Contacts of the strand formed by residues 164 - 176 (chain C) in PDB entry 1TW8
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 PHE 164 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84C THR* 3.7 20.4 - - + -
85C LEU* 3.7 25.6 - - + -
88C LEU* 3.8 15.7 - - + -
122C PHE* 3.8 4.4 - - - -
123C TYR* 3.0 13.7 - - + +
125C LEU* 4.1 21.1 - - + -
148C LEU* 6.4 0.4 - - + -
151C THR* 3.9 20.2 - - + -
155C MET* 3.5 30.2 - - + +
160C GLU* 4.6 3.6 - - + -
162C ASP* 5.8 0.5 - - - -
163C LEU* 1.3 87.3 + - + +
165C ASP* 1.3 74.5 + - - +
166C ILE* 5.0 3.4 - - + -
191C PHE* 3.6 31.9 - + - -
223C ARG* 3.7 9.0 + - - -
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Residues in contact with ASP 165 (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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2C SER 4.7 8.1 + - - +
122C PHE* 3.1 30.7 - - + -
123C TYR 2.6 10.7 + - - +
124C GLU* 3.3 5.9 - - + +
125C LEU* 2.7 34.3 + - - +
164C PHE* 1.3 74.3 - - - +
166C ILE* 1.3 55.6 + - - +
167C ASN* 4.1 17.9 + - - +
189C GLU* 6.1 3.2 - - - -
191C PHE* 3.4 8.4 - - - +
223C ARG* 2.5 42.2 + - - -
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Residues in contact with ILE 166 (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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112C THR* 5.0 10.8 - - + +
125C LEU* 2.8 53.2 - - + +
126C LEU 5.0 0.4 - - - -
127C ASP* 4.7 4.9 - - + +
143C ILE* 5.0 3.6 - - + -
148C LEU* 5.3 2.5 - - + -
164C PHE* 5.0 3.4 - - + -
165C ASP* 1.3 72.4 - - - +
167C ASN* 1.3 70.0 + - - +
168C TYR* 3.5 28.5 - - + +
190C LEU* 3.2 47.5 + - + +
191C PHE* 3.4 24.8 + - + -
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Residues in contact with ASN 167 (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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2C SER* 4.1 11.9 + - - +
124C GLU* 2.6 42.8 + - - +
125C LEU 3.0 11.9 + - - +
126C LEU* 4.6 8.3 - - + -
127C ASP* 3.2 21.8 + - - +
165C ASP* 4.4 8.5 - - - +
166C ILE* 1.3 83.5 + - - +
168C TYR* 1.3 73.8 + - - +
187C PHE* 3.9 11.4 - - + -
188C ALA 3.4 9.4 - - - +
189C GLU* 3.1 28.5 - - - +
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Residues in contact with TYR 168 (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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126C LEU* 4.8 0.4 - - - -
127C ASP* 3.2 47.1 - - + +
129C LYS* 3.7 12.1 - - - -
142C ILE* 3.2 29.8 - - + -
143C ILE* 2.8 38.5 - - - +
166C ILE* 3.5 25.7 - - + +
167C ASN* 1.3 75.6 - - - +
169C LEU* 1.3 59.5 + - - +
170C GLU 4.0 0.2 - - - -
187C PHE* 3.7 3.4 - - - -
188C ALA* 2.9 25.6 + - + +
190C LEU* 4.0 24.2 - - + -
210C PHE* 4.5 8.1 - + + -
212C VAL* 3.1 39.5 - - + +
215C LEU* 5.5 1.1 - - + -
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Residues in contact with LEU 169 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C ILE* 6.0 7.6 - - + -
8C TYR* 5.0 5.8 - - + -
11C ILE* 5.6 4.9 - - + -
15C LEU* 5.2 5.2 - - + -
41C VAL* 3.7 35.4 - - + -
126C LEU* 4.0 26.5 - - + +
127C ASP 3.1 7.9 + - - +
128C VAL* 3.2 10.8 - - + +
129C LYS* 2.8 24.4 + - - -
168C TYR* 1.3 71.4 - - - +
170C GLU* 1.3 64.4 + - - +
171C VAL* 4.6 4.7 - - + -
185C THR* 3.5 30.7 - - + -
186C SER 3.5 6.3 - - - +
187C PHE* 4.7 14.8 - - + +
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Residues in contact with GLU 170 (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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129C LYS* 3.0 16.2 - - + +
131C ARG* 2.6 32.8 + - + +
168C TYR 3.9 1.2 + - - -
169C LEU* 1.3 69.8 - - - +
171C VAL* 1.3 75.0 + - - +
172C ASP* 2.6 30.2 - - - +
185C THR* 3.5 21.7 - - - +
186C SER* 2.7 35.1 + - - +
211C HIS* 3.8 2.1 - - - -
212C VAL* 3.0 21.9 + - + -
213C ARG 3.0 24.4 + - - -
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Residues in contact with VAL 171 (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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15C LEU* 4.6 14.1 - - + -
37C PHE* 3.4 38.4 - - + -
41C VAL* 4.5 15.5 - - + -
128C VAL* 4.0 20.6 - - + -
129C LYS 2.9 8.7 + - - -
130C THR* 3.3 12.7 - - + -
131C ARG 3.0 20.4 + - - -
169C LEU* 4.4 4.0 - - + +
170C GLU* 1.3 81.7 - - - +
172C ASP* 1.3 62.7 + - - +
173C TRP* 3.6 4.2 + - - -
182C CYS* 4.2 14.8 - - - -
184C SER 4.0 3.6 - - - -
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Residues in contact with ASP 172 (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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131C ARG* 3.5 18.2 + - - +
133C ILE* 4.7 8.7 - - + -
170C GLU* 2.6 29.4 - - - +
171C VAL* 1.3 70.5 - - - +
173C TRP* 1.3 59.8 + - - +
182C CYS* 3.4 8.0 - - - -
183C VAL* 3.0 30.1 + - + -
184C SER* 3.1 37.4 + - - +
185C THR 4.4 1.1 + - - -
186C SER* 4.5 3.2 + - - -
213C ARG* 2.5 33.3 + - - +
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Residues in contact with TRP 173 (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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28C LEU* 4.1 15.5 - - + -
33C ALA* 3.5 41.0 + - + -
37C PHE* 3.6 28.0 - + + -
130C THR* 4.2 7.0 - - - -
131C ARG* 2.9 40.3 + - - +
132C ASN* 3.6 31.0 - - + +
133C ILE* 3.0 28.2 + - - +
171C VAL 3.6 11.0 - - - -
172C ASP* 1.3 74.3 - - - +
174C GLU* 1.3 79.3 + - - +
175C LEU* 3.8 19.1 - - + -
180C LEU* 3.3 37.0 - - + -
181C VAL 3.1 15.7 - - - +
183C VAL 4.5 1.3 - - - +
10H C 4.2 3.5 + - - -
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Residues in contact with GLU 174 (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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133C ILE* 4.0 12.4 - - + +
134C SER* 3.9 14.8 - - - +
173C TRP* 1.3 83.2 - - - +
175C LEU* 1.3 61.5 + - - +
176C ASN* 3.0 17.6 + - + +
181C VAL* 2.9 30.7 + - + +
183C VAL* 3.5 28.5 - - + +
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Residues in contact with LEU 175 (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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22C ARG* 4.3 9.9 - - + -
28C LEU* 4.0 20.9 - - + -
132C ASN* 5.7 0.7 - - - +
134C SER* 4.2 7.8 + - - +
173C TRP* 3.8 13.8 - - + -
174C GLU* 1.3 69.5 - - - +
176C ASN* 1.3 56.8 + - - +
177C GLY 3.4 21.8 + - - +
178C GLU* 4.5 3.1 - - - -
179C ASP 3.8 9.9 - - - +
180C LEU* 3.6 28.3 - - + -
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Residues in contact with ASN 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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19C LYS* 3.3 22.2 + - - +
174C GLU* 3.0 12.9 + - + +
175C LEU* 1.3 68.5 - - - +
177C GLY* 1.3 64.9 + - - +
178C GLU 3.0 6.6 + - - -
179C ASP* 2.8 25.4 + - - +
181C VAL* 3.5 23.5 - - + +
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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