Contacts of the strand formed by residues 178 - 187 (chain C) in PDB entry 3IU3
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 178 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112C THR* 3.8 20.6 - - + +
146C ASP* 3.0 22.9 + - - +
147C TYR* 2.7 50.4 + - + +
148C PHE* 3.9 26.5 - + - -
149C PRO* 4.4 4.7 - - + -
150C GLU* 3.7 41.9 + - + -
170C ALA* 4.2 8.7 - - + -
171C VAL 3.7 4.9 - - - -
172C LEU* 3.9 43.9 - - + +
177C LEU* 1.3 75.6 - - - +
179C SER* 1.3 62.4 + - - +
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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
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143C LEU* 4.4 7.3 - - - +
144C VAL 3.4 7.6 + - - -
145C LYS* 3.4 25.4 - - - +
147C TYR* 3.9 2.9 - - - -
170C ALA* 3.5 0.9 - - - -
171C VAL* 3.1 38.7 + - - +
173C GLN* 3.2 28.7 + - - -
178C TYR* 1.3 76.4 - - - +
180C LEU* 1.3 64.7 + - - +
175D THR* 6.1 0.5 - - - +
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Residues in contact with LEU 180 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143C LEU* 3.7 7.4 - - - +
144C VAL* 2.9 51.9 + - + +
147C TYR* 3.4 27.6 - - + +
150C GLU* 5.5 0.7 - - - +
152C VAL* 4.4 11.4 - - + +
154C VAL* 4.4 7.2 - - + -
167C THR* 4.2 16.8 - - + -
168C PHE* 3.4 23.8 - - - +
169C PRO 4.1 3.6 - - - +
170C ALA* 3.9 13.7 - - + +
171C VAL* 5.8 0.9 - - - -
179C SER* 1.3 76.2 + - - +
181C SER* 1.3 76.3 + - - +
182C SER 4.2 0.7 - - - +
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Residues in contact with SER 181 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126C LEU* 4.4 11.0 - - - +
142C CYS 3.4 7.1 + - - -
143C LEU* 3.4 22.7 - - - +
167C THR* 3.8 0.7 - - - -
168C PHE* 3.0 47.2 + - - +
180C LEU* 1.3 80.0 - - - +
182C SER* 1.3 61.3 + - - +
183C VAL* 4.9 2.9 - - - -
130D VAL* 4.4 14.8 - - - +
173D SER* 5.0 9.4 + - - -
175D THR* 4.5 5.0 + - - -
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Residues in contact with SER 182 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126C LEU* 4.2 0.7 - - - +
141C GLY* 3.0 3.3 - - - -
142C CYS* 2.6 41.5 + - - +
144C VAL* 5.4 0.2 - - - -
154C VAL* 3.5 31.6 - - - +
156C TRP* 3.1 26.4 + - - -
165C VAL* 4.3 1.2 - - - +
166C HIS 3.5 3.5 + - - -
167C THR* 3.1 22.3 + - - +
180C LEU* 4.2 1.8 - - - +
181C SER* 1.3 72.9 - - - +
183C VAL* 1.3 64.1 + - - +
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Residues in contact with VAL 183 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126C LEU* 4.2 17.7 - - + -
139C ALA* 5.1 1.3 - - + -
140C LEU 3.5 11.7 - - - +
141C GLY* 4.0 0.2 - - - -
156C TRP* 4.8 1.1 - - - -
164C GLY 5.3 0.2 - - - +
165C VAL* 3.3 6.1 - - - +
166C HIS* 2.6 49.5 + - + +
168C PHE* 4.3 15.5 - - + -
181C SER* 4.9 4.0 - - - -
182C SER* 1.3 80.5 + - - +
184C VAL* 1.3 69.3 + - - +
185C THR* 5.2 1.6 - - + -
115D PHE* 4.9 5.8 - - + -
130D VAL* 5.9 1.6 - - + -
132D LEU* 3.4 39.0 - - + -
134D ASN* 4.7 7.6 - - - +
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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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139C ALA* 3.5 2.1 - - - +
140C LEU* 2.7 69.1 + - + +
156C TRP* 4.2 20.2 - - + -
161C LEU* 3.9 21.1 - - + -
163C SER 3.9 9.0 - - - +
164C GLY 3.2 11.4 - - - +
165C VAL* 3.8 21.8 - - + -
183C VAL* 1.3 76.7 - - - +
185C THR* 1.3 72.2 + - - +
186C VAL* 4.2 5.8 - - + -
196C TYR* 5.0 0.7 - - + -
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Residues in contact with THR 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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137C THR* 3.7 24.5 - - + -
138C ALA 3.3 5.4 - - - +
139C ALA* 4.1 14.1 - - + -
163C SER 4.5 5.2 - - - +
164C GLY* 3.1 23.9 + - - +
166C HIS* 5.5 1.1 + - - +
183C VAL* 5.2 2.9 - - + -
184C VAL* 1.3 78.7 - - - +
186C VAL* 1.3 64.4 + - - +
187C PRO* 4.9 0.7 - - - +
113D PHE* 4.5 4.5 - - + -
134D ASN* 3.5 32.1 + - - +
135D ASN* 5.5 2.4 + - - -
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Residues in contact with VAL 186 (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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137C THR* 3.4 7.0 - - - +
138C ALA* 2.8 37.4 + - + +
140C LEU* 3.9 22.2 - - + -
161C LEU* 4.8 6.3 - - + -
184C VAL* 4.2 13.0 - - + -
185C THR* 1.3 78.3 - - - +
187C PRO* 1.4 81.2 - - + +
191C LEU* 4.2 15.7 - - + -
196C TYR* 3.2 40.6 - - + +
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Residues in contact with PRO 187 (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 GLY 3.4 7.9 - - - +
137C THR* 4.8 0.2 - - - -
185C THR 4.9 0.2 - - - +
186C VAL* 1.4 96.5 - - + +
188C SER* 1.3 64.4 + - - +
189C SER* 4.3 12.1 - - - +
190C SER* 2.7 35.3 + - - +
191C LEU* 3.9 1.7 + - - +
196C TYR* 5.3 0.2 - - - +
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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