Contacts of the helix formed by residues 278 - 291 (chain B) in PDB entry 3KJR
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 ALA 278 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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276B LYS 4.0 1.6 + - - -
277B VAL* 1.3 71.6 - - - +
279B LEU* 1.3 65.3 + - - +
280B ARG* 3.2 3.4 - - + -
281B SER* 3.2 21.5 + - - +
282B ILE* 3.3 16.4 + - - +
423B PHE* 3.9 17.7 - - + -
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Residues in contact with LEU 279 (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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269B PHE* 4.3 7.9 - - + -
271B LEU* 4.1 31.4 - - + -
277B VAL 2.9 9.9 + - - +
278B ALA* 1.3 71.8 - - - +
280B ARG* 1.3 61.6 + - - +
282B ILE* 3.1 14.4 + - + +
283B ILE* 3.0 47.1 + - + +
430B ILE* 4.5 6.7 - - + -
494B ILE 5.5 0.4 - - - +
496B VAL* 3.6 43.1 - - + +
499B TYR* 5.9 1.6 - - + -
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Residues in contact with ARG 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B ALA 3.2 1.6 + - - -
279B LEU* 1.3 79.2 - - - +
281B SER* 1.3 62.5 + - - +
283B ILE* 3.4 2.9 + - - +
284B GLU* 3.0 40.7 + - - +
302B LYS* 2.8 26.2 + - - +
303B ASN* 3.1 33.9 + - - +
304B VAL* 3.9 13.0 - - - +
491B ILE* 3.7 23.1 - - + -
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Residues in contact with SER 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B ALA* 3.2 18.3 + - - +
280B ARG* 1.3 82.4 + - - +
282B ILE* 1.3 58.3 + - - +
284B GLU* 3.9 0.7 - - - +
285B GLU* 2.9 31.7 + - - +
303B ASN 5.2 0.3 + - - -
304B VAL* 3.9 35.2 - - - +
305B ARG 5.5 0.2 + - - -
306B ILE* 4.5 6.4 - - - +
423B PHE* 3.9 20.0 - - - -
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Residues in contact with ILE 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B LEU* 4.1 1.6 - - + -
277B VAL* 3.6 31.6 - - + -
278B ALA 3.3 8.5 + - - +
279B LEU* 3.1 14.5 + - + +
281B SER* 1.3 77.6 - - - +
283B ILE* 1.3 64.1 + - - +
285B GLU* 3.4 6.5 + - - +
286B LEU* 3.0 21.7 + - - +
423B PHE* 3.5 38.6 - - + +
426B ALA* 3.8 23.1 - - + -
427B SER* 3.8 33.9 + - - +
430B ILE* 4.3 11.0 - - + -
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Residues in contact with ILE 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B LEU* 3.0 41.8 + - + +
280B ARG* 5.0 0.9 - - - -
282B ILE* 1.3 74.0 - - - +
284B GLU* 1.3 64.7 + - - +
286B LEU* 3.1 7.7 + - + +
287B LEU* 2.9 30.0 + - + +
430B ILE* 3.9 22.2 - - + -
491B ILE* 3.7 31.9 - - + -
494B ILE* 3.7 55.6 - - + +
496B VAL* 5.6 0.4 - - + -
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Residues in contact with GLU 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B ARG* 3.0 28.5 + - - +
283B ILE* 1.3 76.0 - - - +
285B GLU* 1.3 62.9 + - - +
287B LEU* 3.4 15.0 + - - +
288B TRP* 3.1 23.7 + - - +
299B LEU* 3.9 9.9 - - + +
302B LYS* 3.8 38.9 + - + +
304B VAL* 4.0 24.7 - - + -
491B ILE* 3.6 33.7 - - + +
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Residues in contact with GLU 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B SER 2.9 18.2 + - - +
282B ILE* 3.7 5.8 - - - +
284B GLU* 1.3 74.7 - - - +
286B LEU* 1.3 58.0 + - - +
288B TRP* 3.2 8.4 + - + +
289B PHE* 3.0 57.9 + - + -
299B LEU* 4.1 12.4 - - + +
306B ILE* 3.6 22.2 - - + +
307B TRP* 2.9 29.9 + - + +
394B HIS* 5.2 2.6 + - - -
423B PHE* 4.2 15.0 - - - +
427B SER* 4.7 8.7 + - - -
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Residues in contact with LEU 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B ILE 3.0 18.0 + - - +
283B ILE* 3.1 5.1 + - + +
285B GLU* 1.3 78.1 + - - +
287B LEU* 1.3 62.8 + - + +
289B PHE* 3.2 9.6 + - + +
290B ILE* 2.9 32.1 + - + +
337B TRP* 4.0 27.1 - - + -
427B SER* 3.6 37.0 - - - +
430B ILE* 3.6 31.0 - - + -
431B LEU* 3.9 18.2 - - + +
434B MET* 4.2 11.2 - - + -
494B ILE* 5.9 0.4 - - + -
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Residues in contact with LEU 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B ILE* 2.9 30.3 + - + +
284B GLU* 3.8 20.6 - - - +
286B LEU* 1.3 75.7 - - + +
288B TRP* 1.3 56.6 + - - +
290B ILE* 3.3 13.1 + - + +
291B LYS* 3.0 28.6 + - - +
434B MET* 4.1 13.9 - - + -
486B ILE 5.7 0.7 - - - +
489B PHE* 3.6 20.4 - - + +
490B THR* 3.9 5.8 - - - -
491B ILE* 3.7 26.0 - - - +
494B ILE* 4.0 17.5 - - + -
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Residues in contact with TRP 288 (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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284B GLU 3.1 13.4 + - - +
285B GLU* 3.3 9.9 - - + +
287B LEU* 1.3 73.4 - - - +
289B PHE* 1.3 102.7 + + - +
291B LYS* 3.4 5.3 + - - +
292B GLY 3.3 3.1 + - - -
293B SER* 3.1 62.4 + - - +
294B THR 4.2 0.9 - - - -
295B ASN 3.0 30.1 + - - -
296B GLY* 4.2 0.9 - - - -
298B ASP* 3.7 17.4 - - + +
299B LEU* 3.7 34.0 - - + +
307B TRP* 3.7 18.6 - + - -
329B LEU* 3.6 22.9 - - + -
332B ILE* 3.6 23.6 - - + -
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Residues in contact with PHE 289 (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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285B GLU* 3.0 47.7 + - + -
286B LEU* 3.2 15.9 + - + +
288B TRP* 1.3 106.6 - + - +
290B ILE* 1.3 63.3 + - - +
292B GLY* 2.9 15.4 + - - -
307B TRP* 4.5 0.7 - + - -
332B ILE* 5.4 0.2 - - + -
333B TYR* 3.6 40.6 - + + -
334B GLY* 3.5 17.3 - - - +
337B TRP* 3.5 40.5 - + + -
338B ARG* 4.3 1.7 - - - +
394B HIS* 3.4 23.6 - + - -
427B SER* 4.8 7.0 - - - -
428B TYR* 6.2 0.2 - + - -
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Residues in contact with ILE 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B LEU* 2.9 30.0 + - + +
287B LEU* 3.6 15.0 - - + +
288B TRP 3.3 0.2 - - - -
289B PHE* 1.3 77.0 - - - +
291B LYS* 1.3 56.3 + - - +
292B GLY 3.2 0.9 + - - -
337B TRP* 4.2 14.6 - - + -
338B ARG* 2.6 35.5 + - - -
359B LEU* 4.3 20.9 - - + -
431B LEU* 4.3 3.1 - - + -
434B MET* 3.7 34.5 - - + -
486B ILE* 4.0 29.4 - - + +
487B GLU* 4.2 17.9 - - + -
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Residues in contact with LYS 291 (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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287B LEU 3.0 16.3 + - - +
288B TRP* 3.4 7.1 + - - +
289B PHE 3.2 0.4 - - - -
290B ILE* 1.3 76.5 - - - +
292B GLY* 1.3 62.0 + - - +
293B SER* 4.6 6.6 - - - +
338B ARG* 4.4 6.5 + - - +
339B HIS* 5.9 0.7 + - - -
487B GLU* 5.3 4.0 - - - -
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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