Contacts of the strand formed by residues 194 - 203 (chain E) in PDB entry 2XTJ
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 TYR 194 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91D THR* 4.7 9.0 - - - +
128D THR* 4.1 16.0 - - + +
162E ASP* 3.1 9.5 + - - -
163E TYR* 2.7 67.1 + + + +
164E PHE* 3.8 27.6 - + - -
165E PRO 4.3 0.4 - - - -
166E GLU* 3.9 45.4 - - + +
186E ALA* 4.2 3.4 - - + -
187E VAL 3.3 17.0 - - - -
188E LEU* 3.7 36.6 - - + +
193E LEU* 1.3 73.4 - - - +
195E SER* 1.3 60.9 + - - +
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Residues in contact with SER 195 (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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177C THR* 5.7 3.5 - - - +
159E LEU* 4.3 11.6 - - - +
160E VAL 3.4 7.3 + - - -
161E LYS* 3.5 21.7 - - - +
163E TYR* 4.2 0.4 - - - -
185E PRO 4.7 0.5 - - - +
186E ALA* 4.3 1.1 - - - -
187E VAL* 3.0 40.3 + - - +
189E GLN* 3.4 29.1 + - - -
194E TYR* 1.3 77.4 - - - +
196E LEU* 1.3 62.1 + - - +
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Residues in contact with LEU 196 (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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159E LEU* 3.7 5.7 - - - +
160E VAL* 2.8 59.2 + - + +
163E TYR* 4.2 4.1 - - - +
166E GLU* 5.5 0.7 - - - +
168E VAL* 3.5 33.7 - - + +
170E VAL* 4.3 7.0 - - + -
183E THR* 4.3 17.0 - - + -
184E PHE 3.3 20.6 - - - +
185E PRO 4.1 2.5 - - - +
186E ALA* 3.7 20.9 - - + +
195E SER* 1.3 75.8 + - - +
197E SER* 1.3 73.7 + - - +
198E SER 4.3 0.4 - - - +
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Residues in contact with SER 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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132C VAL* 5.2 4.8 - - - +
175C SER* 3.1 30.2 + - - -
177C THR* 5.1 4.2 + - - -
142E LEU* 4.5 12.3 - - - -
158E CYS 3.4 10.8 - - - -
159E LEU* 4.3 13.0 - - - -
184E PHE* 3.0 37.0 + - - +
196E LEU* 1.3 81.4 - - - +
198E SER* 1.3 61.3 + - - +
199E VAL* 5.1 2.9 - - - -
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Residues in contact with SER 198 (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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157E GLY* 3.1 2.4 - - - -
158E CYS* 2.8 37.4 + - - +
160E VAL* 5.7 0.2 - - - -
170E VAL* 3.6 27.1 - - - +
172E TRP* 3.4 21.1 + - - -
181E VAL* 4.3 0.2 - - - +
182E HIS 3.4 6.2 + - - -
183E THR* 2.9 29.1 + - - +
196E LEU* 4.3 0.6 - - - +
197E SER* 1.3 74.7 - - - +
199E VAL* 1.3 63.2 + - - +
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Residues in contact with VAL 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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117C PHE* 5.1 5.6 - - + -
132C VAL* 6.0 2.2 - - + -
134C LEU* 3.9 33.9 - - + -
136C ASN* 4.8 0.9 - - - +
175C SER* 6.2 1.1 - - - -
142E LEU* 4.3 20.0 - - + -
155E ALA* 5.7 0.2 - - + -
156E LEU 3.3 14.1 - - - +
157E GLY* 4.0 0.9 - - - -
172E TRP* 4.6 2.0 - - - -
181E VAL* 3.4 4.3 - - - +
182E HIS* 2.8 48.3 + - + +
184E PHE* 3.7 26.5 - - + -
197E SER* 5.1 2.9 - - - -
198E SER* 1.3 79.8 - - - +
200E VAL* 1.3 67.5 + - - +
201E THR* 6.4 0.7 - - + -
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Residues in contact with VAL 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 ALA 3.8 0.9 - - - +
155E ALA* 3.4 1.8 - - - -
156E LEU* 2.8 64.9 + - + +
172E TRP* 4.0 21.1 - - + -
177E LEU* 4.3 13.0 - - + -
179E SER 4.1 7.0 - - - +
180E GLY 3.5 9.2 - - - +
181E VAL* 4.0 23.8 - - + -
199E VAL* 1.3 78.9 - - - +
201E THR* 1.3 79.3 + - - +
202E VAL* 4.1 11.0 - - + -
212E TYR* 5.6 0.4 - - + -
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Residues in contact with THR 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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115C PHE* 4.9 5.6 - - + -
134C LEU* 5.8 0.4 - - + -
136C ASN* 3.6 30.2 + - - +
153E THR* 3.7 21.9 - - + +
154E ALA 3.4 3.1 - - - +
155E ALA* 3.9 24.2 - - + +
179E SER 4.3 6.9 - - - +
180E GLY* 3.5 18.6 + - - +
199E VAL* 6.4 0.7 - - + -
200E VAL* 1.3 80.8 - - - +
202E VAL* 1.3 69.0 + - - +
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Residues in contact with VAL 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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153E THR* 3.3 10.6 - - - -
154E ALA 2.7 39.2 + - - +
156E LEU* 3.9 13.9 - - + -
177E LEU* 4.8 8.3 - - + -
200E VAL* 4.1 14.1 - - + +
201E THR* 1.3 83.8 - - - +
203E PRO* 1.4 77.3 - - + +
207E LEU* 4.3 6.3 - - + -
212E TYR* 3.4 47.3 - - + +
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Residues in contact with PRO 203 (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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152E GLY 3.4 9.4 - - - +
153E THR* 4.7 0.4 - - + -
202E VAL* 1.4 96.6 - - + +
204E SER* 1.3 63.0 + - - +
205E SER* 3.7 17.5 - - - +
206E SER* 2.9 32.6 + - - +
207E LEU* 4.1 1.4 + - - +
212E TYR* 4.9 0.4 - - - +
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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