Contacts of the helix formed by residues 281 - 297 (chain A) in PDB entry 1Z1G
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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217A CYS* 4.5 0.7 - - - -
280A LEU* 1.3 76.8 - - - +
282A SER* 1.3 66.4 + - - +
283A GLY* 3.2 5.9 + - - -
284A THR* 2.6 37.5 + - - -
285A VAL* 3.4 5.5 + - - +
4I T 5.9 4.1 - - - +
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Residues in contact with SER 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A VAL* 3.8 16.5 - - - +
214A GLY* 3.8 17.9 + - - -
217A CYS* 3.8 18.9 - - - +
280A LEU 3.8 3.6 + - - -
281A SER* 1.3 70.2 - - - +
283A GLY* 1.3 63.6 + - - +
285A VAL* 3.2 18.2 + - - +
286A SER* 3.4 6.5 + - - -
22J G 4.0 16.4 + - - -
23J C 5.2 0.6 + - - -
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Residues in contact with GLY 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A SER* 2.8 10.0 + - - -
282A SER* 1.3 74.9 - - - +
284A THR* 1.3 65.1 + - - +
286A SER* 3.4 6.3 + - - -
287A ARG* 2.8 29.8 + - - +
23J C 6.0 6.0 - - - +
24J A 5.7 4.8 - - - +
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Residues in contact with THR 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A TRP* 5.3 5.2 - - + -
280A LEU* 5.0 10.1 - - - -
281A SER* 2.6 37.6 + - - -
283A GLY* 1.3 72.7 - - - +
285A VAL* 1.3 55.5 + - - -
287A ARG* 2.6 38.2 + - + +
288A TYR* 2.8 30.0 + - + +
2I A 6.0 2.0 - - - +
3I C 6.4 2.5 - - + -
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Residues in contact with VAL 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A TRP* 4.4 15.9 - - + -
199A LEU* 4.0 6.5 - - + +
202A ALA* 4.8 12.3 - - + -
213A VAL* 3.8 17.5 - - + -
216A LEU* 5.3 2.7 - - + -
217A CYS* 4.3 16.4 - - - -
272A ILE* 5.0 6.1 - - + -
280A LEU* 4.2 21.5 - - + -
281A SER 3.4 2.1 + - - +
282A SER 3.2 8.7 + - - +
283A GLY 3.2 0.4 - - - -
284A THR* 1.3 78.6 - - - +
286A SER* 1.3 66.0 + - - +
288A TYR* 3.4 1.0 + - - -
289A PHE* 3.1 19.2 + - - +
307A PHE* 3.4 33.0 - - + -
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Residues in contact with SER 286 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A VAL* 5.6 0.2 - - - -
282A SER 3.4 6.6 + - - -
283A GLY* 3.8 7.9 - - - -
284A THR 3.3 0.2 - - - -
285A VAL* 1.3 82.6 - - - +
287A ARG* 1.3 64.4 + - - +
289A PHE* 2.9 6.1 + - - +
290A MSE 2.9 21.3 + - - +
306A THR* 4.2 3.5 + - - -
307A PHE* 4.1 14.7 - - - +
22J G 5.8 0.2 - - - -
23J C 3.1 59.1 + - - +
24J A 4.4 2.6 + - - -
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Residues in contact with ARG 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A GLY* 2.8 18.5 + - - +
284A THR* 2.6 34.1 + - - +
286A SER* 1.3 73.3 - - - +
288A TYR* 1.3 67.8 + - + +
290A MSE 3.0 34.8 - - + +
291A ARG* 3.4 17.5 + - - +
3I C 5.8 2.6 - - - +
4I T 4.3 10.0 + - - -
5I C 4.3 1.4 - - - +
24J A 3.9 31.9 + - + +
25J G 2.6 46.9 + - - -
26J A 4.0 16.4 + - - +
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Residues in contact with TYR 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A SER* 4.6 8.8 - - - -
196A PRO* 3.5 38.7 - - + +
198A TRP* 4.2 19.7 - + + -
199A LEU* 3.8 18.0 - - + +
284A THR* 2.8 30.2 + - + +
285A VAL 4.2 0.2 - - - +
287A ARG* 1.3 77.1 - - + +
289A PHE* 1.3 70.3 + - - +
290A MSE 2.9 2.0 - - - -
291A ARG* 2.8 52.5 + - + +
292A ALA* 3.1 10.7 + - - +
1I A 3.9 33.1 + - - -
2I A 4.5 4.8 + - - -
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Residues in contact with PHE 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A LEU* 4.7 15.0 - - + -
188A ILE* 3.8 30.5 - - + -
199A LEU* 3.6 11.7 - - + +
203A MSE 3.7 39.9 - - + -
285A VAL 3.1 12.6 + - - +
286A SER 2.9 11.5 + - - +
288A TYR* 1.3 77.1 - - - +
290A MSE 1.3 67.2 + - - +
292A ALA* 3.2 5.2 + - + +
293A ARG* 3.0 26.4 + - + +
305A PRO 4.4 4.9 - - - -
306A THR* 3.4 17.9 - - - -
307A PHE* 3.2 49.1 - + + -
310A LEU* 5.0 6.3 - - + -
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Residues in contact with MSE 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A SER* 2.9 10.7 + - - +
287A ARG* 3.0 36.1 - - + +
289A PHE* 1.3 80.6 - - - +
291A ARG* 1.3 73.7 + - + +
293A ARG* 2.7 46.5 + - - +
294A LYS* 3.0 36.8 + - + +
24J A 3.6 54.7 - - + +
25J G 4.2 14.6 - - - +
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Residues in contact with ARG 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A ARG* 3.4 23.8 + - - +
288A TYR* 2.8 56.9 + - + +
290A MSE 1.3 93.6 - - + +
292A ALA* 1.3 57.8 - - - +
294A LYS* 3.2 7.8 + - - +
295A ALA* 2.9 30.4 + - - +
1I A 6.3 1.6 - - - -
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Residues in contact with ALA 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A ILE* 3.6 20.1 - - + +
191A ALA* 3.9 7.4 - - - +
192A ALA* 4.4 14.6 - - + +
195A SER* 4.8 2.0 - - - +
199A LEU* 4.3 17.9 - - + -
288A TYR 3.1 6.1 + - - +
289A PHE* 3.3 10.8 - - + +
290A MSE 3.1 0.6 - - - -
291A ARG* 1.3 75.1 - - - +
293A ARG* 1.3 60.8 + - - +
295A ALA* 3.7 6.9 - - - -
296A SER* 3.0 31.5 + - - -
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Residues in contact with ARG 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A ILE* 4.1 13.6 - - + +
289A PHE* 3.0 22.7 + - + +
290A MSE 2.7 25.0 + - - +
292A ALA* 1.3 72.7 - - - +
294A LYS* 1.3 71.4 + - + +
296A SER* 3.2 18.0 + - - -
297A GLY* 3.5 4.5 + - - -
298A LEU* 4.6 3.5 + - - +
300A PHE* 4.5 19.5 - - + -
304A PRO* 3.2 38.8 + - + +
305A PRO 2.1 41.8 + - - -
306A THR* 3.2 17.8 - - - +
24J A 2.9 44.2 + - - -
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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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290A MSE 3.0 36.1 + - + +
291A ARG* 3.5 8.7 - - - +
293A ARG* 1.3 82.2 - - + +
295A ALA* 1.3 57.1 + - - +
297A GLY* 3.0 22.2 + - - -
25J G 6.0 1.3 - - - +
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Residues in contact with ALA 295 (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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191A ALA* 4.1 15.5 - - + +
194A SER* 5.6 4.0 - - - +
291A ARG 2.9 17.7 + - - +
292A ALA* 3.7 8.1 - - - +
293A ARG 3.3 0.4 - - - -
294A LYS* 1.3 73.9 - - - +
296A SER* 1.3 60.5 + - - +
297A GLY* 4.4 0.4 - - - -
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Residues in contact with SER 296 (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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187A LYS* 3.7 45.3 + - - +
188A ILE* 4.2 12.9 - - - +
191A ALA* 4.0 8.1 - - - -
292A ALA 3.0 17.9 + - - -
293A ARG 3.2 6.9 + - - -
295A ALA* 1.3 77.2 - - - +
297A GLY* 1.3 60.8 + - - +
298A LEU* 3.4 10.1 + - - +
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Residues in contact with GLY 297 (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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293A ARG 3.5 2.4 + - - -
294A LYS 3.0 16.7 + - - -
295A ALA 3.3 1.1 - - - -
296A SER* 1.3 77.9 - - - +
298A LEU* 1.3 66.8 + - - +
299A SER* 3.9 0.7 + - - -
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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
------------------------------------------------------------
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