Contacts of the helix formed by residues 282 - 295 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239C ASP* 2.5 35.6 + - - +
271C LEU* 3.4 8.1 - - - +
281C LEU* 1.3 76.9 - - - +
283C VAL* 1.3 64.0 + - - +
284C LYS* 3.3 10.2 + - - +
285C GLY 3.1 10.2 + - - -
286C HIS 3.0 18.0 + - - -
349C HIS* 6.5 0.2 - - - -
350C ILE* 3.4 29.6 - - - +
351C SER 4.3 0.7 - - - -
352C PRO* 3.7 32.1 - - + -
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Residues in contact with VAL 283 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271C LEU* 4.0 18.8 - - + -
282C THR* 1.3 73.6 - - - +
284C LYS* 1.4 57.7 + - - +
286C HIS* 3.4 2.6 + - - +
287C ALA* 2.9 28.6 + - + +
312C ASN 4.4 0.7 - - - +
315C ARG* 4.1 13.9 - - + +
316C CYS* 3.9 30.7 - - - +
319C TYR* 3.8 32.3 - - + -
320C GLU* 4.6 0.5 - - - +
348C LEU* 4.4 4.9 - - + +
349C HIS* 4.1 14.1 + - + +
350C ILE* 3.8 25.5 - - + +
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Residues in contact with LYS 284 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239C ASP* 4.9 1.1 - - - +
282C THR* 3.2 9.0 + - - +
283C VAL* 1.4 79.0 - - - +
285C GLY* 1.3 56.0 + - - +
287C ALA* 3.5 1.4 + - - +
288C LYS* 3.0 30.3 + - - +
291C GLU* 4.8 2.3 - - - +
319C TYR* 4.3 20.6 - - + +
349C HIS* 3.7 44.6 + - + +
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Residues in contact with GLY 285 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239C ASP* 3.3 34.6 + - - +
242C TYR* 5.1 3.8 - - - +
243C GLY* 6.0 1.6 + - - -
281C LEU* 4.8 7.8 - - - +
282C THR* 3.1 9.7 + - - -
284C LYS* 1.3 73.9 - - - +
286C HIS* 1.3 65.0 + - - +
288C LYS* 3.5 17.5 - - - +
289C CYS* 4.1 8.5 + - - -
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Residues in contact with HIS 286 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180C ILE* 3.5 23.1 - - + +
266C CYS 3.2 23.1 - - - -
267C GLY 2.8 22.4 + - - -
268C ALA* 3.9 1.4 - - - -
270C SER* 3.1 20.7 + - - -
271C LEU* 3.7 19.7 - - + -
281C LEU* 4.3 14.0 - - + +
282C THR 3.0 16.1 + - - +
283C VAL 3.7 4.3 - - - +
285C GLY* 1.3 75.7 - - - +
287C ALA* 1.4 60.5 + - - +
289C CYS* 3.2 27.5 + - - +
290C VAL 4.2 0.5 + - - -
316C CYS* 3.2 16.2 - - - -
320C GLU* 2.5 34.8 + - - +
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Residues in contact with ALA 287 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283C VAL 2.9 17.9 + - - +
284C LYS 4.0 1.3 - - - +
286C HIS* 1.4 70.4 - - - +
288C LYS* 1.3 58.9 + - - +
289C CYS 3.1 2.5 - - - -
290C VAL* 2.9 22.0 + - - +
291C GLU* 3.0 16.0 + - - +
319C TYR* 3.5 31.6 - - + -
320C GLU* 3.2 25.7 + - + -
323C VAL* 4.2 7.5 - - + +
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Residues in contact with LYS 288 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243C GLY* 5.5 11.7 - - - -
246C PHE* 5.4 0.2 - - - -
284C LYS 3.0 13.6 + - - +
285C GLY* 3.5 16.4 - - - +
286C HIS 3.3 0.6 - - - -
287C ALA* 1.3 74.9 - - - +
289C CYS* 1.4 56.8 + - - +
291C GLU* 3.2 41.2 + - + +
292C VAL* 2.9 46.7 + - + +
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Residues in contact with CYS 289 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180C ILE* 3.7 21.3 - - + -
242C TYR* 3.6 34.3 - - - -
246C PHE* 3.6 37.9 - - + -
264C LEU* 4.5 3.4 - - + -
285C GLY 4.2 6.7 - - - -
286C HIS* 3.2 18.0 + - - +
287C ALA 3.1 0.2 - - - -
288C LYS* 1.4 77.2 - - - +
290C VAL* 1.3 56.6 + - - +
292C VAL 3.5 0.3 + - - -
293C VAL* 3.0 35.7 + - - +
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Residues in contact with VAL 290 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180C ILE* 5.4 0.7 - - + -
264C LEU* 3.9 21.5 - - + -
266C CYS* 4.3 4.7 - - - -
286C HIS 4.7 1.6 - - - +
287C ALA* 2.9 9.7 + - - +
289C CYS* 1.3 73.4 - - + +
291C GLU* 1.4 59.5 + - - +
293C VAL* 3.4 2.1 + - - +
294C LYS* 2.9 38.2 + - + +
300C LEU* 5.2 1.5 - - + +
302C MET* 3.6 33.9 - - + -
320C GLU* 3.8 37.5 - - + +
323C VAL* 3.8 20.0 - - + -
324C ALA 4.7 0.4 - - - +
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Residues in contact with GLU 291 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284C LYS 4.8 1.9 - - - +
287C ALA* 3.0 9.5 + - - +
288C LYS* 3.2 54.2 + - + +
290C VAL* 1.4 75.9 - - - +
292C VAL* 1.3 61.3 + - + +
294C LYS* 3.4 7.9 + - - +
295C THR* 3.2 26.5 + - - +
319C TYR* 5.2 5.8 + - - -
323C VAL* 3.7 28.2 - - + +
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Residues in contact with VAL 292 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246C PHE* 3.8 24.5 - - + -
247C LYS* 4.2 41.1 - - + +
250C ILE* 4.5 7.9 - - + -
251C SER* 5.4 0.4 - - - +
288C LYS* 2.9 38.8 + - + +
289C CYS 3.7 4.5 - - - +
290C VAL 3.4 0.2 - - - -
291C GLU* 1.3 72.7 - - + +
293C VAL* 1.4 60.4 + - - +
295C THR* 2.6 30.6 + - - +
296C PHE* 3.3 17.0 - - + -
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Residues in contact with VAL 293 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178C ILE* 3.7 24.7 - - + -
246C PHE* 4.1 13.7 - - + -
250C ILE* 4.5 4.7 - - + -
254C MET* 4.7 5.6 - - + +
262C VAL* 3.9 19.1 - - + -
264C LEU* 4.3 14.6 - - + -
289C CYS 3.0 21.4 + - - +
290C VAL 3.9 3.1 - - - +
292C VAL* 1.4 74.6 - - - +
294C LYS* 1.3 61.8 + - - +
296C PHE* 3.2 25.9 + - - +
297C ASN 4.4 1.0 + - - -
298C LEU* 5.3 2.4 + - - +
300C LEU* 3.8 31.0 - - + -
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Residues in contact with LYS 294 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C LYS* 3.1 33.1 + - - +
136C MET* 4.1 13.5 - - + -
290C VAL* 2.9 22.9 + - + +
291C GLU* 3.5 7.6 - - - +
292C VAL 3.3 0.2 - - - -
293C VAL* 1.3 76.7 - - - +
295C THR* 1.4 60.9 + - - +
297C ASN* 3.1 13.2 + - - -
298C LEU 5.0 0.4 + - - +
300C LEU* 4.2 20.6 - - + -
323C VAL* 2.8 36.8 + - + +
324C ALA* 3.6 26.8 + - - -
326C ASP* 4.0 19.8 + - - +
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Residues in contact with THR 295 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C LYS* 5.3 0.2 - - - +
291C GLU 3.2 17.1 + - - +
292C VAL* 2.6 22.6 + - - +
294C LYS* 1.4 73.9 - - - +
296C PHE* 1.3 72.6 + - - +
297C ASN* 3.3 15.5 + - - -
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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