Contacts of the strand formed by residues 237 - 244 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257B ASN* 3.0 13.1 - - - +
166C ALA* 3.7 18.4 - - + -
167C VAL 3.3 11.7 - - - +
168C GLY* 3.1 25.1 - - - +
170C GLU* 4.0 16.6 + - - +
171C PRO 4.3 5.9 + - - -
172C LEU* 4.4 16.1 - - + +
173C ASP* 4.3 3.1 + - - -
235C GLU* 3.5 23.6 + - - +
236C ASN* 1.3 82.7 + - - +
238C ARG* 1.3 78.3 + - - +
239C TYR* 5.8 1.6 - - - -
279C TYR* 4.6 2.0 - - + +
281C SER* 4.9 0.9 - - - +
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Residues in contact with ARG 238 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257B ASN* 3.4 9.3 + - - +
258B THR* 5.1 11.7 - - - -
166C ALA* 2.7 23.6 - - - -
167C VAL 2.8 16.3 + - - +
235C GLU* 4.4 9.3 + - - +
236C ASN* 4.2 5.5 + - - +
237C THR* 1.3 98.7 + - - +
239C TYR* 1.3 60.2 + - - +
240C PHE* 3.3 26.2 - - + -
262C VAL 5.2 0.7 - - - -
263C LEU* 2.7 50.4 + - + +
264C LEU 4.2 4.4 + - - -
265C ASP* 2.9 35.3 - - - +
270C GLY* 3.3 16.9 + - - -
271C PRO* 4.3 4.3 - - + -
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Residues in contact with TYR 239 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B GLU* 2.6 35.3 + - - -
255B PHE* 3.7 7.9 - - + -
256B THR* 2.5 27.4 + - - -
257B ASN* 2.4 72.6 + - + +
98C TRP* 6.4 0.4 - - + -
164C VAL* 4.7 4.3 - - + -
165C PHE 3.0 6.1 - - - +
166C ALA* 3.5 16.6 - - + -
172C LEU* 4.8 9.6 - - + -
229C PRO* 3.6 45.4 + - + -
230C ASP 4.4 8.5 - - - -
231C PRO* 3.8 10.1 - - + +
235C GLU* 5.1 6.5 - - + -
237C THR 5.5 1.1 - - - -
238C ARG* 1.3 75.8 - - - +
240C PHE* 1.3 64.7 + - - +
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Residues in contact with PHE 240 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255B PHE 3.2 10.1 - - - +
256B THR* 3.5 4.9 - - + +
258B THR* 3.3 33.2 - - + -
164C VAL* 3.0 5.5 - - - -
165C PHE* 2.7 76.2 + + + +
238C ARG* 3.3 43.3 - - + -
239C TYR* 1.3 77.8 - - - +
241C GLY* 1.3 55.9 + - - +
261C THR* 4.8 16.4 - - + -
262C VAL 5.5 2.7 - - - -
263C LEU* 4.5 10.1 - - + -
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Residues in contact with GLY 241 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254B GLN* 3.5 5.2 - - - +
255B PHE* 2.7 39.3 + - - +
163C HIS 2.8 15.3 - - - -
164C VAL* 3.5 9.4 - - - +
240C PHE* 1.3 78.4 - - - +
242C ASN* 1.3 59.1 + - - +
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Residues in contact with ASN 242 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252B VAL* 4.6 2.3 - - - +
253B LEU 3.2 14.8 - - - +
254B GLN* 3.6 15.3 + - - +
255B PHE* 4.4 3.4 - - - +
162C TYR* 3.3 13.4 - - - -
163C HIS* 2.8 49.9 + - - +
164C VAL* 4.2 1.8 - - - +
241C GLY* 1.3 75.2 - - - +
243C TYR* 1.3 66.2 + - - +
244C THR* 3.6 23.0 + - - +
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Residues in contact with TYR 243 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132B SER* 3.6 41.0 - - - -
135B LEU* 3.3 46.5 + - + +
136B LEU* 4.0 7.4 - - + -
156B PRO* 4.7 1.9 - - - +
157B VAL 4.5 2.8 + - - -
251B PRO* 3.6 30.2 - - + +
252B VAL* 3.0 8.7 - - - +
253B LEU* 2.8 37.5 + - + -
255B PHE* 5.5 0.4 - - - -
286B MET* 5.2 1.3 - - + -
160C SER* 3.4 13.0 + - - -
161C GLN 3.7 7.0 - - - -
162C TYR* 3.9 13.7 - + + -
242C ASN* 1.3 76.0 - - - +
244C THR* 1.3 67.2 + - - +
245C GLY* 2.7 35.7 - - - -
246C GLY 3.8 1.7 + - - -
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Residues in contact with THR 244 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250B PRO* 6.0 0.7 - - + -
251B PRO 3.6 3.1 - - - -
252B VAL* 3.4 19.1 - - + -
159C GLY 4.6 0.3 - - - +
160C SER* 3.1 4.9 - - - -
161C GLN* 2.9 60.7 + - + +
162C TYR 4.3 0.2 + - - -
163C HIS* 5.7 0.3 - - - -
242C ASN* 3.6 17.1 + - - +
243C TYR* 1.3 76.7 - - - +
245C GLY* 1.3 62.1 + - - +
249C THR* 4.9 10.2 - - + +
252C VAL* 5.9 5.8 - - + -
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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