Contacts of the helix formed by residues 336 - 343 (chain D) in PDB entry 1K9I
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 336 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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295D LYS 5.5 3.8 - - - +
329D TRP* 5.0 2.2 - - - +
333D SER* 6.0 1.1 - - - -
334D PRO* 3.3 27.8 - - + +
335D LEU* 1.3 80.2 - - - +
337D PRO* 1.3 66.8 - - + +
338D SER* 3.1 19.5 - - - +
339D PHE* 2.9 44.5 + - + +
340D LYS* 3.9 1.6 + - - +
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Residues in contact with PRO 337 (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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335D LEU 3.9 3.1 - - - +
336D LEU* 1.3 85.8 - - + +
338D SER* 1.3 61.1 + - - +
339D PHE 3.1 1.3 + - - -
340D LYS* 3.2 49.2 + - + +
341D GLN 4.7 0.9 + - - -
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Residues in contact with SER 338 (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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336D LEU* 3.8 12.8 - - - +
337D PRO* 1.3 79.2 - - - +
339D PHE* 1.3 80.4 + - - +
340D LYS 3.4 0.2 - - - -
341D GLN* 2.8 34.5 + - - +
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Residues in contact with PHE 339 (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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294D ILE* 3.5 35.2 - - + -
295D LYS 3.8 25.1 - - - -
296D SER* 3.8 10.1 - - - -
297D ALA* 4.6 8.3 - - + -
329D TRP* 4.0 20.4 - + - -
335D LEU* 3.6 15.7 - - + -
336D LEU* 2.9 29.9 + - + +
338D SER* 1.3 96.1 - - - +
340D LYS* 1.3 62.7 + - - +
341D GLN 3.1 2.9 - - - -
342D TYR* 3.1 42.0 + + + +
364D TRP* 3.8 17.7 - + + -
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Residues in contact with LYS 340 (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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335D LEU* 4.4 21.1 - - + -
336D LEU 4.3 2.2 - - - +
337D PRO* 3.2 47.3 + - + +
339D PHE* 1.3 73.9 - - - +
341D GLN* 1.3 61.3 + - - +
342D TYR 3.0 6.1 + - - -
343D TRP* 3.3 33.2 + - + +
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Residues in contact with GLN 341 (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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337D PRO 4.7 0.8 + - - -
338D SER* 2.8 27.7 + - - +
340D LYS* 1.3 78.9 - - - +
342D TYR* 1.3 92.8 + - + +
343D TRP 3.3 8.1 + - - +
322H ASN* 4.2 17.2 + - - -
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Residues in contact with TYR 342 (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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297D ALA* 3.3 30.1 + - - +
300D GLN* 3.5 39.9 - - + +
301D ASN* 4.7 6.3 + - - -
338D SER 4.1 2.7 - - - -
339D PHE* 3.2 56.6 - + + +
340D LYS 3.0 1.0 - - - -
341D GLN* 1.3 103.3 + - + +
343D TRP* 1.3 60.0 + - - +
363D GLY* 3.3 9.8 - - - -
364D TRP* 2.8 48.8 + + + +
322H ASN* 6.0 2.9 - - - -
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Residues in contact with TRP 343 (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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318D LEU* 4.7 1.1 - - + -
327D TRP* 3.7 59.0 - + - -
335D LEU* 4.1 19.6 - - + +
339D PHE 4.8 1.3 - - - -
340D LYS* 3.3 33.2 + - + +
341D GLN 3.3 9.7 - - - +
342D TYR* 1.3 80.1 - - - +
344D ASN* 1.3 65.0 + - - +
347D GLU* 3.4 18.8 - - + +
348D PRO* 3.6 30.5 - - + +
357D ALA* 4.3 9.0 - - + -
363D GLY* 5.0 0.2 - - - -
364D TRP* 3.5 42.3 - + + -
365D ASN 4.0 5.2 - - - -
366D ASP* 3.9 21.1 - - + -
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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