Contacts of the strand formed by residues 161 - 168 (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 GLN 161 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136D LEU* 5.3 0.7 - - - -
159E GLY 3.1 11.3 + - - +
160E SER* 1.3 73.9 - - - +
162E TYR* 1.3 64.4 + - - +
163E HIS* 4.2 8.8 + - + +
242E ASN* 4.1 0.4 - - - +
243E TYR* 3.6 3.2 - - - -
244E THR* 2.7 47.2 + - + +
249E THR* 3.0 19.6 + - - +
250E PRO 3.0 13.1 + - - -
251E PRO* 2.9 38.3 - - - +
252E VAL* 3.6 15.5 + - - +
285E ILE* 3.0 17.3 - - - +
286E MET* 3.4 21.0 - - - +
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Residues in contact with TYR 162 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132D SER 4.3 0.2 - - - -
133D GLY* 3.6 16.7 - - - -
136D LEU* 4.0 21.8 - - + -
255D PHE* 3.3 30.2 - + - -
98E TRP* 4.5 5.7 - + - -
161E GLN* 1.3 76.6 - - - +
163E HIS* 1.3 67.9 + - - +
164E VAL* 3.3 15.2 - - + +
224E VAL* 3.2 34.2 - - + +
227E TRP 4.4 3.1 + - - -
228E HIS* 3.8 13.2 + - - -
229E PRO* 4.7 1.6 - - - +
242E ASN 3.5 15.7 - - - -
243E TYR* 4.2 15.3 - + + -
283E VAL* 3.1 34.6 - - + +
285E ILE* 2.7 50.1 + - + +
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Residues in contact with HIS 163 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129E VAL* 4.6 4.5 - - + +
161E GLN* 4.2 9.8 + - + +
162E TYR* 1.3 79.1 + - - +
164E VAL* 1.3 63.3 + - - +
241E GLY* 2.8 20.4 - - - -
242E ASN* 2.9 26.9 + - - +
252E VAL 5.1 4.2 + - - -
253E LEU* 5.0 8.4 - - + +
283E VAL 2.8 6.7 - - - -
284E ASP* 2.8 39.9 + - + +
285E ILE 3.5 24.3 + - - -
286E MET* 3.6 28.5 - - - +
304E ARG* 4.4 6.7 - - - +
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Residues in contact with VAL 164 (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* 3.8 13.2 - - + -
98E TRP* 3.7 22.7 - - + -
162E TYR* 3.3 35.7 - - + +
163E HIS* 1.3 83.9 - - - +
165E PHE* 1.3 80.2 + - - +
229E PRO* 4.8 4.7 - - + -
239E TYR* 4.6 11.9 - - + -
240E PHE 2.9 25.4 - - - +
241E GLY* 3.7 6.7 - - - -
242E ASN 4.3 0.2 - - - +
282E CYS* 3.0 3.4 - - - +
283E VAL* 2.9 26.6 + - + +
304E ARG* 4.2 1.8 + - - -
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Residues in contact with PHE 165 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98E TRP* 4.7 2.5 - - - -
125E VAL* 5.1 10.5 - - + -
127E THR* 4.1 20.2 - - + -
164E VAL* 1.3 83.3 - - - +
166E ALA* 1.3 80.4 + - - +
167E VAL* 4.4 10.8 - - + -
239E TYR* 2.9 4.0 - - - +
240E PHE* 2.7 77.8 + + + -
261E THR* 6.0 5.6 - - + -
263E LEU* 6.1 0.2 - - + -
281E SER 2.9 16.2 - - - +
282E CYS* 3.2 11.4 - - + +
304E ARG* 3.8 28.0 - - - +
306E PHE* 4.2 13.9 - + - -
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Residues in contact with ALA 166 (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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165E PHE* 1.3 81.0 - - - +
167E VAL* 1.3 70.4 + - - +
172E LEU* 4.8 10.5 - - + -
237E THR* 4.0 13.7 - - + -
238E ARG 2.7 22.0 - - - +
239E TYR* 3.2 12.3 - - + -
279E TYR 3.5 1.5 - - - +
280E LEU* 3.5 0.5 - - - -
281E SER* 2.7 39.5 + - - +
306E PHE* 4.5 0.3 - - - -
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Residues in contact with VAL 167 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122E ALA* 4.7 6.7 - - + -
125E VAL* 4.6 13.5 - - + -
165E PHE* 4.4 11.2 - - + -
166E ALA* 1.3 83.1 - - - +
168E GLY* 1.3 61.6 + - - +
237E THR* 3.2 4.4 - - - -
238E ARG* 2.8 30.2 + - - +
240E PHE* 6.1 0.2 - - + -
263E LEU* 4.3 27.6 - - + -
271E PRO* 3.9 7.2 - - + +
278E LEU* 4.0 10.8 - - + -
279E TYR 3.2 3.6 - - - -
280E LEU* 4.0 23.6 - - + -
306E PHE* 4.4 15.5 - - + -
308E ILE* 4.5 6.3 - - + -
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Residues in contact with GLY 168 (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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122E ALA* 6.4 0.2 - - - -
167E VAL* 1.3 76.4 - - - +
169E GLY* 1.3 59.5 + - - -
170E GLU 3.4 4.7 - - - -
236E ASN 3.2 9.0 - - - -
237E THR* 3.0 17.5 - - - +
271E PRO* 4.2 6.7 - - - -
273E CYS* 5.5 0.9 - - - -
278E LEU* 3.6 8.0 - - - +
279E TYR* 2.8 42.6 + - - -
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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