Contacts of the strand formed by residues 171 - 181 (chain A) in PDB entry 1NH1
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 ASN 171 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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166A ALA 3.4 1.6 - - - +
168A LEU* 2.9 37.8 + - + +
169A HIS 3.3 2.6 + - - +
170A GLY* 1.3 77.4 - - - +
172A VAL* 1.3 68.6 + - - +
173A ILE* 3.0 25.8 + - - +
222A TYR* 4.6 6.5 + - - -
225A ILE* 5.0 8.5 - - - +
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Residues in contact with VAL 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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165A THR* 3.9 26.2 - - + +
166A ALA 3.1 10.5 - - - +
167A TYR* 4.1 23.3 - - + -
170A GLY 3.6 6.5 + - - +
171A ASN* 1.3 81.6 + - - +
173A ILE* 1.3 61.4 + - - +
174A PRO* 4.3 2.6 - - - +
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Residues in contact with ILE 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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165A THR* 3.0 8.3 - - - -
166A ALA* 2.7 50.1 + - + +
168A LEU* 4.8 14.1 - - + -
171A ASN* 3.0 39.5 - - + +
172A VAL* 1.3 74.3 - - - +
174A PRO* 1.3 66.9 - - + +
175A LEU* 4.1 22.7 - - + -
222A TYR* 3.5 39.0 - - + +
225A ILE* 4.8 1.3 - - + -
226A ILE* 4.5 11.2 - - + -
257A TRP* 4.5 9.6 - - + -
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Residues in contact with PRO 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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163A ARG* 6.2 3.4 - - + +
164A GLN 3.5 8.3 - - - +
165A THR* 4.3 6.7 - - + -
172A VAL 4.3 3.1 - - - +
173A ILE* 1.3 87.9 - - + +
175A LEU* 1.3 71.8 + - - +
177A THR* 5.2 7.2 - - - +
218A THR* 4.4 2.6 - - - +
219A ASN* 4.9 1.1 + - + -
222A TYR* 3.5 36.2 - - + +
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Residues in contact with LEU 175 (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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164A GLN* 2.7 30.3 + - - +
165A THR 4.5 0.7 - - - -
166A ALA* 3.7 15.0 - - + +
173A ILE* 3.5 17.0 + - + +
174A PRO* 1.3 85.1 - - - +
176A ASN* 1.3 64.1 + - - +
177A THR* 3.9 4.9 + - - -
216A ASP 4.3 0.3 - - - +
217A HIS 4.0 2.6 - - - +
218A THR* 3.3 43.7 + - + +
219A ASN 4.8 0.2 + - - -
226A ILE* 4.0 17.3 - - + -
256A TRP* 3.4 36.1 - - + -
257A TRP* 4.6 5.2 - - + -
260A SER* 3.7 15.0 - - - +
261A ALA* 5.4 0.2 - - - -
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Residues in contact with ASN 176 (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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162A TYR 3.9 1.6 - - - +
164A GLN* 2.8 51.8 + - - +
175A LEU* 1.3 81.0 - - - +
177A THR* 1.3 59.9 + - - +
178A PHE* 4.1 11.5 + - + -
215A ILE* 4.0 10.8 - - + -
216A ASP 3.6 3.4 - - - -
217A HIS* 2.6 39.2 + - - +
218A THR* 3.3 3.2 + - - +
260A SER* 2.6 31.3 + - - +
301A MET* 2.9 21.8 - - + +
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Residues in contact with THR 177 (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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161A VAL* 4.1 7.0 - - + -
162A TYR 3.5 3.4 - - - +
163A ARG* 3.3 47.7 + - + +
164A GLN 5.3 0.7 + - - -
174A PRO* 5.2 6.8 - - - +
175A LEU 3.9 5.6 + - - -
176A ASN* 1.3 75.3 + - - +
178A PHE* 1.3 64.1 + - - +
179A ARG* 3.4 24.5 - - - +
214A ARG 3.7 0.9 - - - +
215A ILE* 3.4 2.3 - - - -
216A ASP* 2.8 47.3 + - - +
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Residues in contact with PHE 178 (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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127A LEU* 4.6 0.9 - - + -
134A VAL* 3.8 13.0 - - + -
138A VAL* 3.6 35.7 - - + -
160A LYS 4.5 0.4 - - - -
161A VAL* 3.4 12.5 - - - +
162A TYR* 2.8 45.2 + + + +
176A ASN* 4.3 13.9 - - + -
177A THR* 1.3 77.6 - - - +
179A ARG* 1.3 60.0 + - - +
214A ARG 3.5 4.5 - - - +
215A ILE* 3.5 33.7 - - + +
298A ILE* 4.7 5.2 - - + -
301A MET* 3.4 46.2 - - + -
302A LEU* 3.3 24.0 - - + -
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Residues in contact with ARG 179 (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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127A LEU* 4.1 1.2 - - - +
147A GLU* 4.0 13.7 + - - -
149A MET* 4.4 12.9 - - - +
159A VAL* 4.2 9.3 - - + +
160A LYS 3.7 3.1 - - - -
161A VAL* 3.5 22.4 - - - +
163A ARG* 3.8 17.3 - - - +
177A THR* 3.4 23.5 + - - +
178A PHE* 1.3 75.0 - - - +
180A VAL* 1.3 65.9 + - - +
212A PRO 3.6 8.7 - - - +
213A ASP* 3.3 3.3 - - - -
214A ARG* 2.8 63.7 + - - +
216A ASP* 2.6 33.7 + - - +
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Residues in contact with VAL 180 (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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127A LEU* 4.2 2.7 - - + -
135A LEU* 3.8 30.1 - - + +
138A VAL* 3.4 37.9 - - + -
139A VAL* 3.5 27.1 - - + -
159A VAL* 4.1 2.2 - - - +
160A LYS* 2.9 33.1 + - - +
179A ARG* 1.3 79.6 - - - +
181A ALA* 1.3 71.8 + - - +
182A THR* 3.3 0.9 + - - -
213A ASP* 3.2 13.2 - - - +
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Residues in contact with ALA 181 (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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157A LEU* 4.7 6.5 - - + -
158A ASN 3.4 9.0 - - - +
159A VAL* 3.8 9.4 - - + +
180A VAL* 1.3 81.9 - - - +
182A THR* 1.3 61.4 + - - +
183A ASP 4.9 0.2 - - - +
184A THR* 5.2 2.9 + - - -
187A LEU* 3.2 32.4 - - + +
212A PRO* 3.5 27.8 + - + +
213A ASP* 3.0 11.6 + - - +
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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