Contacts of the helix formed by residues 281 - 297 (chain B) in PDB entry 1Z19
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 SER 281 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B CYS* 4.6 0.2 - - - -
280B LEU* 1.3 76.7 - - - +
282B SER* 1.3 62.3 + - - +
283B GLY* 3.0 4.8 + - - -
284B THR* 2.9 37.8 + - - -
285B VAL* 3.3 11.1 + - - +
5C T 3.5 16.4 + - - -
6C T 4.1 28.0 - - - +
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Residues in contact with SER 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B VAL* 3.8 38.2 - - - +
214B GLY* 3.9 10.7 - - - -
217B CYS* 3.9 16.6 - - - +
280B LEU 3.7 2.4 + - - -
281B SER* 1.3 72.1 - - - +
283B GLY* 1.3 62.1 + - - +
285B VAL* 3.6 1.1 + - - -
286B SER* 3.1 23.4 + - - -
57E G 3.9 13.3 + - - -
58E C 5.0 0.2 + - - -
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Residues in contact with GLY 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B SER* 3.0 6.8 + - - -
282B SER* 1.3 84.0 + - - +
284B THR* 1.3 56.2 + - - +
286B SER* 3.5 1.2 + - - -
287B ARG* 2.8 33.7 + - - +
6C T 5.8 2.7 - - - -
59E T 3.4 27.8 - - - +
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Residues in contact with THR 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B TRP* 4.0 13.0 - - + -
280B LEU* 4.7 3.6 - - + -
281B SER* 2.9 19.7 + - - -
283B GLY* 1.3 74.1 - - - +
285B VAL* 1.3 60.3 + - - +
287B ARG* 2.9 11.0 + - - +
288B TYR* 2.8 52.6 + - + -
4C G 4.0 11.0 - - + -
5C T 2.5 46.3 + - + +
6C T 4.6 0.5 - - - +
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Residues in contact with VAL 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B TRP* 3.7 24.7 - - + -
199B LEU* 4.0 3.5 - - + +
202B ALA* 3.9 18.4 - - + -
213B VAL* 4.2 7.9 - - + -
216B LEU* 6.1 0.4 - - + -
217B CYS* 3.6 25.4 - - - -
272B ILE* 4.9 1.3 - - + -
280B LEU* 4.0 15.5 - - + -
281B SER 3.3 6.6 + - - +
282B SER 3.9 6.1 - - - +
283B GLY 3.4 0.2 - - - -
284B THR* 1.3 79.0 - - - +
286B SER* 1.3 64.7 + - - +
288B TYR* 3.3 2.1 + - - +
289B PHE* 3.1 21.1 + - - +
307B PHE* 3.6 31.0 - - + -
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Residues in contact with SER 286 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B VAL* 4.9 1.1 - - - +
282B SER 3.1 16.0 + - - -
283B GLY* 3.6 5.4 - - - -
285B VAL* 1.3 79.0 - - - +
287B ARG* 1.3 63.4 + - - +
289B PHE* 3.4 4.3 + - - +
290B MSE 3.2 22.5 + - - +
307B PHE* 4.0 17.6 + - - +
58E C 2.7 50.6 + - - +
59E T 4.2 7.7 + - - +
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Residues in contact with ARG 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B GLY* 2.8 28.3 + - - +
284B THR 2.9 9.4 + - - +
286B SER* 1.3 77.4 - - - +
288B TYR* 1.3 65.7 + - + +
290B MSE 2.9 37.8 + - + +
291B ARG* 3.2 40.6 + - - +
5C T 3.8 24.4 - - - +
6C T 3.4 18.2 + - - +
7C C 4.5 0.8 - - - +
59E T 3.4 36.0 - - + +
60E G 2.8 38.2 + - - -
61E A 3.4 14.1 + - - +
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Residues in contact with TYR 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B SER* 4.9 4.5 + - - -
196B PRO* 3.6 29.8 - - + -
198B TRP* 3.6 24.0 - + + -
199B LEU* 3.7 18.0 - - + +
284B THR* 2.8 37.5 + - + +
285B VAL 4.0 2.2 - - - +
287B ARG* 1.3 74.6 - - + +
289B PHE* 1.3 67.1 + - - +
291B ARG* 3.1 41.0 + - + +
292B ALA 3.0 19.1 + - - -
3C C 3.4 52.9 + - + +
4C G 4.0 9.2 - + - -
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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
----------------------------------------------------------
180B LEU* 4.3 13.5 - - + -
188B ILE* 3.8 29.8 - - + -
199B LEU* 3.8 11.3 - - + +
203B MSE 3.8 38.6 - - + -
285B VAL 3.1 12.9 + - - +
286B SER 3.6 9.0 - - - +
287B ARG 3.3 0.2 - - - -
288B TYR* 1.3 75.8 - - - +
290B MSE 1.3 58.1 + - + +
292B ALA* 3.1 4.3 + - - +
293B ARG* 2.8 38.0 + - + +
305B PRO* 4.2 8.7 - - + -
306B THR* 3.6 28.5 - - - -
307B PHE* 3.6 37.2 - + + -
310B LEU* 4.3 12.1 - - + -
59E T 5.9 0.2 - - - -
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Residues in contact with MSE 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B SER 3.2 5.8 + - - +
287B ARG* 2.9 47.6 - - + +
289B PHE* 1.3 83.8 - - + +
291B ARG* 1.3 73.6 + - + +
293B ARG* 3.1 30.1 + - - +
294B LYS* 2.9 60.9 + - - +
59E T 3.4 39.3 - - + +
60E G 4.4 17.0 - - - +
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Residues in contact with ARG 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287B ARG* 3.2 40.2 + - - +
288B TYR* 3.1 53.3 + - + +
290B MSE 1.3 91.8 - - + +
292B ALA* 1.3 56.5 + - - +
294B LYS* 2.9 11.1 + - + +
295B ALA* 2.7 35.9 + - - +
2C T 5.5 3.6 + - - -
3C C 5.2 3.4 + - - -
4C G 5.2 9.1 + - - -
5C T 5.7 0.6 + - - -
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Residues in contact with ALA 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B ILE* 4.0 11.9 - - + -
191B ALA* 3.5 9.4 - - - +
192B ALA* 3.7 34.5 - - + +
195B SER* 4.1 5.3 + - - +
199B LEU* 3.9 7.0 - - + -
203B MSE 5.7 0.2 - - - -
288B TYR 3.0 12.7 + - - +
289B PHE* 3.5 8.3 - - - +
291B ARG* 1.3 76.0 - - - +
293B ARG* 1.3 62.7 - - - +
295B ALA* 3.1 11.5 + - - +
296B SER* 3.0 17.8 + - - -
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Residues in contact with ARG 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B ILE* 3.9 29.3 - - + +
289B PHE* 2.8 18.3 + - + +
290B MSE 3.2 34.4 + - - +
291B ARG 3.0 0.2 - - - -
292B ALA* 1.3 77.1 - - - +
294B LYS* 1.3 79.2 + - - +
296B SER* 2.7 31.4 + - - +
297B GLY 3.7 1.0 + - - -
298B LEU* 4.6 1.7 + - - +
300B PHE* 4.1 16.3 - - + -
304B PRO* 3.2 35.6 - - - +
305B PRO* 2.9 37.6 + - - -
306B THR* 4.7 0.6 - - - +
59E T 3.3 21.8 + - - -
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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
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290B MSE 2.9 37.0 + - - +
291B ARG* 2.9 11.9 + - + +
293B ARG* 1.3 91.1 - - - +
295B ALA* 1.3 62.7 + - - +
296B SER 3.0 1.4 + - - -
297B GLY* 3.1 13.6 + - - +
60E G 3.5 25.5 + - - -
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Residues in contact with ALA 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B ALA* 4.1 16.3 - - + +
194B SER* 6.0 0.7 - - - +
291B ARG 2.7 15.9 + - - +
292B ALA* 3.3 17.0 - - - +
293B ARG 3.1 0.2 - - - -
294B LYS* 1.3 73.0 - - - +
296B SER* 1.3 59.5 + - - +
297B GLY 3.3 0.4 + - - -
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Residues in contact with SER 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B LYS* 4.5 7.0 - - - +
188B ILE* 4.4 14.2 - - - +
191B ALA* 3.9 15.5 - - - -
292B ALA 3.0 8.0 + - - -
293B ARG* 2.7 20.5 + - - +
295B ALA* 1.3 80.0 - - - +
297B GLY* 1.3 62.0 + - - +
298B LEU* 3.0 35.8 + - - +
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Residues in contact with GLY 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293B ARG 3.7 0.2 + - - -
294B LYS 3.1 13.3 + - - -
295B ALA 3.3 1.2 - - - -
296B SER* 1.3 79.0 + - - +
298B LEU* 1.3 66.5 + - - +
299B SER* 3.9 6.2 + - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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