Contacts of the helix formed by residues 306 - 315 (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 LYS 306 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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303B ARG 5.4 0.4 + - - -
305B VAL* 1.3 94.7 - - + +
307B THR* 1.3 60.9 + - - +
308B TYR 3.5 0.2 - - - -
309B GLU* 3.4 24.0 - - + +
310B LYS* 3.7 15.2 + - - +
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Residues in contact with THR 307 (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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409A GLN 4.3 3.5 + - - -
410A HIS* 3.1 34.2 - - - +
435A ILE* 3.2 25.3 - - - +
245B PHE* 3.9 4.8 - - + -
303B ARG 5.0 1.1 - - - +
304B MET* 3.1 54.0 - - + +
306B LYS* 1.3 78.1 - - - +
308B TYR* 1.3 64.9 + - + +
309B GLU 3.1 4.2 + - - -
310B LYS* 3.7 4.2 + - - +
311B LEU 3.6 1.9 + - - -
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Residues in contact with TYR 308 (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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239B PHE* 3.4 15.6 - + - -
241B THR* 3.3 22.2 - - - +
243B ASP 3.4 8.8 + - - -
244B GLY 3.8 5.5 + - - -
245B PHE* 4.0 22.9 - + - -
298B PHE* 3.7 41.1 - + + -
300B VAL* 3.3 36.1 - - + -
304B MET* 2.9 39.8 + - + +
305B VAL* 4.2 3.8 - - - +
307B THR* 1.3 80.5 - - + +
309B GLU* 1.3 59.4 + - - +
311B LEU* 3.2 20.9 + - + +
312B THR* 3.0 28.8 + - - -
320B VAL* 3.8 3.9 - - + +
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Residues in contact with GLU 309 (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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305B VAL* 3.1 17.3 + - + +
306B LYS* 3.4 22.0 - - + +
307B THR 3.1 0.2 - - - -
308B TYR* 1.3 75.9 - - - +
310B LYS* 1.3 67.6 + - + +
312B THR* 3.1 23.4 + - - +
313B GLU* 3.6 18.9 + - - +
320B VAL* 3.1 34.0 - - - +
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Residues in contact with LYS 310 (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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409A GLN* 5.7 2.4 + - - -
411A THR* 5.5 9.4 - - + +
435A ILE* 3.5 26.2 - - + +
306B LYS 3.7 14.0 + - - +
307B THR* 4.0 8.3 - - - +
308B TYR 3.4 0.4 - - - -
309B GLU* 1.3 81.5 - - + +
311B LEU* 1.3 61.4 + - - +
313B GLU* 3.4 27.7 - - + +
314B ILE* 3.9 2.4 + - - +
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Residues in contact with LEU 311 (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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435A ILE* 3.6 26.9 - - + +
215B LEU* 6.2 3.8 - - + -
245B PHE* 4.9 14.4 - - + -
282B VAL* 4.9 14.6 - - + +
298B PHE* 3.2 35.9 - - + -
307B THR 3.6 1.0 + - - -
308B TYR* 3.3 27.7 - - + +
309B GLU 3.1 0.6 - - - -
310B LYS* 1.3 78.9 - - - +
312B THR* 1.3 62.8 + - - +
314B ILE* 3.6 6.4 + - + -
315B ILE* 3.4 30.0 + - + +
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Residues in contact with THR 312 (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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298B PHE* 3.9 6.5 - - - -
308B TYR 3.0 14.0 + - - -
309B GLU* 3.1 15.6 + - - +
311B LEU* 1.3 76.1 - - - +
313B GLU* 1.3 67.7 + - - +
315B ILE 2.9 15.9 - - - +
318B SER* 3.2 23.3 + - - +
319B ALA* 5.2 0.4 - - - -
320B VAL* 3.2 22.0 - - + +
344B ARG* 2.9 37.9 + - - +
375B ARG* 5.6 0.7 + - - -
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Residues in contact with GLU 313 (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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309B GLU* 3.8 21.2 - - + +
310B LYS* 3.4 25.4 - - + +
312B THR* 1.3 82.6 - - - +
314B ILE* 1.3 70.2 + - + +
375B ARG* 4.2 13.9 + - - -
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Residues in contact with ILE 314 (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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434A GLN* 3.0 44.0 - - + +
435A ILE* 3.7 25.6 - - + -
465A TYR* 2.9 36.8 - - + +
466A GLU* 6.3 0.9 - - - -
282B VAL* 5.6 6.7 - - + +
286B ALA* 5.2 0.4 - - + +
310B LYS 3.9 2.0 + - - +
311B LEU* 3.6 10.4 + - + +
312B THR 3.3 0.6 - - - -
313B GLU* 1.3 88.4 - - + +
315B ILE* 1.3 69.5 + - + +
316B PRO* 3.6 3.1 - - - +
375B ARG* 3.9 9.4 + - - -
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Residues in contact with ILE 315 (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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282B VAL 6.1 0.2 - - - +
285B LEU* 4.3 6.7 - - + -
286B ALA* 3.7 28.7 - - + +
289B LEU* 3.6 31.6 - - + -
290B ALA* 6.1 0.7 - - + +
295B GLN* 4.7 4.0 - - - +
296B PRO* 5.3 2.9 - - + -
298B PHE* 4.5 8.1 - - + -
311B LEU* 3.4 27.1 + - + +
312B THR 2.9 20.8 - - - +
313B GLU 4.3 0.2 - - - +
314B ILE* 1.3 83.1 - - + +
316B PRO* 1.3 81.7 - - + +
318B SER* 3.3 21.8 + - - +
344B ARG* 4.2 0.2 + - - -
375B ARG* 4.9 0.2 + - - -
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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