Contacts of the helix formed by residues 336 - 343 (chain D) in PDB entry 6K71
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 ILE 336 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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239D ILE* 5.2 0.7 - - + -
240D LEU 4.3 18.2 - - - +
241D ALA* 4.9 4.9 - - - -
242D ASN 5.5 0.2 - - - -
243D GLY* 4.1 15.5 - - - +
274D LEU* 4.5 11.0 - - + -
324D PHE* 3.5 36.3 - - + -
331D ASN* 5.2 1.6 - - + -
332D ALA 3.4 16.4 - - - +
333D PRO 3.3 26.9 - - - +
334D SER 3.3 2.6 - - - -
335D TYR* 1.3 73.7 - - + +
337D TYR* 1.3 62.5 + - - +
338D ARG 3.2 0.9 - - - -
339D LEU* 3.1 17.4 + - + +
340D MET* 3.0 40.3 + - + +
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Residues in contact with TYR 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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288A LEU* 4.8 12.1 + - + +
290A VAL* 3.6 22.9 - - + -
291A LEU* 3.7 21.9 - - + +
292A THR* 4.2 24.2 - - + -
294A SER* 5.7 0.4 - - - +
295A ALA* 3.6 27.1 - - + -
298A ASP* 4.6 10.1 - - + +
241D ALA* 5.6 9.4 - - + +
334D SER 4.8 0.6 + - - -
335D TYR 2.8 4.1 + - - +
336D ILE* 1.3 79.3 - - - +
338D ARG* 1.3 57.8 + - - +
340D MET* 4.3 10.3 - - + +
341D SER* 2.7 54.8 + - - -
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Residues in contact with ARG 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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298A ASP* 5.1 10.6 + - - +
335D TYR* 3.2 36.5 + - + +
336D ILE 3.2 0.8 - - - -
337D TYR* 1.3 79.6 - - - +
339D LEU* 1.3 63.4 + - + +
341D SER* 3.1 25.5 + - - -
342D GLU* 3.0 43.5 + - - +
514G VAL* 4.9 1.8 - - + -
517G ARG* 3.1 58.1 - - - +
522G ASP* 5.4 5.1 + - - -
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Residues in contact with LEU 339 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271D MET* 4.9 14.6 - - + -
274D LEU* 5.8 5.2 - - + -
324D PHE* 5.8 4.0 - - + -
326D SER* 5.6 4.7 - - - +
328D ILE* 4.4 23.6 - - + -
331D ASN* 3.5 29.4 - - - +
335D TYR* 3.9 20.6 - - + -
336D ILE* 3.1 19.4 + - + +
338D ARG* 1.3 78.9 - - + +
340D MET* 1.3 74.1 + - + +
342D GLU* 3.2 3.9 + - - +
343D LEU* 2.9 40.7 + - + +
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Residues in contact with MET 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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241D ALA* 4.8 10.8 - - + -
271D MET* 6.4 0.4 - - + -
274D LEU* 3.6 38.8 - - + -
276D PRO* 4.7 13.7 - - + -
336D ILE* 3.0 28.8 + - + +
337D TYR* 3.3 16.0 + - + +
338D ARG 3.2 0.2 - - - -
339D LEU* 1.3 104.6 - - + +
341D SER* 1.3 60.9 + - - +
343D LEU* 4.0 13.9 - - + +
344D TYR* 3.2 55.6 + - + +
346D PRO* 5.2 3.5 - - - +
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Residues in contact with SER 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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87D LYS* 5.6 0.2 - - - -
337D TYR* 2.7 50.1 + - - -
338D ARG* 3.1 31.0 + - - -
340D MET* 1.3 79.0 - - - +
342D GLU* 1.3 63.5 + - - +
344D TYR 3.8 7.9 - - - +
345D HIS* 5.4 0.3 - - - -
346D PRO* 5.2 6.0 - - - +
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Residues in contact with GLU 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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87D LYS* 3.0 36.4 + - - +
338D ARG* 3.0 33.9 + - - +
339D LEU* 3.2 8.0 + - - +
341D SER* 1.3 80.7 - - - +
343D LEU* 1.3 73.3 + - + +
344D TYR 3.4 0.3 + - - -
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Residues in contact with LEU 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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84D ARG* 2.9 50.5 + - - +
87D LYS* 3.3 7.8 - - - +
271D MET* 3.8 44.9 - - + +
274D LEU* 6.2 0.2 - - + -
339D LEU* 2.9 36.5 + - + +
340D MET* 4.0 10.1 - - + -
342D GLU* 1.3 86.6 - - + +
344D TYR* 1.3 94.2 + - + +
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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