Contacts of the helix formed by residues 414 - 420 (chain A) in PDB entry 5HG1
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 GLY 414 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229A ILE* 4.5 5.6 - - - -
230A VAL 3.0 16.2 - - - -
231A GLY* 4.0 3.6 - - - -
413A ASP* 1.3 91.5 + - - -
415A SER* 1.3 64.8 + - - -
417A TYR 3.1 3.3 + - - -
418A LYS* 3.1 26.5 + - - +
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Residues in contact with SER 415 (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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230A VAL 3.3 1.6 + - - -
231A GLY* 3.4 12.6 - - - -
232A THR* 4.3 11.4 + - - -
299A GLY* 6.2 0.7 - - - -
336A THR* 6.5 0.4 - - - -
414A GLY* 1.3 69.8 - - - -
416A VAL* 1.3 68.4 + - - +
418A LYS* 5.3 1.1 - - - -
419A LYS* 3.0 46.6 + - - +
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Residues in contact with VAL 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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230A VAL* 3.1 17.7 + - + +
231A GLY* 4.0 6.3 - - - +
298A SER 4.6 0.7 - - - -
299A GLY* 3.5 35.9 - - - +
302A MET* 4.6 14.4 - - - -
336A THR* 4.4 13.7 - - + -
382A SER* 5.1 0.7 - - - +
415A SER* 1.3 78.1 - - - +
417A TYR* 1.3 65.1 + - - +
420A HIS* 3.1 37.4 + - + +
423A PHE* 3.8 35.3 - - + +
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Residues in contact with TYR 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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230A VAL* 3.3 8.7 + - + +
412A VAL* 3.2 42.4 - - + -
413A ASP 3.9 11.4 - - - +
414A GLY 3.1 8.0 + - - +
416A VAL* 1.3 81.6 - - - +
418A LYS* 1.3 75.1 + - + +
420A HIS 4.0 6.8 - - - +
423A PHE* 3.9 19.7 - + + -
424A ALA* 3.6 36.7 + - + +
427A LEU* 4.1 14.8 - - + -
428A HIS* 2.6 33.7 + - - -
442A PHE* 3.5 12.6 - - - +
443A LEU 4.7 5.0 + - - -
444A ARG* 4.9 12.8 - - + -
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Residues in contact with LYS 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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412A VAL 4.5 0.2 - - - -
413A ASP* 3.3 28.8 + - - +
414A GLY 3.1 14.1 + - - +
415A SER* 4.4 0.9 - - - +
417A TYR* 1.3 87.7 - - + +
419A LYS* 1.3 67.6 + - + +
420A HIS 4.0 3.1 - - - +
444A ARG* 3.4 70.0 + - + +
445A SER 3.0 28.1 + - - -
446A GLU* 4.0 10.1 + - - +
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Residues in contact with LYS 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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337A LYS* 6.4 2.0 - - + -
340A SER* 4.5 8.9 - - - +
415A SER* 3.0 28.2 + - - +
418A LYS* 1.3 81.6 - - + +
420A HIS* 1.3 67.9 + - - +
421A PRO* 3.4 6.2 - - - +
444A ARG* 6.3 0.2 - - - +
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Residues in contact with HIS 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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302A MET* 5.4 2.0 - - + -
336A THR* 6.3 2.5 - - + -
339A ILE* 4.5 6.3 + - + +
340A SER* 3.7 26.4 + - - +
343A GLU* 2.6 30.7 + - - -
379A SER* 3.3 28.2 + - - -
415A SER 4.0 1.2 + - - -
416A VAL* 3.1 32.9 + - + +
417A TYR 4.0 6.9 - - - +
418A LYS 4.0 5.9 - - - +
419A LYS* 1.3 78.6 - - - +
421A PRO* 1.3 72.7 - - + +
422A HIS* 3.0 35.8 + - + -
423A PHE* 3.0 22.0 + - + +
424A ALA* 5.2 1.0 + - - +
426A ARG* 4.5 1.8 - - - -
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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