 - - - +
429A ARG* 1.3 54.6 + - - +
430A THR 3.1 8.8 + - - +
432A ARG* 2.7 35.3 + - - +
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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