Contacts of the strand formed by residues 175 - 181 (chain C) in PDB entry 1UDY
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 TRP 175 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104C GLY 3.5 26.7 - - - -
105C GLN* 4.1 10.8 - - + -
108C LEU* 3.5 26.7 - - + -
120C TYR* 3.2 42.2 + + + -
121C LEU* 4.4 0.9 - - + -
123C ARG* 4.3 4.0 - - - -
124C MET* 3.5 15.1 - - - -
130C MET 4.0 0.2 + - - -
131C CYS* 3.3 33.3 - - + +
132C ALA 3.2 20.3 + - - -
173C ALA* 3.3 3.5 - - - +
174C ASN* 1.3 99.2 - - + +
176C TYR* 1.3 71.0 + - - +
177C PHE* 4.2 13.0 - - + -
198C ILE* 3.4 30.5 - - + -
199C VAL 3.5 11.9 - - - +
200C GLU* 4.1 5.8 - - + -
201C ALA 3.9 2.0 - - - +
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Residues in contact with TYR 176 (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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132C ALA* 3.5 25.4 - - + -
134C CYS* 3.9 19.7 - - + -
170C GLY 2.4 30.6 + - - -
171C GLY* 4.3 0.3 - - - -
173C ALA* 3.5 18.7 + - + -
175C TRP* 1.3 83.6 - - - +
177C PHE* 1.3 61.8 + - - +
178C LEU* 3.7 2.2 + - + -
198C ILE* 3.4 3.8 - - - -
199C VAL* 2.7 54.5 + - + +
200C GLU 4.9 0.2 - - - -
201C ALA* 3.6 27.9 - - + +
206C VAL* 4.5 13.5 - - + -
208C ILE* 3.3 22.0 - - - +
225C ILE* 4.1 15.0 - - + -
227C PHE* 4.6 15.0 - + + -
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Residues in contact with PHE 177 (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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104C GLY 4.0 16.6 - - - +
107C PRO* 3.5 27.8 - - + -
108C LEU* 6.2 2.0 - - + -
132C ALA 2.9 14.5 + - - +
133C TYR* 3.4 42.0 - + + -
134C CYS* 2.8 32.6 + - - +
135C VAL* 4.5 2.9 - - + -
175C TRP* 4.1 5.9 - - + -
176C TYR* 1.3 72.2 - - - +
178C LEU* 1.3 62.3 + - - +
179C LEU* 4.4 23.1 - - + -
196C GLY* 3.9 23.1 - - - -
197C PHE 3.6 7.2 - - - -
198C ILE* 4.6 2.2 - - + +
238C LEU* 3.7 20.6 - - + -
244C GLY 5.1 0.9 - - - -
247C ILE* 4.4 11.7 - - + -
248C ALA* 5.3 4.3 - - + -
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Residues in contact with LEU 178 (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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134C CYS* 3.6 8.5 - - + -
149C THR* 4.8 1.1 - - + +
160C ILE* 4.6 11.7 - - + -
164C LYS* 3.5 26.5 - - - -
176C TYR* 3.7 1.3 + - + -
177C PHE* 1.3 78.1 - - - +
179C LEU* 1.3 78.5 + - - +
180C ALA* 3.6 15.7 - - + -
195C THR 3.5 0.9 - - - +
196C GLY* 3.4 3.0 - - - -
197C PHE* 2.7 50.6 + - + +
199C VAL* 3.9 21.5 - - + -
227C PHE* 3.5 38.6 - - + -
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Residues in contact with LEU 179 (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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134C CYS 3.2 14.3 + - - +
135C VAL* 4.0 18.6 - - + -
144C VAL* 3.9 24.2 - - + -
147C ILE* 3.6 22.7 - - + +
149C THR* 3.2 3.1 - - - +
164C LYS* 2.9 26.9 + - - -
177C PHE* 4.4 9.1 - - + -
178C LEU* 1.3 75.3 - - - +
180C ALA* 1.3 60.4 + - - +
194C PHE* 4.0 14.1 - - + -
195C THR 3.9 9.9 - - - +
196C GLY* 4.2 3.1 - - - +
244C GLY* 3.7 37.7 - - - +
245C PHE* 5.3 1.1 - - - -
248C ALA* 4.4 11.9 - - + -
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Residues in contact with ALA 180 (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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147C ILE* 4.3 0.4 - - - -
149C THR* 3.5 17.7 - - + +
150C LYS 4.1 6.1 - - - +
151C ALA* 4.1 22.9 - - + -
160C ILE* 4.6 1.8 - - + -
178C LEU* 3.6 15.7 - - + -
179C LEU* 1.3 76.4 - - - +
181C ARG* 1.3 62.9 + - - +
194C PHE* 3.4 5.5 - - - -
195C THR* 2.8 33.3 + - - +
197C PHE* 4.3 5.8 - - + -
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Residues in contact with ARG 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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145C ALA 4.5 5.7 + - - -
147C ILE* 4.2 14.7 + - - +
148C LYS* 5.2 6.7 - - - +
149C THR* 2.8 16.9 + - - +
150C LYS* 2.7 35.5 - - + +
151C ALA 3.3 10.3 + - - -
180C ALA* 1.3 71.6 - - - +
182C SER* 1.3 55.6 + - - +
183C ASP 2.8 21.0 + - - +
184C PRO* 4.4 5.6 + - - -
185C ASP 2.8 29.1 + - - -
186C PRO* 4.1 9.0 + - - +
188C ALA* 3.4 20.4 + - - +
190C ALA* 5.9 0.4 - - - +
193C ALA* 3.3 30.5 - - - +
194C PHE* 3.5 32.6 - - + -
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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