Contacts of the helix formed by residues 200 - 207 (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 VAL 200 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100E TRP* 4.2 18.6 - - + -
103E VAL* 3.8 31.9 - - + -
105E VAL* 5.1 4.5 - - + -
132E LEU* 4.4 11.2 - - + -
175E VAL* 4.5 9.4 - - + -
179E GLY 2.9 25.8 + - - +
181E LEU* 4.1 20.4 - - + +
198E ALA 3.5 1.0 + - - -
199E PRO* 1.3 69.9 - - - +
201E ALA* 1.3 63.5 + - - +
203E ILE* 3.2 9.0 + - - +
204E PHE* 3.1 37.0 + - + -
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Residues in contact with ALA 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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100E TRP* 5.6 3.9 - - + -
179E GLY 4.7 0.6 + - - -
199E PRO* 3.2 4.3 - - + +
200E VAL* 1.3 79.9 - - - +
202E ASP* 1.3 64.9 + - - +
204E PHE* 3.4 7.5 + - - +
205E SER* 3.0 28.9 + - - -
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Residues in contact with ASP 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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199E PRO* 3.0 22.2 + - + +
201E ALA* 1.3 83.4 - - - +
203E ILE* 1.3 64.2 + - - +
205E SER* 3.5 8.5 + - - +
206E SER* 2.9 31.0 + - - -
216E VAL* 4.1 10.3 - - + +
217E SER* 5.1 4.3 + - - +
218E SER* 2.6 34.9 + - - +
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Residues in contact with ILE 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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132E LEU* 3.9 24.9 - - + -
141E ALA* 4.6 1.8 - - + -
142E GLU 3.8 20.5 - - - +
143E TYR* 3.6 38.6 - - + -
181E LEU* 3.8 24.5 - - + -
198E ALA* 3.9 26.5 - - + +
199E PRO 2.9 13.0 + - - +
200E VAL* 3.2 10.1 + - - +
202E ASP* 1.3 78.9 - - - +
204E PHE* 1.3 62.2 + - - +
206E SER* 3.6 4.9 + - - -
207E TYR* 3.2 23.7 + - - +
214E TRP* 5.1 1.1 + - - +
216E VAL* 4.7 4.9 - - + -
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Residues in contact with PHE 204 (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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103E VAL* 4.3 9.2 - - + -
132E LEU* 3.6 31.4 - - + -
133E ALA 4.1 16.6 - - - -
134E GLN* 4.5 9.6 - - + -
139E ARG* 3.9 58.4 + - + +
140E ARG 4.1 11.7 - - - -
141E ALA* 3.6 22.8 - - + +
200E VAL* 3.1 41.1 + - + -
201E ALA* 3.7 9.6 - - - +
202E ASP 3.3 0.2 - - - -
203E ILE* 1.3 78.0 - - - +
205E SER* 1.3 62.3 + - - +
207E TYR* 3.4 18.4 + - - +
208E ARG* 5.1 0.3 + - - -
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Residues in contact with SER 205 (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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139E ARG* 5.2 2.9 - - - +
201E ALA 3.0 17.1 + - - -
202E ASP* 3.5 12.5 + - - +
204E PHE* 1.3 76.9 - - - +
206E SER* 1.3 61.6 + - - +
208E ARG* 3.1 29.3 + - - -
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Residues in contact with SER 206 (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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202E ASP 2.9 20.0 + - - -
203E ILE 3.6 2.3 + - - -
205E SER* 1.3 79.6 + - - +
207E TYR* 1.3 63.7 + - - +
208E ARG* 3.6 15.6 + - - +
214E TRP* 3.7 19.2 + - - -
215E HIS 5.3 1.8 - - - -
216E VAL* 3.5 30.1 - - - +
217E SER* 5.6 2.2 - - - -
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Residues in contact with TYR 207 (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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75E GLU* 5.5 2.1 + - - -
140E ARG* 4.0 11.7 - - + -
141E ALA* 3.7 21.8 - - + -
142E GLU* 3.4 53.4 + - + +
203E ILE 3.2 18.1 + - - +
204E PHE 3.7 10.3 - - - +
205E SER 3.3 1.2 - - - -
206E SER* 1.3 77.1 + - - +
208E ARG* 1.3 84.8 + - - +
209E PRO* 3.7 38.7 - - + +
210E GLY 4.8 1.6 + - - -
211E ILE 5.1 2.5 - - - -
214E TRP* 3.8 28.9 - + + +
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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