Contacts of the helix formed by residues 282 - 295 (chain B) in PDB entry 4LXZ
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 THR 282 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239B ASP* 2.5 36.1 + - - +
271B LEU* 3.5 8.8 - - - +
281B LEU* 1.3 76.9 - - - +
283B VAL* 1.3 63.5 + - - +
284B LYS* 3.3 17.8 + - - +
285B GLY 3.3 1.7 + - - -
286B HIS* 3.1 17.5 + - - +
349B HIS* 6.3 0.2 - - - -
350B ILE* 3.4 31.9 - - - +
351B SER 4.2 0.4 - - - -
352B PRO* 3.7 32.8 - - + -
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Residues in contact with VAL 283 (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 13.5 - - + -
282B THR* 1.3 72.8 - - - +
284B LYS* 1.4 57.5 + - - +
286B HIS* 3.4 2.8 + - - +
287B ALA* 2.8 28.6 + - + +
312B ASN 4.4 0.7 - - - +
315B ARG* 4.1 13.5 - - + +
316B CYS* 3.8 37.0 - - + +
319B TYR* 3.7 35.0 - - + -
320B GLU* 4.7 0.2 - - - +
348B LEU* 4.5 6.1 - - + +
349B HIS* 4.0 14.8 + - + +
350B ILE* 3.8 21.2 - - + +
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Residues in contact with LYS 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B ASP* 4.8 2.2 - - - +
282B THR* 3.2 9.5 + - - +
283B VAL* 1.4 77.7 - - - +
285B GLY* 1.3 56.5 + - - +
287B ALA* 3.7 0.7 - - - +
288B LYS* 2.9 30.1 + - - +
291B GLU* 5.1 2.1 - - - +
319B TYR* 4.5 13.2 - - + +
349B HIS* 3.6 26.6 + - + +
406B PG4 2.8 107.5 + - - +
67C GLU* 4.3 2.6 - - - +
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Residues in contact with GLY 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B ASP* 3.2 33.3 + - - -
242B TYR* 5.0 5.9 - - - +
281B LEU* 4.9 6.1 - - - -
282B THR* 3.3 8.3 + - - -
284B LYS* 1.3 75.7 - - - +
286B HIS* 1.3 65.9 + - - +
288B LYS* 3.5 16.9 - - - +
289B CYS* 4.0 8.7 + - - -
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Residues in contact with HIS 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180B ILE* 3.4 24.6 - - + +
266B CYS 3.3 22.7 - - - -
267B GLY 2.8 22.2 + - - -
268B ALA* 3.9 1.4 - - - -
270B SER* 3.2 20.5 + - - -
271B LEU* 3.7 21.8 - - + -
281B LEU* 4.3 13.8 - - + +
282B THR 3.1 15.4 + - - +
283B VAL 3.7 3.8 - - - +
285B GLY* 1.3 76.8 - - - +
287B ALA* 1.4 61.0 + - - +
289B CYS* 3.1 25.7 + - - +
290B VAL 4.1 0.3 + - - -
316B CYS* 3.2 15.7 - - - -
320B GLU* 2.5 35.2 + - - +
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Residues in contact with ALA 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B VAL 2.8 21.5 + - - +
284B LYS 4.0 1.6 - - - +
286B HIS* 1.4 68.5 - - - +
288B LYS* 1.3 64.8 + - - +
290B VAL* 2.9 16.3 + - - +
291B GLU* 3.1 15.7 + - - +
319B TYR* 3.4 32.8 - - + -
320B GLU* 3.2 26.4 + - + -
323B VAL* 4.2 6.6 - - + +
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Residues in contact with LYS 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243B GLY* 5.4 12.6 - - - -
246B PHE* 5.4 0.2 - - - -
247B LYS* 5.5 10.1 - - - +
284B LYS 2.9 17.6 + - - +
285B GLY* 3.5 12.3 - - - +
286B HIS 3.2 0.6 - - - -
287B ALA* 1.3 74.9 - - - +
289B CYS* 1.3 57.2 + - - +
291B GLU* 3.2 32.9 + - - +
292B VAL* 2.9 52.6 + - + +
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Residues in contact with CYS 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180B ILE* 3.7 20.4 - - + -
242B TYR* 3.5 35.2 - - - -
246B PHE* 3.6 38.7 - - + -
264B LEU* 4.5 3.8 - - + -
281B LEU* 6.1 0.2 - - - -
285B GLY 4.1 6.3 - - - -
286B HIS* 3.1 17.9 + - - +
288B LYS* 1.3 77.2 - - - +
290B VAL* 1.4 62.1 + - - +
292B VAL 3.4 0.7 + - - -
293B VAL* 3.0 30.0 + - - +
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Residues in contact with VAL 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180B ILE* 5.5 0.9 - - + -
264B LEU* 3.7 24.0 - - + -
266B CYS* 4.1 8.7 - - - -
286B HIS 4.9 1.1 - - - +
287B ALA 2.9 8.5 + - - +
289B CYS* 1.4 73.1 - - + +
291B GLU* 1.3 66.8 + - - +
293B VAL* 3.3 3.1 + - - +
294B LYS* 3.0 31.7 + - + +
300B LEU* 5.1 1.7 - - + +
302B MET* 3.8 29.6 - - + -
320B GLU* 3.8 33.4 - - + +
323B VAL* 3.7 21.3 - - + -
324B ALA 4.7 0.7 - - - +
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Residues in contact with GLU 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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284B LYS 5.1 1.6 - - - +
287B ALA 3.1 10.8 + - - +
288B LYS* 3.2 40.4 + - - +
290B VAL* 1.3 73.8 - - - +
292B VAL* 1.3 63.8 + - - +
294B LYS* 3.2 16.6 + - - +
295B THR* 3.3 18.5 + - + +
319B TYR* 4.4 11.4 + - - -
323B VAL* 3.5 33.5 - - + +
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Residues in contact with VAL 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B PHE* 3.9 24.9 - - + -
247B LYS* 4.1 39.9 - - + +
250B ILE* 4.5 5.8 - - + -
288B LYS* 2.9 45.9 + - + +
289B CYS 3.7 4.0 - - - +
290B VAL 3.3 0.2 - - - -
291B GLU* 1.3 74.7 - - - +
293B VAL* 1.3 61.1 + - - +
295B THR* 2.8 29.8 + - - +
296B PHE* 3.3 18.3 - - + -
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Residues in contact with VAL 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B ILE* 3.6 25.6 - - + -
246B PHE* 4.0 15.3 - - + -
250B ILE* 4.5 4.5 - - + -
254B MET* 4.7 3.3 - - + +
262B VAL* 3.8 31.6 - - + +
264B LEU* 4.3 13.5 - - + -
289B CYS 3.0 21.3 + - - +
290B VAL 3.9 3.4 - - - +
292B VAL* 1.3 74.8 - - - +
294B LYS* 1.4 62.2 + - - +
296B PHE* 3.2 25.2 + - - +
297B ASN 4.4 1.0 + - - -
298B LEU* 5.3 2.3 + - - +
300B LEU* 3.8 21.3 - - + -
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Residues in contact with LYS 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B LYS* 3.1 30.9 + - - +
136B MET* 3.9 16.4 - - - -
290B VAL* 3.0 20.2 + - + +
291B GLU* 3.2 10.5 + - - +
293B VAL* 1.4 76.8 - - - +
295B THR* 1.3 57.0 + - - +
296B PHE 3.0 0.4 - - - -
297B ASN* 3.0 19.3 + - - +
298B LEU 6.1 0.4 - - - +
300B LEU* 4.1 20.4 - - + -
323B VAL* 2.8 35.9 + - + +
324B ALA* 3.2 26.1 + - - -
326B ASP* 3.7 22.2 + - - +
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Residues in contact with THR 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B LYS* 5.3 0.2 - - - +
247B LYS* 6.2 0.2 - - - -
291B GLU* 3.3 18.2 - - + +
292B VAL* 2.8 20.2 + - - +
294B LYS* 1.3 74.5 - - + +
296B PHE* 1.3 72.7 + - - +
297B ASN* 3.3 15.4 + - - -
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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