Contacts of the strand formed by residues 173 - 182 (chain C) in PDB entry 3TWI
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 PRO 173 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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172A ALA* 4.2 11.0 - - + -
173A PRO* 3.6 29.2 - - + +
175A VAL* 4.8 5.6 - - + +
173B PRO* 3.5 34.3 - - + +
139C ILE* 4.8 4.0 - - + -
140C ALA 3.4 10.3 - - - +
141C ASN* 4.1 17.5 - - - +
167C LEU* 5.6 0.2 - - - +
171C GLY 4.1 4.3 - - - +
172C ALA* 1.3 89.6 - - + +
174C ILE* 1.3 60.9 + - - +
175C VAL* 3.9 14.8 - - + -
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Residues in contact with ILE 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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138C VAL* 3.6 1.6 - - + +
139C ILE* 3.5 3.8 - - - -
140C ALA* 2.8 39.8 + - + +
142C THR* 4.0 19.5 - - + -
150C GLY* 4.8 0.4 - - - -
151C LEU* 4.2 16.6 - - + +
165C SER* 3.7 34.3 - - - +
166C SER 5.0 3.4 - - - +
167C LEU* 4.4 26.9 - - + +
173C PRO* 1.3 75.8 - - - +
175C VAL* 1.3 61.9 + - - +
176C ILE* 4.0 16.4 - - + -
198C LEU* 3.9 28.5 - - + -
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Residues in contact with VAL 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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175A VAL* 4.3 25.6 - - + -
139B ILE* 3.7 44.0 - - + +
141B ASN* 4.8 4.9 + - - +
173B PRO* 4.7 4.9 - - + +
175B VAL* 4.4 18.4 - - + -
137C THR* 5.0 6.3 - - + -
138C VAL 3.4 7.2 - - - +
139C ILE* 4.6 13.2 - - + -
165C SER* 4.5 7.2 + - - -
173C PRO* 3.9 20.9 + - + +
174C ILE* 1.3 79.8 - - - +
176C ILE* 1.3 68.6 + - - +
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Residues in contact with ILE 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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139B ILE* 4.1 2.9 - - - -
136C ILE 3.7 0.9 - - - +
137C THR* 3.2 7.1 - - - +
138C VAL* 2.8 54.0 + - + +
151C LEU* 4.0 29.2 - - + +
152C THR 4.6 1.6 - - - +
153C ILE* 3.9 15.9 - - + -
162C GLY 5.2 0.4 - - - +
163C THR* 3.6 47.6 - - + +
165C SER* 4.1 9.0 - - - -
174C ILE* 4.0 15.9 - - + -
175C VAL* 1.3 81.1 - - - +
177C GLN* 1.3 64.6 - - - +
191C VAL* 5.4 0.7 - - + -
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Residues in contact with GLN 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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88B TYR* 3.2 16.6 + - - -
137B THR* 2.8 51.6 + - - -
139B ILE* 3.5 23.0 - - + +
207B SER* 3.2 37.1 + - - +
208B ILE* 3.7 2.0 - - - +
209B ILE* 3.7 21.8 - - + +
135C LYS* 5.1 1.6 - - - -
136C ILE 3.4 4.9 - - - -
137C THR* 4.3 13.5 - - + +
176C ILE* 1.3 81.5 - - - +
178C ALA* 1.3 63.7 + - - +
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Residues in contact with ALA 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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88B TYR* 3.8 20.0 - - + -
209B ILE* 3.8 4.1 - - - +
134C TYR 3.8 0.2 - - - +
135C LYS* 3.4 5.5 - - - +
136C ILE* 2.8 39.4 + - + +
153C ILE* 4.9 3.6 - - + -
160C VAL* 3.9 11.0 - - + -
163C THR* 3.7 27.1 - - + -
177C GLN* 1.3 77.5 - - - +
179C ILE* 1.3 62.5 + - - +
180C THR* 4.2 0.9 - - - -
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Residues in contact with ILE 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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86B GLY* 4.3 2.0 - - - -
87B LEU 4.0 25.8 - - - +
88B TYR* 3.5 27.2 - - + +
111B GLY 4.7 0.7 - - - -
112B SER* 3.4 32.4 - - - +
114B PHE* 4.1 19.1 - - + -
209B ILE* 3.9 28.5 - - + -
211B GLU* 4.6 6.7 - - - +
133C PHE* 4.3 16.8 - - + -
134C TYR 3.2 14.1 - - - +
135C LYS* 4.5 11.0 - - + -
160C VAL* 4.8 1.6 - - - +
178C ALA* 1.3 78.0 - - - +
180C THR* 1.3 65.3 + - - +
213C VAL* 4.9 1.8 - - + -
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Residues in contact with THR 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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112B SER* 4.6 3.1 - - - -
132C GLY 3.7 0.7 - - - +
133C PHE* 3.5 1.3 - - - -
134C TYR* 2.8 37.5 + - + +
136C ILE* 3.9 28.5 - - + -
155C VAL* 4.4 8.7 - - + +
160C VAL* 4.0 27.3 - - + +
161C PRO* 5.5 1.7 - - - +
178C ALA* 5.5 0.2 - - - -
179C ILE* 1.3 80.9 - - - +
181C GLN* 1.3 66.8 + - - +
182C ILE* 3.8 19.5 + - + +
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Residues in contact with GLN 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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112B SER* 4.5 5.4 + - - +
132C GLY* 3.5 9.4 - - - +
133C PHE* 3.6 41.9 - - + -
180C THR* 1.3 80.4 + - - +
182C ILE* 1.3 67.6 + - - +
183C THR* 3.6 27.3 + - + +
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Residues in contact with ILE 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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128C ILE* 4.2 27.1 - - + -
130C GLU 4.3 5.6 - - - +
131C THR* 3.3 8.0 - - - -
132C GLY* 2.8 32.4 + - - +
134C TYR* 3.5 30.1 - - + -
155C VAL* 3.6 37.5 - - + -
180C THR* 4.2 10.5 - - + +
181C GLN* 1.3 77.5 - - - +
183C THR* 1.3 60.2 + - - +
184C THR 3.3 24.0 - - - +
187C SER* 3.4 15.5 - - - +
189C VAL* 5.2 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