Contacts of the strand formed by residues 356 - 359 (chain B) in PDB entry 3K72
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 LEU 356 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85B LEU* 4.4 6.7 - - + -
352B LEU* 3.1 30.3 - - + +
353B PRO* 3.1 32.1 + - + +
354B ASP 3.0 1.7 - - - +
355B THR* 1.3 92.1 - - - +
357B LYS* 1.3 80.4 + - - +
358B VAL* 5.4 2.7 - - + -
393B VAL* 4.8 7.0 - - + -
394B THR 4.0 8.1 - - - +
395B ALA* 3.9 15.7 - - + +
396B THR* 5.5 0.4 - - - +
399B ILE* 3.8 29.4 - - + -
402B GLN* 5.3 4.3 - - + +
404B PHE* 5.3 15.3 - - + -
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Residues in contact with LYS 357 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352B LEU* 4.6 3.3 - - + +
354B ASP* 3.8 20.4 + - - +
356B LEU* 1.3 90.5 + - - +
358B VAL* 1.3 63.8 + - - +
359B THR* 5.3 3.2 - - + +
392B LYS 4.1 1.6 - - - +
393B VAL* 4.1 0.3 - - - +
394B THR* 3.3 37.3 + - - +
396B THR* 5.0 14.8 - - + -
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Residues in contact with VAL 358 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349B HIS* 4.1 14.0 - - + +
352B LEU* 3.2 31.2 - - + +
356B LEU* 5.4 1.3 - - + -
357B LYS* 1.3 77.2 - - - +
359B THR* 1.3 83.2 + - - +
360B TYR* 3.8 28.1 - - + +
374B PRO* 5.4 5.4 - - - +
391B VAL* 4.2 12.3 - - + -
392B LYS 4.0 3.6 - - - +
393B VAL* 4.2 22.2 - - + -
404B PHE* 4.9 10.1 - - + -
406B ILE* 5.4 2.2 - - + -
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Residues in contact with THR 359 (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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357B LYS* 5.3 3.1 - - + +
358B VAL* 1.3 85.4 - - - +
360B TYR* 1.3 79.6 + - - +
361B ASP* 5.2 0.5 + - - -
372B ASN* 5.2 5.7 + - + -
373B GLN* 4.9 10.8 - - - -
374B PRO* 5.0 4.7 - - + -
391B VAL* 3.7 2.6 - - - -
392B LYS* 3.2 47.8 + - - +
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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