Contacts of the helix formed by residues 419 - 425 (chain B) in PDB entry 2H3W
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 LYS 419 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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418B GLY* 1.3 69.9 - - - -
420B ASP* 1.3 66.0 + - - +
422B PRO* 3.5 1.6 - - - +
423B LYS* 3.0 40.1 + - - +
429B PRO* 3.9 23.3 - - + +
580B PRO* 3.6 34.2 + - + +
581B MET* 2.9 24.4 + - - +
582B GLU* 3.1 15.4 + - - +
1701B COA 2.7 47.7 + - - +
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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
----------------------------------------------------------
417B PHE* 3.5 11.1 - - - +
418B GLY 3.0 18.0 + - - +
419B LYS* 1.3 78.1 - - - +
421B PHE* 1.3 73.0 + - - -
423B LYS* 3.7 4.6 - - - +
424B SER* 2.9 30.5 + - - -
582B GLU* 3.0 38.0 + - + +
583B ALA* 3.5 17.0 - - - +
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Residues in contact with PHE 421 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417B PHE* 3.8 20.6 - + + -
420B ASP* 1.3 81.5 + - - +
422B PRO* 1.3 77.7 - - + +
424B SER* 2.6 27.1 + - - -
425B GLU* 3.0 34.3 + - + +
432B PHE* 3.9 14.8 - + - -
615B ARG* 3.5 59.7 - - + +
618B LEU* 3.6 23.6 - - + -
619B GLN* 3.7 20.2 - - + -
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Residues in contact with PRO 422 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417B PHE* 4.2 4.3 - - + -
418B GLY 2.9 29.2 - - - +
419B LYS 3.5 3.8 - - - +
421B PHE* 1.3 92.2 - - + +
423B LYS* 1.3 59.9 + - - +
425B GLU* 3.1 8.5 + - + +
427B LEU* 2.7 43.5 + - + +
429B PRO* 3.6 25.4 - - + +
432B PHE* 3.9 33.4 - - + -
433B ILE* 6.0 1.3 - - + -
585B ILE* 6.4 0.4 - - + -
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Residues in contact with LYS 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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419B LYS* 3.0 35.6 + - - +
420B ASP* 3.7 3.4 - - - +
422B PRO* 1.3 78.9 - - - +
424B SER* 1.3 55.3 + - - +
426B LYS* 2.7 29.3 + - - +
427B LEU 3.8 0.2 - - - -
429B PRO* 3.8 5.2 - - + -
582B GLU* 3.2 26.5 + - - -
1701B COA 3.3 81.1 + - + +
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Residues in contact with SER 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 ASP 2.9 14.4 + - - -
421B PHE* 2.6 32.5 + - - -
423B LYS* 1.3 75.8 - - - +
425B GLU* 1.3 63.5 + - - +
426B LYS* 3.2 9.7 + - - +
623B ARG* 5.0 1.6 + - - -
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Residues in contact with GLU 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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421B PHE* 3.0 43.7 + - + +
422B PRO 3.5 9.4 - - - +
423B LYS 3.0 1.0 - - - -
424B SER* 1.3 81.2 + - - +
426B LYS* 1.3 72.1 + - - +
427B LEU* 3.3 22.1 + - + +
497B ARG* 4.4 6.6 + - - -
618B LEU* 4.0 34.8 - - + +
619B GLN* 4.9 3.1 + - - +
622B PRO* 6.1 1.4 - - - +
623B ARG* 3.3 31.6 + - - +
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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