Contacts of the strand formed by residues 176 - 185 (chain C) in PDB entry 3SO3
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 TYR 176 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144C ASP* 3.0 24.8 + - - -
145C TYR* 2.9 48.1 + - + +
146C PHE* 3.8 29.9 - + - -
147C PRO* 4.4 0.9 - - + -
148C GLU* 3.7 51.0 + - + +
168C ALA* 4.2 6.5 - - + -
169C VAL 3.3 17.5 - - - -
170C LEU* 3.9 35.3 - - + +
171C GLN* 3.8 0.4 - - - -
175C LEU* 1.3 75.5 - - - +
177C SER* 1.3 62.2 + - - +
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Residues in contact with SER 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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141C LEU* 3.7 14.0 - - - +
142C VAL 3.3 12.6 + - - -
143C LYS* 3.6 15.5 + - - +
145C TYR* 3.9 4.5 - - - -
168C ALA* 3.4 1.7 - - - -
169C VAL* 2.9 39.0 + - - +
171C GLN* 3.6 26.4 + - - -
176C TYR* 1.3 77.0 - - - +
178C LEU* 1.3 65.0 + - - +
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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
----------------------------------------------------------
141C LEU* 3.6 6.7 - - - +
142C VAL* 2.7 58.3 + - + +
145C TYR* 3.5 9.2 - - - +
150C VAL* 3.5 33.4 - - + +
152C VAL* 4.1 9.2 - - + -
165C THR* 4.0 19.1 - - + -
166C PHE* 3.7 20.9 - - - +
167C PRO 4.4 2.0 - - - +
168C ALA* 4.0 11.0 - - + +
177C SER* 1.3 77.5 + - - +
179C SER* 1.3 76.0 + - - +
180C SER 4.1 0.2 - - - +
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Residues in contact with SER 179 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B VAL* 4.5 7.4 - - - +
176B SER* 5.0 9.9 - - - -
178B THR* 5.0 2.1 + - - -
124C LEU* 3.6 21.6 - - - +
140C CYS 3.3 7.5 + - - -
141C LEU* 3.4 23.0 - - - +
166C PHE* 2.9 45.8 + - - +
178C LEU* 1.3 79.8 - - - +
180C SER* 1.3 61.5 + - - +
181C VAL* 4.8 3.6 - - - -
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Residues in contact with SER 180 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139C GLY* 3.1 2.4 - - - -
140C CYS* 2.8 35.9 + - - +
142C VAL* 5.9 0.4 - - - -
152C VAL* 3.8 24.0 - - - +
154C TRP* 3.0 27.3 + - - -
163C VAL* 3.8 3.1 - - - +
164C HIS 3.4 4.5 - - - -
165C THR* 2.6 30.1 + - - +
178C LEU* 4.1 0.6 - - - +
179C SER* 1.3 74.7 - - - +
181C VAL* 1.3 63.2 + - - +
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Residues in contact with VAL 181 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B PHE* 5.0 6.1 - - + -
133B VAL* 5.8 2.5 - - + -
135B LEU* 3.8 36.1 - - + -
137B ASN* 4.7 0.7 - - - +
124C LEU* 4.5 18.2 - - + -
138C LEU 3.3 14.6 - - - +
154C TRP* 4.6 1.8 - - - -
162C GLY 5.1 0.2 - - - +
163C VAL* 3.3 6.8 - - - +
164C HIS* 2.9 56.6 + - + +
166C PHE* 4.0 17.9 - - + -
179C SER* 4.8 2.7 - - - -
180C SER* 1.3 78.8 - - - +
182C VAL* 1.3 65.2 + - - +
183C THR* 5.8 0.7 - - + -
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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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136C ALA 4.0 0.2 - - - +
137C ALA* 3.6 1.2 - - - -
138C LEU* 2.9 59.2 + - + +
154C TRP* 4.0 22.9 - - + -
159C LEU* 4.1 13.5 - - + -
161C SER 3.9 11.0 - - - +
162C GLY 3.4 5.2 - - - -
163C VAL* 3.7 23.1 - - + -
181C VAL* 1.3 77.6 - - - +
183C THR* 1.3 70.6 + - - +
184C VAL* 3.5 22.5 + - + +
194C TYR* 5.2 0.7 - - + -
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Residues in contact with THR 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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116B PHE* 4.7 9.4 - - + -
135B LEU* 5.0 2.9 - - + -
137B ASN* 3.5 31.4 + - - +
138B ASN* 5.4 0.5 + - - -
135C THR* 5.1 10.1 - - - -
136C ALA 3.3 7.0 - - - +
137C ALA* 4.1 19.5 - - + -
161C SER 4.5 1.9 - - - +
162C GLY* 3.3 22.9 + - - +
181C VAL* 5.8 1.3 - - + -
182C VAL* 1.3 80.0 - - - +
184C VAL* 1.3 66.5 + - - +
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Residues in contact with VAL 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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135C THR* 3.4 6.9 - - - -
136C ALA 2.7 39.8 + - - +
138C LEU* 3.9 15.0 - - + -
159C LEU* 4.8 5.4 - - + -
182C VAL* 3.5 21.8 - - + -
183C THR* 1.3 80.8 - - - +
185C PRO* 1.4 69.7 - - + +
188C SER* 4.2 0.7 - - - +
189C LEU* 3.8 25.6 - - + -
194C TYR* 3.5 33.7 - - + +
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Residues in contact with PRO 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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134C GLY 4.0 6.1 - - - +
135C THR* 4.1 8.9 - - + -
184C VAL* 1.4 88.1 - - + +
186C SER* 1.3 61.5 + - - +
187C SER* 4.4 9.9 - - - +
188C SER* 2.5 46.8 + - - +
189C LEU* 3.8 4.9 + - - +
194C TYR* 4.5 1.8 - - - +
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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