Contacts of the strand formed by residues 237 - 244 (chain E) in PDB entry 1SID
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 237 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257D ASN* 3.2 12.2 + - - +
166E ALA* 4.0 11.4 - - + -
167E VAL* 3.2 13.2 - - - +
168E GLY* 3.0 28.9 - - - +
170E GLU* 4.2 11.2 + - - +
171E PRO 4.1 11.8 + - - -
172E LEU* 4.5 13.6 - - - +
173E ASP* 4.2 2.3 + - - -
235E GLU* 3.5 25.8 + - - +
236E ASN* 1.3 79.3 + - - +
238E ARG* 1.3 76.1 + - - +
239E TYR* 5.2 3.1 - - - -
279E TYR* 4.4 3.1 - - + +
281E SER* 4.9 2.5 - - - +
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Residues in contact with ARG 238 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257D ASN* 2.7 16.0 + - - +
258D THR* 4.6 13.2 - - - -
166E ALA* 2.7 24.9 - - - +
167E VAL 2.8 18.0 + - - +
235E GLU* 4.1 14.5 + - - +
236E ASN* 4.2 2.8 + - - +
237E THR* 1.3 96.4 + - - +
239E TYR* 1.3 62.3 + - - +
240E PHE* 3.6 18.7 - - + -
262E VAL 5.0 1.1 - - - -
263E LEU* 2.5 49.9 + - + +
264E LEU 4.3 1.0 + - - -
265E ASP* 2.9 37.2 - - - +
270E GLY 3.2 21.4 + - - -
271E PRO* 4.1 5.5 - - + +
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Residues in contact with TYR 239 (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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128D GLU* 2.8 34.3 + - - -
255D PHE* 4.1 9.4 - - + -
256D THR* 2.5 26.0 + - - -
257D ASN* 2.9 54.7 + - + +
98E TRP* 6.4 0.2 - - + -
164E VAL* 4.6 4.3 - - + -
165E PHE 2.9 13.9 - - - +
166E ALA* 3.2 13.0 - - + -
172E LEU* 5.7 4.0 - - + -
229E PRO* 3.6 45.5 + - + -
230E ASP 4.8 7.6 - - - -
231E PRO* 4.0 12.4 - - + +
235E GLU* 5.1 11.2 - - + -
237E THR* 4.9 4.9 - - - -
238E ARG* 1.3 76.7 - - - +
240E PHE* 1.3 69.6 + - - +
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Residues in contact with PHE 240 (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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255D PHE* 3.0 10.8 - - - +
256D THR* 3.3 5.8 - - - +
258D THR* 3.1 35.9 - - + -
125E VAL* 6.2 0.4 - - + -
164E VAL* 2.9 6.9 - - - -
165E PHE* 2.7 78.0 + + + +
167E VAL 5.5 0.2 - - - -
238E ARG* 3.6 27.4 - - + -
239E TYR* 1.3 94.4 - - - +
241E GLY* 1.3 58.7 + - - +
261E THR* 5.1 16.4 - - + -
262E VAL 5.7 2.0 - - - -
263E LEU* 5.2 5.2 - - + -
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Residues in contact with GLY 241 (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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254D GLN* 3.6 3.1 - - - +
255D PHE* 2.6 37.8 + - - +
163E HIS 2.8 16.6 - - - -
164E VAL* 3.4 8.1 - - - -
240E PHE* 1.3 80.5 - - - +
242E ASN* 1.3 60.3 + - - +
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Residues in contact with ASN 242 (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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252D VAL* 5.5 0.3 - - - +
253D LEU 3.0 8.1 - - - +
254D GLN* 3.0 27.6 + - - +
255D PHE* 4.1 5.0 - - - +
161E GLN 4.1 0.2 - - - +
162E TYR* 3.5 9.4 - - - -
163E HIS* 2.9 43.9 + - - +
241E GLY* 1.3 73.4 - - - -
243E TYR* 1.3 61.9 + - - +
244E THR* 3.1 24.4 + - - -
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Residues in contact with TYR 243 (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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132D SER* 3.6 34.2 - - - -
135D LEU* 3.3 38.4 + - + +
136D LEU* 3.5 25.4 - - + -
156D PRO* 4.8 3.8 - - - +
157D VAL 4.9 0.9 + - - -
251D PRO* 3.5 24.3 - - + +
252D VAL* 3.0 8.8 - - - +
253D LEU* 2.9 33.3 + - + +
286D MET* 6.1 0.4 - - + -
160E SER* 3.2 10.1 + - - -
161E GLN 3.6 7.4 - - - -
162E TYR* 4.2 15.5 - + + -
242E ASN* 1.3 76.8 - - - +
244E THR* 1.3 79.9 + - - +
245E GLY* 2.8 36.0 - - - -
246E GLY 3.9 0.9 + - - -
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Residues in contact with THR 244 (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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250D PRO* 5.8 0.7 - - + -
251D PRO 3.5 5.2 - - - +
252D VAL* 4.0 11.3 - - + +
160E SER* 2.9 6.8 - - - -
161E GLN* 2.7 61.6 + - - +
242E ASN* 3.1 17.8 + - - -
243E TYR* 1.3 76.2 + - - +
245E GLY* 1.3 58.2 + - - +
249E THR* 3.5 25.4 - - + -
250E PRO 5.5 0.9 - - - +
252E VAL* 6.2 2.0 - - + -
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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