Contacts of the helix formed by residues 417 - 423 (chain P) in PDB entry 5X22
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 417 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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668N PRO 5.6 5.6 - - - -
669N ASN* 4.6 2.9 + - - -
353P GLU* 3.3 29.7 + - - +
356P LYS* 5.8 3.6 - - - +
412P GLU* 3.7 3.8 + - - +
415P THR* 3.6 31.2 + - - +
416P ARG* 1.3 74.5 - - - +
418P LEU* 1.3 74.0 + - + +
419P ARG 3.1 8.3 + - - -
420P ASP* 3.4 17.5 + - - +
421P PHE* 4.2 9.2 - - - -
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Residues in contact with LEU 418 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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774M LEU* 3.6 24.2 - - + +
777M ILE* 4.4 9.6 - - + -
778M PHE* 3.8 9.7 - - + -
350P LEU* 5.3 2.9 - - + -
353P GLU* 4.2 20.9 - - + +
354P LEU* 3.6 37.5 - - + +
357P ALA* 4.2 22.0 - - + -
412P GLU* 3.2 17.0 + - - +
415P THR* 5.7 0.2 - - - +
417P LYS* 1.3 89.3 - - + +
419P ARG* 1.3 65.8 + - - +
420P ASP 3.3 0.9 - - - -
421P PHE* 2.9 30.4 + - + +
422P LEU 3.9 1.6 + - - -
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Residues in contact with ARG 419 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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778M PHE* 3.4 37.8 - - - -
780M GLU* 5.4 4.4 - - - +
412P GLU* 3.7 10.6 + - - +
416P ARG* 4.6 10.8 - - + +
417P LYS 3.1 1.4 - - - -
418P LEU* 1.3 75.1 - - - +
420P ASP* 1.3 65.0 + - - +
422P LEU* 2.9 54.3 + - - +
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Residues in contact with ASP 420 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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668N PRO* 4.5 8.8 - - - +
669N ASN* 2.9 38.3 + - - +
671N LYS* 3.3 25.2 - - + +
672N ALA* 3.4 19.2 - - + +
675N ARG* 3.5 24.2 + - - +
416P ARG 4.3 7.4 - - - +
417P LYS 3.4 10.9 - - - +
418P LEU 3.3 0.6 - - - -
419P ARG* 1.3 78.8 - - - +
421P PHE* 1.3 61.0 + - + +
422P LEU 3.2 2.1 + - - -
423P ASP* 4.0 5.3 + - - -
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Residues in contact with PHE 421 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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774M LEU* 3.6 13.9 - - + +
669N ASN* 4.6 22.2 - - + -
671N LYS* 4.2 23.3 + - + +
346P THR* 4.0 10.8 - - + -
349P LEU* 3.7 18.2 - - + -
350P LEU* 3.5 57.0 - - + +
353P GLU* 3.9 28.7 - - + -
417P LYS 4.2 10.5 - - - -
418P LEU* 2.9 26.9 + - + +
420P ASP* 1.3 78.8 - - - +
422P LEU* 1.3 59.0 + - - +
423P ASP* 3.2 9.6 + - - +
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Residues in contact with LEU 422 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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728M HIS* 4.1 9.4 + - + -
774M LEU* 3.9 28.0 - - + +
775M ARG* 3.3 37.3 + - - +
778M PHE* 4.0 27.1 - - + -
780M GLU* 4.5 13.7 - - + -
418P LEU 3.9 2.4 + - - +
419P ARG* 2.9 43.7 + - - +
421P PHE* 1.3 77.7 - - - +
423P ASP* 1.3 70.7 + - - +
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Residues in contact with ASP 423 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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728M HIS* 3.2 44.9 - - + +
671N LYS* 2.9 32.3 + - - +
419P ARG 4.6 0.6 + - - -
420P ASP 4.0 6.7 + - - -
421P PHE 3.2 4.4 - - - +
422P LEU* 1.3 85.1 - - - +
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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