Contacts of the helix formed by residues 449 - 458 (chain B) in PDB entry 4XHS
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 ARG 449 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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386B GLU* 3.1 37.4 + - - -
387B LEU* 3.9 13.2 - - + +
388B GLU* 4.3 3.6 + - - +
391B GLU* 2.9 43.9 + - - +
444B PHE* 2.8 30.0 + - + +
447B ILE* 4.2 7.9 - - + +
448B ASN* 1.3 82.3 - - - +
450B LYS* 1.3 58.9 + - - +
451B ASP* 2.9 44.9 + - - +
452B LEU* 3.0 35.3 + - + +
453B TRP 3.3 7.1 + - - -
455B ARG* 4.0 0.6 - - - +
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Residues in contact with LYS 450 (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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445B GLU* 3.7 46.1 + - + +
448B ASN* 3.6 22.0 + - - +
449B ARG* 1.3 77.1 - - - +
451B ASP* 1.3 57.2 + - - +
453B TRP* 3.2 12.6 + - + +
454B GLU* 2.8 41.0 + - - +
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Residues in contact with ASP 451 (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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448B ASN 4.7 0.3 - - - +
449B ARG* 2.9 51.5 + - - -
450B LYS* 1.3 79.2 + - - +
452B LEU* 1.3 57.8 + - - -
454B GLU* 3.4 12.5 + - - +
455B ARG* 2.9 55.7 + - + +
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Residues in contact with LEU 452 (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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383B TYR* 3.7 33.9 - - + +
386B GLU* 3.5 20.0 - - + +
387B LEU* 3.5 31.6 - - + -
441B LEU* 4.0 2.8 - - - +
444B PHE* 3.6 21.5 - - + -
449B ARG* 3.0 35.6 + - + +
451B ASP* 1.3 78.2 - - - +
453B TRP* 1.3 61.1 + - - +
455B ARG* 3.3 25.1 - - - +
456B GLY* 2.8 29.1 + - - -
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Residues in contact with TRP 453 (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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441B LEU* 3.2 41.7 - - + +
442B SER* 4.2 3.0 - - - +
444B PHE* 4.1 1.4 - - - +
445B GLU* 3.5 40.9 + - + +
449B ARG 3.3 4.5 + - - +
450B LYS* 3.2 19.7 + - + +
452B LEU* 1.3 80.5 - - - +
454B GLU* 1.3 90.4 + - + +
456B GLY* 3.7 0.5 - - - -
457B GLN* 2.9 71.2 + - + +
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Residues in contact with GLU 454 (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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450B LYS* 2.8 29.7 + - - +
451B ASP* 3.7 13.4 + - - +
452B LEU 3.3 0.2 - - - -
453B TRP* 1.3 96.7 - - + +
455B ARG* 1.3 64.6 + - + +
457B GLN* 3.3 13.2 + - - +
458B ARG* 3.3 29.0 + - - +
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Residues in contact with ARG 455 (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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383B TYR* 3.5 22.4 + - + +
386B GLU* 2.8 43.0 + - - -
449B ARG* 4.0 1.0 - - - +
451B ASP* 2.9 45.5 + - + +
452B LEU* 3.3 16.6 - - - +
454B GLU* 1.3 78.3 - - + +
456B GLY* 1.3 62.3 + - - +
458B ARG* 3.2 20.5 + - - +
459B GLU* 3.6 7.8 + - - +
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Residues in contact with GLY 456 (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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383B TYR* 3.7 17.2 + - - -
437B TRP* 3.5 20.1 + - - -
441B LEU* 3.8 11.1 - - - +
452B LEU 2.8 19.0 + - - -
453B TRP 3.7 0.9 - - - -
455B ARG* 1.3 78.4 - - - +
457B GLN* 1.3 60.9 + - - +
459B GLU* 3.1 20.1 + - - +
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Residues in contact with GLN 457 (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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441B LEU* 4.0 17.7 - - - +
453B TRP* 2.9 73.8 + - + +
454B GLU* 3.3 7.5 + - - +
456B GLY* 1.3 75.4 - - - +
458B ARG* 1.3 61.3 + - + +
459B GLU 3.3 6.0 + - - +
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Residues in contact with ARG 458 (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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454B GLU* 3.3 26.4 + - - +
455B ARG* 3.2 11.4 + - - +
456B GLY 3.1 1.4 - - - -
457B GLN* 1.3 78.4 - - + +
459B GLU* 1.3 64.3 + - - +
460B ASP* 3.4 9.2 - - - +
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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