Contacts of the strand formed by residues 180 - 185 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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175C VAL* 3.3 3.8 - - - +
176C THR* 2.9 53.1 + - + +
178C ALA* 4.2 17.1 - - + +
179C GLY* 1.3 75.8 - - - +
181C LEU* 1.3 64.2 + - - +
182C VAL* 3.5 7.0 + - + +
197C GLN* 5.5 7.5 - - + +
198C ALA 3.8 10.5 - - - +
199C PRO* 4.0 18.4 - - + +
251C THR* 4.6 8.1 + - - -
253C TYR* 5.2 5.5 + - - +
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Residues in contact with LEU 181 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98C VAL* 4.7 3.8 - - + -
105C VAL* 4.0 31.0 - - + -
130C CYS* 4.9 2.9 - - + -
132C LEU* 4.3 8.5 - - + -
143C TYR* 4.1 11.8 - - + -
173C SER* 4.8 1.3 - - - -
174C VAL 3.8 4.7 - - - +
175C VAL* 3.9 21.8 - - + -
179C GLY 3.8 2.4 + - - -
180C GLU* 1.3 72.1 - - - +
182C VAL* 1.3 62.6 + - - +
183C LEU* 3.8 28.0 - - + -
196C ALA 3.6 1.6 - - - +
197C GLN* 3.2 6.1 - - - -
198C ALA 2.8 36.7 + - - +
200C VAL* 4.1 11.8 - - + +
203C ILE* 3.7 22.9 - - + -
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Residues in contact with VAL 182 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173C SER* 3.4 6.4 - - - -
174C VAL* 2.8 52.3 + - + +
176C THR* 4.2 9.2 - - + -
180C GLU* 3.7 11.4 - - + +
181C LEU* 1.3 76.3 - - - +
183C LEU* 1.3 64.0 + - - +
184C GLY 4.1 0.2 + - - -
195C LEU* 3.9 31.2 - - + -
196C ALA 3.6 4.9 - - - +
197C GLN* 4.4 7.4 - - + +
239C VAL* 4.4 5.0 - - + +
253C TYR* 4.0 37.7 - - + +
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Residues in contact with LEU 183 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130C CYS* 3.6 30.5 - - + -
143C TYR* 3.7 33.2 - - + +
145C PRO* 4.5 5.2 - - + -
169C ALA* 4.5 12.6 - - + -
170C GLY 3.7 19.7 - - - +
172C SER 3.9 1.1 - - - +
173C SER* 3.9 13.0 - - - -
181C LEU* 3.8 22.0 + - + -
182C VAL* 1.3 79.9 - - - +
184C GLY* 1.3 60.9 + - - +
185C ALA* 5.1 0.6 - - + +
194C LEU 3.9 0.2 - - - +
195C LEU* 3.1 11.1 - - - +
196C ALA* 2.7 46.0 + - + +
239C VAL* 5.3 0.4 - - - -
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Residues in contact with GLY 184 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170C GLY 3.3 5.4 + - - -
171C PHE* 3.2 27.9 + - - +
172C SER* 3.1 27.8 + - - -
182C VAL 4.1 0.6 + - - -
183C LEU* 1.3 73.4 - - - +
185C ALA* 1.3 58.6 + - - -
194C LEU 3.8 3.1 - - - -
195C LEU* 3.8 11.2 - - - -
236C GLY* 3.6 11.7 - - - -
239C VAL* 4.5 2.5 - - - +
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Residues in contact with ALA 185 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146C CYS* 4.7 0.2 - - - -
167C CYS* 3.1 40.6 - - + +
168C GLU 4.0 1.1 - - - -
169C ALA* 3.8 11.0 - - + -
183C LEU* 5.1 1.6 - - + +
184C GLY* 1.3 73.3 - - - +
186C PRO* 1.3 55.9 - - - +
188C GLY 2.9 11.8 + - - -
194C LEU* 2.7 50.4 + - + +
196C ALA* 6.0 0.9 - - + +
235C TRP 4.2 0.7 - - - -
236C GLY* 4.0 1.2 + - - -
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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