Contacts of the strand formed by residues 166 - 173 (chain A) in PDB entry 1T0P
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 166 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127A MET* 3.7 25.8 - - - +
130A VAL* 3.3 39.5 - - + +
132A LEU* 3.9 27.4 - - + -
161A LEU* 3.9 28.4 - - + +
164A THR* 3.0 28.6 + - - +
165A SER* 1.3 84.9 - - - +
167A GLN* 1.3 66.2 + - - +
168A PHE* 3.7 19.1 - + + -
186A TYR* 4.0 11.1 - - - -
298A LEU* 2.8 49.5 + - + +
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Residues in contact with GLN 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A VAL 3.1 5.6 + - - +
131A ASP* 3.6 7.0 + - - +
132A LEU* 3.0 24.9 + - - +
164A THR 5.5 0.9 - - - +
165A SER 5.0 0.4 - - - -
166A TYR* 1.3 77.9 - - - +
168A PHE* 1.3 65.8 + - - +
183A PHE* 3.7 10.8 - - + +
186A TYR* 3.9 13.0 - - + -
187A VAL* 3.5 32.0 - - + +
225A GLY 4.3 12.1 + - - -
227A ARG* 3.3 47.8 + - - +
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Residues in contact with PHE 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A LEU* 3.3 33.0 - - + +
134A PHE* 3.5 24.2 - + + -
158A MET* 3.8 30.7 - - + -
161A LEU* 3.5 42.4 - - + -
166A TYR* 3.7 22.4 - + + -
167A GLN* 1.3 76.6 - - - +
169A ALA* 1.3 63.2 + - - +
181A PHE* 3.4 9.7 - - + -
182A ASP 3.4 5.9 - - - +
183A PHE* 3.3 25.6 - - - -
186A TYR* 3.4 44.1 - + + +
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Residues in contact with ALA 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A LEU 3.2 3.9 + - - +
133A VAL* 3.3 7.0 - - + -
134A PHE* 2.9 26.5 + - - -
168A PHE* 1.3 75.9 - - - +
170A ALA* 1.3 61.3 + - - +
181A PHE* 3.4 20.2 - - - +
182A ASP* 4.0 9.2 - - - -
183A PHE* 3.8 23.1 - - + -
219A VAL* 3.9 20.9 - - + -
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Residues in contact with ALA 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A PHE* 3.3 16.8 - - + +
136A PHE* 4.1 15.3 - - + -
154A MET* 4.7 2.2 - - - -
169A ALA* 1.3 74.9 - - - +
171A VAL* 1.3 58.2 + - - +
179A THR* 3.6 1.2 - - - -
180A GLU* 2.8 32.0 + - + -
181A PHE* 3.0 41.3 + - + +
196A LEU* 4.1 7.4 - - + -
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Residues in contact with VAL 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A VAL* 4.1 13.2 - - + -
134A PHE 2.8 9.5 + - - +
135A LEU* 3.4 25.2 - - + +
136A PHE* 3.0 28.5 + - - -
170A ALA* 1.3 79.0 - - - +
172A GLN* 1.3 69.1 + - - +
177A TYR* 4.4 2.9 - - + -
178A LYS 3.3 13.2 - - - +
179A THR* 4.0 9.4 - - + +
214A TYR* 3.9 23.3 - - + -
215A VAL* 4.2 2.7 - - + -
219A VAL* 3.6 32.1 - - + -
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Residues in contact with GLN 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A PHE* 3.4 26.5 - - + +
138A GLY* 3.3 17.9 - - - -
147A PHE* 3.7 11.6 - - - -
171A VAL* 1.3 74.2 - - - +
173A PHE* 1.3 63.0 + - - +
177A TYR* 3.5 3.5 - - - -
178A LYS* 2.9 32.3 + - - +
180A GLU* 3.0 27.6 + - + +
199A VAL* 3.7 8.1 - - - +
200A LYS 2.9 21.0 + - - +
202A MET* 2.9 48.7 + - + +
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Residues in contact with PHE 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A LEU* 3.5 36.3 - - + -
136A PHE 3.0 25.9 + - - -
137A ASP* 3.4 33.1 - - + +
138A GLY 2.8 26.6 + - - -
139A SER 4.0 0.5 + - - -
172A GLN* 1.3 74.7 - - - +
174A SER* 1.3 63.2 + - - +
176A SER 3.5 4.3 - - - -
177A TYR* 3.6 20.4 - - + -
202A MET* 4.1 1.8 - - - -
206A THR* 3.8 14.1 - - + -
207A ASN 4.4 3.1 - - - -
208A THR* 3.4 41.5 - - + -
211A ALA* 3.6 15.9 - - + -
236A ILE* 4.3 4.5 - - + -
238A THR* 4.1 10.1 - - - -
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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