Contacts of the strand formed by residues 194 - 199 (chain E) in PDB entry 1TYE
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 LEU 194 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146E CYS* 4.3 5.4 - - - -
164E LYS* 4.3 9.9 - - + -
167E CYS* 4.0 15.3 - - - -
184E GLY* 3.8 0.2 - - - -
185E ALA* 2.7 58.6 + - + -
188E GLY* 3.8 20.0 - - - -
189E TYR* 3.6 41.3 - - + +
193E GLY* 1.3 74.8 - - - +
195E LEU* 1.3 77.5 + - - +
196E ALA* 4.2 8.7 - - + +
221E LEU* 4.7 7.2 - - + -
222E SER* 3.2 14.1 - - - +
235E TRP* 3.2 10.3 + - - +
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Residues in contact with LEU 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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182E VAL* 3.9 22.4 - - + -
183E LEU 3.3 12.1 - - - +
184E GLY* 4.0 2.7 - - - -
194E LEU* 1.3 84.8 - - - +
196E ALA* 1.3 59.9 + - - +
220E SER 3.6 0.9 - - - +
221E LEU* 3.3 5.9 - - - +
222E SER* 2.7 34.3 + - - +
235E TRP* 3.6 20.4 - - + -
236E GLY* 4.4 0.9 - - - -
239E VAL* 3.8 25.1 - - + -
253E TYR* 4.1 13.7 - - + -
255E VAL* 3.6 27.1 - - + -
270E LEU* 5.8 0.2 - - + -
274E TYR* 3.8 25.8 + - + +
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Residues in contact with ALA 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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143E TYR* 4.1 6.4 - - + +
145E PRO* 3.8 34.3 - - + -
169E ALA* 5.9 1.1 - - + -
181E LEU 3.7 0.9 - - - +
182E VAL* 3.5 2.2 - - - +
183E LEU* 2.7 46.1 + - + +
185E ALA* 6.0 0.4 - - + -
194E LEU* 4.2 8.9 - - + +
195E LEU* 1.3 74.4 - - - +
197E GLN* 1.3 60.7 + - - +
220E SER 3.5 4.7 - - - -
221E LEU* 4.2 11.9 - - + -
274E TYR* 4.4 0.2 - - - -
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Residues in contact with GLN 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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143E TYR* 4.1 2.8 + - - -
180E GLU* 3.2 39.1 - - - +
181E LEU 3.1 10.9 + - - +
182E VAL* 3.8 16.2 - - + +
196E ALA* 1.3 75.8 - - - +
198E ALA* 1.3 76.4 + - - +
199E PRO* 4.3 4.7 - - - +
218E SER 3.9 9.9 - - - +
219E GLN* 3.4 1.9 - - - +
220E SER* 2.8 48.7 + - - -
253E TYR* 3.5 21.1 + - - +
274E TYR* 3.6 15.5 - - + +
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Residues in contact with ALA 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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143E TYR* 3.7 25.5 - - + +
181E LEU* 2.8 33.2 + - - +
197E GLN* 1.3 82.6 - - - +
199E PRO* 1.3 74.6 - - + +
200E VAL 3.5 0.5 + - - -
203E ILE* 3.9 15.5 - - + +
216E VAL* 4.3 5.8 - - + -
218E SER 4.4 0.4 - - - -
219E GLN* 4.1 10.5 - - - -
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Residues in contact with PRO 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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179E GLY 3.7 8.1 - - - +
180E GLU* 4.1 15.7 - - + +
197E GLN* 4.3 4.3 - - - +
198E ALA* 1.3 85.5 - - + +
200E VAL* 1.3 66.2 + - - +
201E ALA* 4.4 3.6 - - + +
202E ASP* 3.0 29.9 + - + +
203E ILE* 2.9 21.4 + - - +
218E SER* 3.2 30.5 - - - +
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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