Contacts of the strand formed by residues 196 - 202 (chain E) in PDB entry 1XSK
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 ASN 196 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165E LEU 4.4 3.4 - - - -
168E ARG* 3.0 27.5 + - - -
180E GLU 3.1 15.1 - - - +
181E THR* 3.5 21.2 - - + -
182E TRP 3.2 10.8 + - - +
183E ASN* 2.7 40.8 + - - +
193E ALA* 3.1 26.1 + - - +
195E LYS* 1.3 72.0 - - - +
197E ILE* 1.3 76.2 + - - +
198E PRO* 4.5 3.3 - - - +
438E ASN* 4.9 5.7 - - - +
468E ALA 3.9 7.5 + - - +
469E SER* 4.0 5.5 + - - -
470E VAL 4.5 0.2 + - - -
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Residues in contact with ILE 197 (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 LEU* 3.0 25.9 + - - +
166E GLY* 3.8 22.0 - - - +
181E THR* 3.9 3.9 - - - +
195E LYS* 4.4 4.7 - - + +
196E ASN* 1.3 88.5 - - - +
198E PRO* 1.3 59.3 - - - +
199E PHE* 2.7 28.9 + - + -
254E TYR* 3.4 25.1 - - - +
468E ALA 4.9 0.9 - - - -
469E SER* 3.7 6.7 - - - +
470E VAL* 3.6 28.9 - - + +
503E SER* 4.4 9.6 - - - +
505E PHE* 3.6 31.4 - - + -
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Residues in contact with PRO 198 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82E TYR* 3.2 33.2 - - + +
181E THR* 3.9 22.4 - - + +
196E ASN 4.5 2.9 - - - +
197E ILE* 1.3 78.1 - - - +
199E PHE* 1.3 56.5 + - - +
208E VAL 3.8 1.2 - - - +
209E LEU* 3.5 5.6 - - + -
210E VAL* 2.8 57.7 + - + +
212E HIS 4.3 2.5 - - - +
216E VAL* 4.2 5.8 - - + -
218E PHE* 3.9 25.1 - - + -
470E VAL* 3.8 10.3 - - + -
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Residues in contact with PHE 199 (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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164E GLY 3.8 0.2 - - - -
165E LEU* 2.7 34.9 + - - +
166E GLY 4.5 0.2 + - - -
197E ILE* 2.7 24.8 + - + +
198E PRO* 1.3 75.4 - - - +
200E TYR* 1.3 75.2 + - - +
201E MET* 4.2 5.4 - - + -
207E GLY* 4.0 2.2 - - - -
208E VAL 3.3 24.2 - - - +
209E LEU* 3.9 5.6 - - + -
242E ILE* 3.8 14.8 - - + -
250E VAL* 3.9 21.1 - - + -
251E LEU* 4.1 12.8 - - + -
254E TYR* 3.7 45.5 - + + +
502E LEU 3.6 24.0 - - - -
503E SER* 4.2 11.6 + - - -
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Residues in contact with TYR 200 (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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154E LEU* 3.5 20.6 - - - +
162E VAL* 3.8 22.4 - - + -
163E TYR 3.3 12.8 - - - +
164E GLY* 4.7 0.2 - - - -
165E LEU* 3.8 12.3 - - + -
199E PHE* 1.3 81.0 - - - +
201E MET* 1.3 67.3 + - - +
202E THR* 4.0 18.8 - - + -
206E TYR* 4.5 7.3 + + - -
207E GLY* 3.2 2.3 - - - -
208E VAL* 2.9 77.4 + - + +
218E PHE* 4.0 21.1 - + - -
228E VAL* 3.6 41.5 - - + +
230E PHE* 4.5 3.8 - + - -
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Residues in contact with MET 201 (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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162E VAL* 3.6 2.4 - - - +
163E TYR* 2.8 41.0 + - + +
199E PHE* 4.2 4.7 - - + -
200E TYR* 1.3 78.7 - - - +
202E THR* 1.3 68.0 + - - +
206E TYR 3.4 11.2 - - - +
207E GLY* 4.0 4.3 - - - -
247E PRO* 3.3 45.5 - - + +
250E VAL* 3.4 20.2 - - + -
251E LEU* 4.1 18.2 - - - -
502E LEU* 3.9 42.6 - - + +
592E MET* 5.8 1.6 - - + +
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Residues in contact with THR 202 (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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156E LEU* 4.3 1.6 - - + -
160E GLU* 3.0 32.5 + - + +
161E THR 3.0 15.9 - - - +
162E VAL* 4.2 8.3 - - + -
163E TYR* 4.6 5.2 - - - -
200E TYR* 4.0 18.8 - - + -
201E MET* 1.3 84.3 - - - +
203E ASN* 1.3 59.8 + - - +
204E ARG* 3.0 17.2 + - - +
205E GLY* 3.3 10.4 + - - -
206E TYR* 3.2 28.7 + - + +
247E PRO* 4.8 5.0 - - - +
592E MET* 4.5 5.1 - - - +
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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