Contacts of the helix formed by residues 393 - 397 (chain K) in PDB entry 4KRM
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 393 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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381K LEU* 6.1 0.7 - - + -
383K ILE* 4.1 18.2 - - + -
386K TRP* 3.7 39.3 - - + +
392K ASP* 1.3 70.7 - - - +
394K HIS* 1.3 63.6 + - - +
395K ALA 3.2 3.4 - - - -
396K PHE* 3.1 21.0 + - + -
397K GLU 3.8 3.5 + - - -
414K LEU* 6.1 0.2 - - + -
416K VAL* 4.1 26.5 - - + -
419K LEU* 4.2 16.4 - - + -
421K ILE* 4.3 9.0 - - + -
424K LEU* 3.1 31.2 + - + +
425K GLY 4.3 4.4 - - - +
426K LEU* 4.2 20.9 - - + +
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Residues in contact with HIS 394 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369K ASP* 4.0 19.5 - - - +
372K LYS* 5.4 1.5 - - + +
386K TRP* 4.2 2.7 - - + -
390K ARG* 6.1 2.2 - - + -
392K ASP* 2.6 31.5 + - - +
393K LEU* 1.3 73.0 - - - +
395K ALA* 1.3 57.6 + - - +
396K PHE 3.1 0.4 - - - -
397K GLU* 3.1 60.7 + - - +
425K GLY 5.5 0.7 - - - -
427K ARG* 5.2 6.6 + - - +
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Residues in contact with ALA 395 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368K LEU* 3.2 34.5 - - + +
369K ASP* 4.2 12.3 - - - +
371K LEU* 3.1 32.7 - - + +
372K LYS* 3.4 11.8 - - - +
386K TRP* 4.2 20.7 - - + -
393K LEU 3.2 1.2 - - - -
394K HIS* 1.3 79.5 - - - +
396K PHE* 1.3 57.7 + - + +
397K GLU 3.4 1.3 - - - -
398K ASN 5.1 0.2 + - - -
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Residues in contact with PHE 396 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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345K LEU* 3.8 21.5 - - + -
347K ILE* 4.1 13.9 - - + -
371K LEU* 3.9 29.4 - - + -
374K VAL* 5.1 5.8 - - + -
377K ILE* 4.4 5.2 - - + -
381K LEU* 3.7 25.8 - - + -
383K ILE* 3.8 26.7 - - + -
386K TRP* 4.1 15.9 - + - -
393K LEU* 3.1 10.1 + - + +
394K HIS 3.1 0.6 - - - -
395K ALA* 1.3 80.2 - - - +
397K GLU* 1.3 56.1 + - - +
398K ASN 3.0 10.9 + - - -
399K LEU* 3.1 39.5 + - + +
426K LEU* 3.6 30.7 - - + +
428K SER* 4.4 0.2 + - - -
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Residues in contact with GLU 397 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372K LYS* 4.9 8.1 - - + +
393K LEU 3.8 0.6 + - - -
394K HIS* 3.1 52.6 + - - +
395K ALA 3.4 2.2 - - - -
396K PHE* 1.3 74.7 - - - +
398K ASN* 1.3 75.8 + - - +
425K GLY 3.8 19.5 - - - +
427K ARG* 3.5 36.1 + - - +
428K SER* 2.3 23.8 + - - -
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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
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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