Contacts of the strand formed by residues 167 - 174 (chain A) in PDB entry 1N3Y
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 THR 167 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A GLN 5.5 0.2 + - - -
131A GLN* 3.3 22.9 + - - +
133A ILE* 3.7 24.0 - - + -
162A PHE* 3.6 22.1 - - + +
163A GLN 3.0 9.8 + - - +
164A ARG* 3.4 27.2 + - - +
166A SER* 1.3 88.1 + - - +
168A GLN* 1.3 64.2 - - - +
169A PHE* 3.6 26.5 - - + -
187A PHE* 4.4 1.9 - - - -
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Residues in contact with GLN 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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131A GLN 3.0 6.6 + - - +
132A ASP* 4.1 2.0 - - - +
133A ILE* 2.9 26.7 + - - +
164A ARG* 3.4 16.3 - - - +
165A PRO* 3.4 26.6 - - - +
167A THR* 1.3 79.7 - - - +
169A PHE* 1.3 66.5 + - - +
184A PHE* 3.5 18.6 - - + +
187A PHE* 3.2 23.4 - - + -
188A ARG* 3.5 46.9 + - - +
228A ARG* 3.6 20.0 - - - +
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Residues in contact with PHE 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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133A ILE* 3.2 41.7 - - + -
135A PHE* 3.7 24.2 - + + -
158A VAL* 5.0 1.8 - - + -
159A ILE* 3.8 33.4 - - + -
162A PHE* 3.8 34.3 - + + -
167A THR* 3.6 22.4 - - + -
168A GLN* 1.3 77.1 - - - +
170A SER* 1.3 60.1 + - - +
182A PHE* 3.4 8.2 - - + -
184A PHE* 3.5 11.8 - - - -
187A PHE* 3.1 60.3 - + + +
236A ILE* 5.3 0.4 - - + -
314A ILE* 5.9 0.2 - - + -
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Residues in contact with SER 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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133A ILE 3.0 5.1 + - - +
134A VAL* 3.3 7.9 - - - -
135A PHE* 2.9 27.2 + - - +
169A PHE* 1.3 77.2 - - - +
171A LEU* 1.3 59.5 + - - +
172A MET 4.3 0.2 - - - -
182A PHE* 2.8 25.2 + - - -
183A THR* 3.7 5.5 - - - -
184A PHE* 3.7 33.4 - - - -
220A LEU* 3.7 21.5 + - - +
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Residues in contact with LEU 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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135A PHE* 3.5 31.4 - - + +
137A ILE* 4.0 19.1 - - + -
152A MET* 4.2 6.3 - - + -
155A VAL* 4.9 7.0 - - + -
170A SER* 1.3 75.9 + - - +
172A MET* 1.3 66.5 + - - +
180A THR* 3.6 3.3 - - - +
181A HIS* 2.8 48.4 + - + -
182A PHE* 3.0 35.3 + - + +
197A LEU* 3.5 27.1 - - + -
200A VAL* 4.0 14.1 - - + -
220A LEU* 4.9 0.7 - - - -
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Residues in contact with MET 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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135A PHE 3.0 8.1 + - - +
136A LEU* 3.3 20.0 - - + -
137A ILE* 2.9 24.8 + - - +
171A LEU* 1.3 77.7 - - - +
173A GLN* 1.3 69.6 + - - +
178A PHE* 4.4 16.6 - - + -
179A GLN 3.3 16.4 - - - +
180A THR* 3.6 18.6 - - - +
212A ALA 4.2 7.0 - - - +
215A ASN* 4.1 24.7 - - + +
216A VAL* 3.6 25.8 - - + -
219A ARG* 5.5 6.1 - - - +
220A LEU* 3.9 25.9 - - + +
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Residues in contact with GLN 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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137A ILE* 3.2 23.3 - - + +
139A GLY* 3.3 20.1 - - - -
148A PHE* 3.5 13.0 - - - -
172A MET* 1.3 77.8 - - - +
174A PHE* 1.3 64.0 + - - +
178A PHE* 3.6 2.1 - - - -
179A GLN 2.9 31.4 + - - +
181A HIS* 3.0 30.3 + - + +
200A VAL* 4.1 0.8 - - - +
201A HIS 2.9 24.4 + - - -
202A GLN* 3.3 5.2 - - - -
203A LEU* 2.8 41.3 + - + +
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Residues in contact with PHE 174 (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 LEU* 3.6 30.7 - - + -
137A ILE 2.9 16.5 + - - -
138A ASP* 3.4 34.8 - - + +
139A GLY 2.8 31.1 + - - -
172A MET* 5.3 0.2 - - - -
173A GLN* 1.3 76.2 - - - +
175A SER* 1.3 70.6 + - - +
177A LYS 3.3 4.9 - - - -
178A PHE* 3.7 11.4 - - + -
203A LEU* 4.1 3.4 - - - -
207A THR* 3.7 16.4 - - + -
208A TYR 4.0 2.7 - - - -
209A THR* 3.6 39.3 - - + -
212A ALA* 3.4 26.0 - - + -
237A VAL* 4.6 3.6 - - + -
238A ILE 4.2 4.5 - - - -
239A THR* 4.5 6.1 - - - -
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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