Contacts of the helix formed by residues 406 - 414 (chain B) in PDB entry 4XK8
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 ASN 406 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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315B LEU 4.5 2.0 - - - -
317B ARG* 4.4 3.1 - - + +
318B GLY 3.2 19.5 - - - +
319B HIS* 4.9 0.4 - - - -
320B LYS 3.6 23.8 + - - +
322B LEU* 3.9 14.1 - - - +
403B ASN* 2.9 52.3 + - - +
404B ALA 3.0 5.9 + - - +
405B ASP* 1.3 79.5 - - - +
407B VAL* 1.3 60.4 + - + +
408B LEU* 2.9 16.8 + - - +
409B ALA* 3.0 8.2 + - - +
410B ARG* 2.9 29.7 + - - +
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Residues in contact with VAL 407 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315B LEU* 4.4 25.1 - - + +
318B GLY* 2.9 28.9 + - - +
319B HIS* 4.2 18.4 - - + +
322B LEU* 3.8 28.3 - - + -
406B ASN* 1.3 72.7 - - - +
408B LEU* 1.3 60.2 + - + +
410B ARG* 3.8 6.0 - - - +
411B MET* 2.9 33.0 + - - +
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Residues in contact with LEU 408 (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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322B LEU* 4.6 11.0 - - + -
325B THR* 4.9 1.3 - - - +
332B PHE* 4.1 17.9 - - + -
393B PHE* 3.5 34.3 - - + -
394B PHE* 4.0 23.3 - - + -
398B TYR* 3.7 19.7 - - + -
403B ASN* 4.2 9.9 - - - +
406B ASN* 2.9 12.2 + - - +
407B VAL* 1.3 80.9 - - + +
409B ALA* 1.3 65.1 + - - +
411B MET* 3.0 12.8 + - + +
412B LEU* 3.0 23.6 + - - +
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Residues in contact with ALA 409 (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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398B TYR* 3.5 20.8 + - - +
400B PRO 5.2 1.3 - - - +
403B ASN 3.2 25.4 - - - +
404B ALA* 4.7 0.9 - - - -
405B ASP* 3.9 13.7 - - - +
406B ASN* 3.0 5.8 + - - +
408B LEU* 1.3 76.3 - - - +
410B ARG* 1.3 58.7 + - - +
412B LEU* 3.1 8.1 + - - +
413B GLU* 2.9 33.2 + - + +
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Residues in contact with ARG 410 (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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313B GLY 3.2 15.6 + - - -
314B ARG* 2.8 33.5 + - - +
315B LEU* 3.8 18.6 - - - +
316B GLY* 3.3 12.4 - - - +
405B ASP* 2.9 29.8 + - - +
406B ASN 2.9 19.3 + - - +
407B VAL* 3.8 6.5 - - - +
409B ALA* 1.3 76.9 - - - +
411B MET* 1.3 59.4 + - - +
413B GLU* 3.2 34.1 + - - +
414B HIS* 2.9 24.3 + - + -
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Residues in contact with MET 411 (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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394B PHE* 5.7 4.0 - - + -
407B VAL* 2.9 19.8 + - - +
408B LEU* 3.0 22.6 + - + +
410B ARG* 1.3 78.8 - - - +
412B LEU* 1.3 60.0 - - + +
413B GLU 3.3 0.7 + - - -
414B HIS* 3.7 17.4 + - + +
415B LYS* 3.6 15.1 + - - +
418B ILE* 3.7 30.7 - - + +
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Residues in contact with LEU 412 (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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394B PHE* 3.9 39.5 - - + -
398B TYR* 3.7 35.2 - - + +
408B LEU 3.0 9.0 + - - +
409B ALA* 3.1 8.5 + - - +
411B MET* 1.3 75.4 - - - +
413B GLU* 1.3 63.1 + - - +
415B LYS* 3.5 34.1 - - + +
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Residues in contact with GLU 413 (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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405B ASP* 4.6 10.2 + - - +
409B ALA* 2.9 19.9 + - + +
410B ARG* 3.3 34.9 + - - +
411B MET 3.1 0.4 - - - -
412B LEU* 1.3 80.9 - - - +
414B HIS* 1.3 60.1 + - + +
415B LYS 3.3 2.8 + - - -
416B GLU* 3.6 10.2 - - - +
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Residues in contact with HIS 414 (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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709A TRP* 6.1 3.1 - - + -
410B ARG* 2.9 27.9 + - + -
411B MET* 3.7 24.6 + - - +
413B GLU* 1.3 77.4 - - + +
415B LYS* 1.3 63.2 + - - +
416B GLU* 3.2 4.7 - - - -
417B ALA* 3.1 27.2 + - + +
418B ILE* 3.3 28.4 + - + +
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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