Contacts of the strand formed by residues 237 - 244 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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257C ASN* 3.2 13.5 - - - +
166D ALA* 3.9 17.7 - - + -
167D VAL 3.3 7.9 - - - +
168D GLY* 3.2 29.6 - - - +
170D GLU* 4.3 8.2 + - - +
171D PRO 4.2 12.8 + - - -
172D LEU* 4.3 18.9 - - + +
173D ASP* 4.2 2.1 + - - -
235D GLU* 3.4 26.7 + - - +
236D ASN* 1.3 79.3 + - - +
238D ARG* 1.3 75.5 + - - +
239D TYR* 5.0 2.0 - - - -
279D TYR* 5.0 1.3 - - + +
281D SER* 5.2 1.3 - - - +
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Residues in contact with ARG 238 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257C ASN* 4.0 8.8 + - - +
258C THR* 4.9 15.3 - - - -
166D ALA* 2.8 26.7 - - - +
167D VAL 2.9 13.8 + - - +
235D GLU* 4.2 9.7 + - - +
236D ASN* 4.0 4.0 + - - -
237D THR* 1.3 108.1 + - - +
239D TYR* 1.3 60.3 + - - +
240D PHE* 3.4 20.2 - - + -
262D VAL 5.0 1.3 - - - -
263D LEU* 2.7 44.7 + - + +
264D LEU 4.3 1.7 + - - -
265D ASP* 3.0 37.3 - - - +
270D GLY* 3.2 23.6 + - - -
271D PRO* 4.4 2.0 - - + +
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Residues in contact with TYR 239 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128C GLU* 2.7 33.0 + - - -
255C PHE* 3.8 2.7 - - + -
256C THR* 2.8 34.7 + - - -
257C ASN* 2.7 51.9 + - + +
164D VAL* 5.1 3.8 - - + -
165D PHE 3.0 8.7 - - - +
166D ALA* 3.4 16.4 - - + -
172D LEU* 4.9 9.4 - - + -
229D PRO* 3.7 38.9 + - + -
230D ASP 4.6 9.4 - - - -
231D PRO* 3.8 16.5 - - + +
235D GLU* 5.1 8.3 - - + -
237D THR* 5.0 3.1 - - - -
238D ARG* 1.3 78.9 - - - +
240D PHE* 1.3 76.1 + - - +
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Residues in contact with PHE 240 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255C PHE 3.1 11.7 - - - -
256C THR* 3.7 7.9 - - + -
258C THR* 3.4 32.8 - - + -
164D VAL* 3.0 5.7 - - - +
165D PHE* 2.7 77.2 + + + -
166D ALA* 4.7 0.2 - - - -
167D VAL 5.2 0.4 - - - -
238D ARG* 3.4 28.0 - - + -
239D TYR* 1.3 93.8 - - - +
241D GLY* 1.3 60.0 + - - +
261D THR* 4.6 20.2 - - + -
262D VAL 5.6 1.8 - - - -
263D LEU* 4.8 5.2 - - + -
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Residues in contact with GLY 241 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254C GLN* 3.4 5.3 - - - +
255C PHE* 2.7 38.7 + - - +
256C THR* 4.6 1.1 - - - +
163D HIS 2.9 15.5 - - - -
164D VAL* 3.3 5.6 - - - -
165D PHE* 5.6 0.4 - - - -
240D PHE* 1.3 79.3 - - - +
242D ASN* 1.3 59.9 - - - +
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Residues in contact with ASN 242 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252C VAL* 4.8 3.3 - - - +
253C LEU 3.0 23.0 - - - +
254C GLN* 3.9 12.9 + - - +
255C PHE* 4.3 4.7 - - - +
162D TYR* 3.4 11.1 - - - -
163D HIS* 2.9 41.9 + - - +
164D VAL* 4.1 1.0 - - - +
241D GLY* 1.3 77.0 - - - +
243D TYR* 1.3 61.4 + - - +
244D THR* 3.0 26.7 + - - +
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Residues in contact with TYR 243 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132C SER* 3.6 38.8 - - - +
135C LEU* 3.3 36.9 + - + +
136C LEU* 3.5 22.9 - - + -
156C PRO* 4.8 2.3 - - - +
157C VAL* 4.8 3.5 + - - +
251C PRO* 3.6 25.2 - - + +
252C VAL* 3.1 9.7 - - - +
253C LEU* 3.0 31.6 + - + +
255C PHE* 5.0 1.0 - - - -
286C MET* 5.9 0.7 - - - -
160D SER* 3.3 10.9 + - - -
161D GLN 3.7 7.2 - - - -
162D TYR* 4.2 14.4 - + + -
242D ASN* 1.3 74.1 - - - +
244D THR* 1.3 71.7 + - - +
245D GLY* 2.8 37.1 - - - -
246D GLY 3.9 1.2 + - - -
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Residues in contact with THR 244 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250C PRO* 6.1 1.3 - - + -
251C PRO 3.2 4.3 - - - +
252C VAL* 3.6 19.7 - - + -
159D GLY 4.4 0.2 - - - +
160D SER* 3.1 2.3 - - - -
161D GLN* 3.0 51.7 + - + +
163D HIS* 5.8 1.2 - - - -
242D ASN* 3.0 18.0 + - - +
243D TYR* 1.3 81.8 - - - +
245D GLY* 1.3 66.9 + - - +
249D THR* 4.4 12.2 - - + +
250D PRO 6.0 0.2 - - - +
252D VAL* 6.0 4.0 - - + -
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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