Contacts of the helix formed by residues 501 - 506 (chain A) in PDB entry 4LEY
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 PHE 501 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150A LEU* 4.8 12.1 - - + -
404A LEU* 4.5 8.7 - - + -
449A PHE* 4.0 20.2 - + - -
450A ASP* 5.7 1.1 - - - -
453A LEU* 3.5 33.4 - - + -
493A ILE 5.3 0.9 - - - -
496A GLU* 2.8 35.2 + - + +
497A ARG* 3.8 23.3 - - + -
500A GLY* 1.3 84.4 - - - +
502A PRO* 1.3 69.4 - - - +
503A ILE 3.3 2.6 + - - -
504A PHE* 3.6 45.6 + + + +
505A ASP* 3.4 9.4 - - - +
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Residues in contact with PRO 502 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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495A TYR* 4.3 17.7 - - + +
496A GLU* 3.1 23.3 - - - +
499A ASN* 4.0 13.7 - - + +
500A GLY 3.5 3.8 - - - +
501A PHE* 1.3 89.3 - - - +
503A ILE* 1.3 58.4 + - - +
505A ASP* 2.9 36.6 + - - +
506A LYS* 3.7 12.8 + - - +
464B LYS* 4.8 15.7 - - - +
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Residues in contact with ILE 503 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404A LEU* 4.0 13.2 - - + -
407A GLN* 2.7 58.5 + - + +
408A LEU* 3.6 30.5 - - + +
411A GLU* 3.6 18.6 - - - +
412A PHE* 5.7 0.4 - - + -
496A GLU* 3.1 32.1 + - - +
502A PRO* 1.3 75.1 - - - +
504A PHE* 1.3 73.6 + - + +
505A ASP 3.0 5.4 - - - -
506A LYS* 3.1 33.2 + - + +
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Residues in contact with PHE 504 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A LEU* 4.8 8.3 - - + -
153A VAL* 4.2 30.8 - - + +
156A LYS* 2.8 32.7 + - - +
400A LEU* 3.9 12.3 - - + -
403A TYR* 3.5 28.9 + + + -
404A LEU* 3.4 55.9 - - + -
407A GLN* 4.9 0.7 - - + -
449A PHE* 4.1 18.2 - + - -
501A PHE* 3.6 40.8 - + + +
502A PRO 3.1 0.4 - - - -
503A ILE* 1.3 84.6 - - + +
505A ASP* 1.3 56.9 + - - +
506A LYS 3.2 0.9 - - - -
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Residues in contact with ASP 505 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A VAL* 5.4 4.2 - - - +
156A LYS* 4.5 3.4 - - - +
500A GLY 4.6 2.8 - - - +
501A PHE 3.4 16.9 - - - +
502A PRO* 2.9 16.3 + - - +
504A PHE* 1.3 85.2 - - - +
506A LYS* 1.3 58.9 + - - +
458B GLU* 4.2 0.6 - - - +
461B ARG* 3.1 20.4 + - - -
462B THR* 4.5 10.3 - - + +
464B LYS* 6.0 1.9 - - - +
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Residues in contact with LYS 506 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156A LYS* 3.9 10.2 + - - -
407A GLN* 4.0 7.5 + - - +
410A LYS* 6.4 0.2 - - - -
411A GLU* 2.9 36.5 + - - +
496A GLU* 4.7 5.0 + - - -
502A PRO* 3.7 11.9 - - - +
503A ILE* 3.1 49.2 + - + +
504A PHE 3.2 1.2 - - - -
505A ASP* 1.3 81.4 - - - +
507A LEU* 1.3 81.2 + - - +
433B GLN* 4.8 10.9 + - - -
455B PHE* 6.6 0.4 - - - -
458B GLU* 4.1 23.6 - - + +
461B ARG* 4.2 5.6 - - - +
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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