Contacts of the helix formed by residues 419 - 425 (chain B) in PDB entry 2H5G
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 ALA 419 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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417B ARG 4.0 1.4 + - - -
418B LEU* 1.4 76.9 - - - +
420B ALA* 1.3 65.7 + - - +
421B PRO* 3.4 11.0 - - + -
422B LEU* 3.0 17.4 + - + +
423B LEU* 3.0 17.7 + - - -
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Residues in contact with ALA 420 (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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418B LEU 3.6 2.8 + - - -
419B ALA* 1.3 67.2 - - - +
421B PRO* 1.4 72.1 - - + +
423B LEU* 3.8 10.4 - - + +
424B LYS* 2.9 27.0 + - - +
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Residues in contact with PRO 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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419B ALA* 3.4 13.5 - - + -
420B ALA* 1.4 93.8 - - + +
422B LEU* 1.3 64.8 + - + +
424B LYS* 3.8 5.8 + - + +
425B ARG* 3.3 28.6 + - - +
608B TYR* 5.2 0.2 + - - -
610B ALA* 5.8 9.0 - - + -
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Residues in contact with LEU 422 (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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418B LEU* 3.9 29.8 - - + -
419B ALA* 3.0 17.9 + - + +
421B PRO* 1.3 82.2 - - + +
423B LEU* 1.3 66.5 + - - +
425B ARG* 3.2 5.7 + - - -
426B LEU* 3.4 1.7 + - - +
481B GLU* 3.7 45.5 - - + +
482B SER* 2.7 36.5 + - - -
483B ARG* 4.9 4.7 - - - +
508B GLU* 4.8 10.1 - - + +
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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
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411B LEU* 4.0 26.5 - - + +
414B ALA* 4.3 25.4 - - + +
415B GLU* 4.8 10.5 - - - +
416B GLY 5.0 2.9 - - - +
418B LEU* 3.7 29.8 - - + +
419B ALA 3.0 12.7 + - - +
420B ALA* 3.2 11.9 + - - +
422B LEU* 1.3 75.4 - - - +
424B LYS* 1.3 65.9 + - - +
426B LEU* 3.1 14.3 + - + +
427B SER* 4.2 3.8 + - - -
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Residues in contact with LYS 424 (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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420B ALA 2.9 16.2 + - - +
421B PRO* 4.2 6.1 - - + +
422B LEU 3.4 0.2 - - - -
423B LEU* 1.3 76.8 - - - +
425B ARG* 1.3 58.7 + - - +
426B LEU 3.5 0.9 + - - -
427B SER* 4.1 12.6 + - - +
607B GLU 5.2 2.6 + - - -
608B TYR* 3.5 48.3 + - + +
609B PRO* 4.5 11.5 - - - +
610B ALA* 5.6 3.8 - - + -
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Residues in contact with ARG 425 (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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303B SO4 3.6 26.3 + - - -
304B SO4 4.8 5.7 + - - -
421B PRO* 3.3 20.0 + - - +
422B LEU* 3.2 3.1 + - - +
423B LEU 3.1 0.8 - - - -
424B LYS* 1.3 76.3 - - - +
426B LEU* 1.3 58.8 + - - +
427B SER 3.6 4.4 - - - +
482B SER* 3.2 15.5 - - - +
483B ARG* 3.3 63.8 + - + +
484B PRO* 3.7 1.6 - - - +
485B ASP* 4.4 4.9 - - - +
608B TYR* 3.5 33.1 + - - +
610B ALA* 3.4 29.9 + - - +
611B ALA* 4.2 5.7 - - - +
612B CYS 4.6 2.4 - - - +
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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