Contacts of the strand formed by residues 401 - 404 (chain D) in PDB entry 4LQL
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 401 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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394D SER* 3.1 28.6 + - - +
396D PHE* 4.6 14.8 - - + -
399D GLY 5.2 0.2 - - - +
400D TYR* 1.3 80.3 - - - +
402D PHE* 1.3 65.4 + - - +
403D ILE* 3.2 7.3 + - + +
443D GLY* 5.9 0.9 - - - -
469D ASP* 3.8 26.9 - - + -
471D ILE* 4.1 25.6 - - + -
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Residues in contact with PHE 402 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391D ILE* 4.8 13.5 - - + -
392D THR 3.6 11.7 - - - -
393D LEU* 3.5 35.5 - - + +
400D TYR 4.1 0.6 - - - -
401D LYS* 1.3 71.3 - - - +
403D ILE* 1.3 61.3 + - - +
404D GLY* 4.0 1.3 - - - -
463D ALA* 5.3 9.0 - - + -
468D VAL* 5.5 3.0 - - + +
469D ASP 3.3 12.7 + - - +
470D PHE* 3.1 19.5 - + + -
471D ILE* 2.8 23.7 + - - +
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Residues in contact with ILE 403 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391D ILE* 4.2 0.3 - - - -
392D THR* 3.1 29.1 + - - +
394D SER* 5.4 0.2 - - - +
401D LYS* 3.2 7.7 + - + +
402D PHE* 1.3 73.7 - - - +
404D GLY* 1.3 58.8 + - - +
438D GLN 4.8 7.6 - - - +
439D TRP* 3.9 24.1 - - + -
442D TYR* 3.8 24.2 - - + +
443D GLY* 5.3 1.1 - - - -
444D GLY* 4.4 19.1 - - - +
471D ILE* 3.4 29.2 - - + +
473D ILE* 5.2 2.0 - - + -
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Residues in contact with GLY 404 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390D ASP 3.8 8.5 - - - -
391D ILE* 4.9 3.8 - - - -
402D PHE* 4.0 2.6 + - - -
403D ILE* 1.3 76.6 - - - +
405D TYR* 1.3 61.2 - - - -
439D TRP* 4.7 1.6 - - - -
470D PHE* 5.2 4.6 - - - -
471D ILE 2.5 17.6 + - - +
472D ASN* 3.1 11.0 - - - -
473D ILE* 2.9 29.9 + - - +
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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
------------------------------------------------------------
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