Contacts of the strand formed by residues 180 - 185 (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 GLU 180 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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175E VAL* 3.0 5.8 - - - +
176E THR* 2.7 58.7 + - + +
178E ALA* 3.9 19.9 - - + +
179E GLY* 1.3 78.7 - - - +
181E LEU* 1.3 61.7 + - - +
182E VAL* 3.6 1.3 + - + -
197E GLN* 3.2 27.0 - - - +
198E ALA 3.8 3.8 - - - -
199E PRO* 4.1 15.3 - - + +
251E THR* 4.8 7.6 + - - -
253E TYR* 5.7 1.7 + - - -
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Residues in contact with LEU 181 (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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98E VAL* 4.6 0.2 - - + -
105E VAL* 4.1 27.8 - - + -
130E CYS* 4.9 3.4 - - + -
132E LEU* 4.6 10.1 - - + -
143E TYR* 4.2 12.5 - - + -
173E SER* 4.6 4.9 - - - -
174E VAL 3.6 9.0 - - - +
175E VAL* 4.0 16.8 - - + +
179E GLY 3.9 2.0 + - - -
180E GLU* 1.3 70.8 - - - +
182E VAL* 1.3 62.1 + - - +
183E LEU* 3.6 32.8 - - + -
196E ALA 3.7 1.0 - - - +
197E GLN* 3.1 24.9 - - - +
198E ALA 2.8 20.1 + - - +
200E VAL* 4.1 12.1 - - + +
203E ILE* 3.8 21.5 - - + -
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Residues in contact with VAL 182 (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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173E SER* 3.3 4.9 - - - -
174E VAL* 2.6 47.1 + - + +
176E THR* 4.6 9.0 - - + -
180E GLU 4.2 6.3 - - - +
181E LEU* 1.3 76.2 - - - +
183E LEU* 1.3 65.6 + - - +
184E GLY 4.2 0.2 + - - -
195E LEU* 3.9 31.6 - - + -
196E ALA 3.5 4.3 - - - +
197E GLN* 3.8 15.7 - - + +
239E VAL* 4.3 11.9 - - + +
241E VAL* 4.7 4.5 - - + -
253E TYR* 3.6 31.6 - - + -
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Residues in contact with LEU 183 (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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130E CYS* 3.5 32.1 - - + -
143E TYR* 3.7 34.3 - - + +
145E PRO* 4.6 9.2 - - + -
169E ALA* 4.6 5.6 - - + -
170E GLY* 3.7 17.0 - - - +
172E SER 3.7 1.1 - - - +
173E SER* 3.7 15.5 - - - -
181E LEU* 3.6 24.9 - - + -
182E VAL* 1.3 82.3 - - - +
184E GLY* 1.3 60.4 + - - +
185E ALA* 3.8 1.2 + - + +
195E LEU* 3.3 11.6 - - - +
196E ALA* 2.7 42.3 + - + +
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Residues in contact with GLY 184 (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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170E GLY 3.3 18.8 + - - -
171E PHE* 3.3 12.0 + - - +
172E SER* 2.9 17.7 + - - +
182E VAL 4.2 0.4 + - - -
183E LEU* 1.3 73.2 - - - +
185E ALA* 1.3 59.5 + - - -
186E PRO* 3.5 8.0 - - - +
194E LEU 3.8 3.6 - - - -
195E LEU* 4.0 10.3 - - - -
236E GLY 3.4 16.8 - - - -
239E VAL* 4.2 3.2 - - - +
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Residues in contact with ALA 185 (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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167E CYS* 3.3 21.8 - - + +
168E GLU 4.0 0.9 - - - -
169E ALA* 3.8 18.2 - - + -
183E LEU 5.0 1.1 - - - +
184E GLY* 1.3 74.4 - - - +
186E PRO* 1.3 53.8 - - - +
187E GLY 3.1 4.5 - - - -
188E GLY 2.8 17.7 + - - -
194E LEU* 2.7 60.9 + - + -
196E ALA* 6.0 0.7 - - + -
235E TRP 4.2 0.2 - - - -
236E GLY 4.1 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