Contacts of the helix formed by residues 282 - 295 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239A ASP* 2.6 35.1 + - - +
271A LEU* 3.4 8.8 - - - +
272A SER* 5.4 0.2 - - - -
281A LEU* 1.3 77.1 - - - +
283A VAL* 1.3 57.9 + - - +
284A LYS* 3.3 10.5 + - - +
285A GLY 3.2 9.0 + - - -
286A HIS 3.0 22.2 + - - -
349A HIS* 6.4 0.2 - - - -
350A ILE* 3.6 31.2 - - - +
351A SER 4.3 0.7 - - - -
352A PRO* 3.8 32.1 - - + -
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Residues in contact with VAL 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A LEU* 4.0 16.4 - - + -
282A THR* 1.3 74.0 - - - +
284A LYS* 1.3 58.1 + - - +
286A HIS* 3.3 2.1 + - - +
287A ALA* 2.8 29.4 + - + +
312A ASN 4.4 0.7 - - - +
315A ARG* 4.2 13.5 - - + +
316A CYS* 3.9 35.9 - - + +
319A TYR* 3.7 35.0 - - + -
320A GLU* 4.6 0.2 - - - +
348A LEU 4.6 5.4 - - - +
349A HIS* 4.0 14.8 + - + +
350A ILE* 3.8 18.0 - - + +
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Residues in contact with LYS 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A ASP* 4.9 1.3 - - - +
282A THR* 3.2 9.1 + - - +
283A VAL* 1.3 77.7 - - - +
285A GLY* 1.3 57.0 + - - +
287A ALA* 3.8 1.0 - - - +
288A LYS* 3.0 29.5 + - - +
291A GLU* 5.4 1.0 - - - +
319A TYR* 4.4 18.8 - - + +
349A HIS* 3.5 46.2 + - + +
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Residues in contact with GLY 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A ASP* 3.3 34.2 + - - -
242A TYR* 5.2 4.5 - - - +
281A LEU* 4.9 7.1 - - - +
282A THR* 3.2 10.7 + - - -
284A LYS* 1.3 75.0 - - - +
286A HIS* 1.3 62.4 + - - +
288A LYS* 3.5 20.2 - - - +
289A CYS* 4.1 8.7 + - - -
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Residues in contact with HIS 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A ILE* 3.4 25.4 - - + +
266A CYS* 3.3 23.6 - - - -
267A GLY 2.8 22.0 + - - -
268A ALA* 3.9 0.8 - - - -
270A SER* 3.1 18.3 + - - -
271A LEU* 3.8 21.5 - - + -
281A LEU* 4.3 15.1 - - + +
282A THR 3.0 17.0 + - - +
283A VAL 3.6 4.5 - - - +
285A GLY* 1.3 76.4 - - - +
287A ALA* 1.3 56.9 + - - +
289A CYS* 3.1 32.2 + - - +
290A VAL 4.1 0.5 + - - -
316A CYS* 3.3 15.8 - - - -
320A GLU* 2.5 29.4 + - - +
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Residues in contact with ALA 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A VAL 2.8 21.8 + - - +
284A LYS 3.9 1.6 - - - +
286A HIS* 1.3 67.7 - - - +
288A LYS* 1.3 64.0 + - - +
289A CYS 3.0 2.2 - - - -
290A VAL* 3.0 14.5 + - - +
291A GLU* 3.0 17.0 + - - +
319A TYR* 3.4 32.8 - - + -
320A GLU* 3.2 24.0 + - + -
323A VAL* 4.3 6.6 - - + +
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Residues in contact with LYS 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A ASP 5.0 3.7 + - - +
240A GLU* 6.2 0.2 - - - +
243A GLY* 3.6 35.6 + - - -
247A LYS* 6.0 4.5 - - - -
284A LYS 3.0 13.6 + - - +
285A GLY* 3.5 16.8 - - - +
286A HIS 3.3 0.4 - - - -
287A ALA* 1.3 76.0 - - - +
289A CYS* 1.4 51.6 + - - +
291A GLU* 3.2 20.6 + - - +
292A VAL* 2.8 52.2 + - + +
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Residues in contact with CYS 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A ILE* 3.7 20.2 - - + -
242A TYR* 3.6 35.7 - - - -
246A PHE* 3.5 35.6 - - + -
264A LEU* 4.5 2.9 - - + -
281A LEU* 6.0 0.2 - - - -
285A GLY 4.2 6.5 - - - -
286A HIS* 3.1 18.0 + - - +
287A ALA 3.0 0.6 - - - -
288A LYS* 1.4 73.8 - - - +
290A VAL* 1.3 59.1 + - - +
292A VAL 3.4 0.7 + - - -
293A VAL* 3.0 34.3 + - - +
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Residues in contact with VAL 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A ILE* 5.4 0.9 - - + -
264A LEU* 3.9 22.2 - - + -
266A CYS* 4.2 10.3 - - - -
286A HIS 4.7 1.1 - - - +
287A ALA* 3.0 7.5 + - - +
289A CYS* 1.3 73.1 - - + +
291A GLU* 1.3 62.1 + - - +
293A VAL* 3.3 2.3 + - - +
294A LYS* 2.9 38.0 + - + +
300A LEU* 5.1 2.1 - - + +
302A MET* 3.8 28.3 - - + -
320A GLU* 3.8 38.4 - - + +
323A VAL* 3.8 18.2 - - + -
324A ALA 4.8 2.5 - - - +
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Residues in contact with GLU 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284A LYS 5.4 1.1 - - - +
287A ALA 3.0 12.8 + - - +
288A LYS* 3.4 25.0 + - + +
290A VAL* 1.3 77.4 - - - +
292A VAL* 1.4 63.8 + - + +
294A LYS* 3.3 9.1 + - - +
295A THR* 3.2 27.9 + - + +
319A TYR* 4.2 11.8 + - - -
323A VAL* 3.6 31.5 - - + +
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Residues in contact with VAL 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246A PHE* 3.9 25.1 - - + -
247A LYS* 4.0 44.2 - - + +
250A ILE* 4.5 6.3 - - + -
288A LYS* 2.8 39.1 + - + +
289A CYS 3.7 4.7 - - - +
291A GLU* 1.4 73.1 - - + +
293A VAL* 1.3 60.7 + - - +
295A THR* 2.9 27.0 + - - +
296A PHE* 3.4 19.2 - - + -
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Residues in contact with VAL 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178A ILE* 3.6 24.7 - - + -
246A PHE* 4.1 14.8 - - + -
250A ILE* 4.6 4.5 - - + -
254A MET* 4.7 3.4 - - + -
262A VAL* 3.8 32.3 - - + +
264A LEU* 4.2 14.1 - - + -
289A CYS 3.0 17.1 + - - +
290A VAL 4.0 2.7 - - - +
292A VAL* 1.3 75.4 - - - +
294A LYS* 1.3 62.8 + - - +
296A PHE* 3.3 24.8 + - - +
297A ASN 4.4 1.0 + - - -
298A LEU* 5.4 2.3 + - - +
300A LEU* 3.8 21.2 - - + +
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Residues in contact with LYS 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A GLY 4.5 4.6 + - - -
14A LYS* 4.5 15.7 + - - +
136A MET* 4.0 21.1 - - + -
290A VAL* 2.9 21.2 + - + +
291A GLU* 3.3 8.5 - - - +
293A VAL* 1.3 77.8 - - - +
295A THR* 1.4 61.4 + - + +
297A ASN* 3.2 21.8 + - - +
300A LEU* 4.6 9.1 - - + +
323A VAL* 3.4 23.1 - - + +
324A ALA* 3.3 31.2 - - - -
326A ASP* 2.7 30.1 + - - +
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Residues in contact with THR 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A LYS* 5.9 4.9 - - - -
291A GLU* 3.2 17.5 + - + +
292A VAL* 2.9 19.6 + - - +
293A VAL 3.3 0.2 - - - -
294A LYS* 1.4 75.5 - - + +
296A PHE* 1.3 69.5 + - - +
297A ASN* 3.2 16.5 + - - -
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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