Contacts of the helix formed by residues 283 - 293 (chain E) in PDB entry 1SSP
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 HIS 283 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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180E ASP* 4.0 0.2 + - - -
243E LEU* 3.8 22.7 - - + -
245E TRP* 3.1 33.7 - + + +
264E LEU* 3.6 42.2 - - + +
265E GLN 3.7 6.9 - - - -
266E THR* 3.5 21.1 + - + +
281E CYS* 3.0 39.0 + - + -
282E ARG* 1.3 77.2 - - - +
284E PHE* 1.3 58.4 + - + +
286E LYS* 3.9 2.7 - - + +
287E THR* 2.6 38.7 + - - -
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Residues in contact with PHE 284 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141E ILE* 4.8 1.3 - - + -
173E ILE* 3.9 16.6 - - + -
176E GLU* 3.8 26.0 - - + -
177E LEU* 3.5 46.4 - - + -
180E ASP* 3.1 15.8 + - - +
181E ILE* 4.1 3.1 - - + -
195E TRP* 4.5 4.9 - + - -
243E LEU* 5.0 2.0 - - + -
245E TRP* 3.5 39.9 - + - -
278E PHE* 4.2 3.4 - + - -
281E CYS* 5.4 0.2 - - - -
283E HIS* 1.3 80.7 - - + +
285E SER* 1.3 62.2 + - - +
287E THR* 3.4 1.7 + - - -
288E ASN* 3.3 15.6 + - - -
301E TRP* 3.1 59.1 + + + +
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Residues in contact with SER 285 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180E ASP* 2.6 44.6 + - - -
181E ILE* 3.9 11.1 - - - +
282E ARG* 3.0 19.8 + - - +
284E PHE* 1.3 70.6 - - - +
286E LYS* 1.3 74.7 + - - +
288E ASN* 3.1 8.5 + - - +
289E GLU* 3.0 36.4 + - - +
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Residues in contact with LYS 286 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264E LEU* 3.9 20.2 - - + -
281E CYS 3.7 18.8 - - - +
282E ARG* 3.0 29.7 + - + +
283E HIS* 3.9 5.4 - - + +
285E SER* 1.3 86.2 + - - +
287E THR* 1.3 61.2 + - - +
289E GLU* 3.2 19.7 + - - +
290E LEU* 3.0 32.7 + - + +
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Residues in contact with THR 287 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139E VAL* 3.5 36.1 - - + -
241E VAL* 3.5 18.8 - - + +
243E LEU* 3.4 26.2 - - - +
264E LEU* 4.2 0.4 - - - +
283E HIS 2.6 24.9 + - - -
284E PHE 3.6 5.4 - - - -
285E SER 3.2 0.2 - - - -
286E LYS* 1.3 75.2 - - - +
288E ASN* 1.3 58.9 + - - +
290E LEU* 3.2 4.9 + - - +
291E LEU* 2.8 34.7 + - + +
301E TRP* 4.1 12.1 - - + -
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Residues in contact with ASN 288 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181E ILE* 4.8 5.7 - - - +
284E PHE 3.3 2.4 + - - +
285E SER* 3.1 11.2 + - - +
287E THR* 1.3 77.1 - - - +
289E GLU* 1.3 58.8 + - + +
291E LEU* 3.5 8.6 - - - +
292E GLN* 2.8 37.9 + - + +
298E PRO* 3.4 18.9 - - + +
299E ILE* 2.7 48.2 + - - +
301E TRP* 3.1 22.6 + - - +
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Residues in contact with GLU 289 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282E ARG* 5.6 2.6 + - - -
285E SER* 3.0 30.9 + - - +
286E LYS* 3.5 26.0 + - - +
288E ASN* 1.3 75.7 - - - +
290E LEU* 1.3 60.6 + - + +
292E GLN* 3.4 6.8 + - - +
293E LYS* 3.0 37.1 + - + +
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Residues in contact with LEU 290 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239E GLY 6.1 0.2 - - - -
241E VAL* 3.9 10.5 - - + -
262E HIS* 3.7 55.7 + - + +
264E LEU* 3.7 22.0 - - + -
286E LYS* 3.0 23.5 + - + +
287E THR 3.6 6.3 - - - +
289E GLU* 1.3 77.9 - - + +
291E LEU* 1.3 63.1 - - - +
293E LYS* 3.3 15.3 + - + +
294E SER* 3.1 26.3 + - - -
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Residues in contact with LEU 291 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138E LYS* 4.1 19.3 - - + +
139E VAL* 3.9 19.3 - - + -
239E GLY 4.5 3.8 - - - +
241E VAL* 4.0 15.9 - - + -
287E THR* 2.8 20.8 + - + +
288E ASN* 3.5 25.1 - - - +
290E LEU* 1.3 76.5 - - - +
292E GLN* 1.3 56.9 + - - +
294E SER* 2.9 17.6 + - - -
295E GLY 3.0 0.2 + - - -
296E LYS* 2.9 56.1 + - + +
297E LYS 3.7 16.8 - - - +
298E PRO* 4.5 1.3 - - + -
299E ILE* 3.9 10.3 - - + -
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Residues in contact with GLN 292 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288E ASN* 2.8 26.9 + - + +
289E GLU* 3.7 7.0 - - - +
291E LEU* 1.3 72.9 - - - +
293E LYS* 1.3 62.9 + - + +
295E GLY* 3.0 14.4 + - - -
296E LYS 3.6 12.5 + - - +
297E LYS* 5.0 0.3 - - - -
298E PRO* 4.0 31.0 - - + +
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Residues in contact with LYS 293 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262E HIS* 6.2 0.7 - - - +
289E GLU* 3.0 24.2 + - - +
290E LEU* 3.7 15.2 - - + +
291E LEU 3.2 0.2 - - - -
292E GLN* 1.3 76.5 - - + +
294E SER* 1.3 61.2 + - - +
295E GLY 3.1 0.9 + - - -
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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