Contacts of the helix formed by residues 173 - 185 (chain A) in PDB entry 1NPR
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 LYS 173 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A TRP* 5.1 0.4 - - - -
172A LEU* 1.3 74.8 - - - +
174A GLU* 1.3 66.9 + - - +
175A GLU* 3.4 31.0 - - + +
176A GLU* 2.7 45.3 + - + +
177A VAL* 3.1 14.4 + - - +
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Residues in contact with GLU 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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13A TRP* 3.0 36.2 + - + -
142A LYS* 3.8 15.6 + - - -
172A LEU 4.0 1.4 + - - -
173A LYS* 1.3 71.6 - - - +
175A GLU* 1.3 58.7 + - - +
177A VAL* 3.2 3.8 + - - +
178A GLN* 2.7 68.8 + - + +
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Residues in contact with GLU 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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173A LYS* 3.4 33.3 - - + +
174A GLU* 1.3 77.5 - - - +
176A GLU* 1.3 67.1 + - + +
178A GLN* 3.7 7.1 - - - +
179A ASN* 2.6 56.1 + - - +
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Residues in contact with GLU 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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171A PRO 4.8 0.3 - - - +
172A LEU* 3.5 19.4 - - + +
173A LYS* 2.7 55.3 + - + +
175A GLU* 1.3 87.0 - - + +
177A VAL* 1.3 57.6 + - + +
179A ASN* 3.6 6.8 + - - +
180A ILE* 3.0 37.9 + - + +
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Residues in contact with VAL 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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13A TRP* 3.6 56.5 - - + +
140A LEU* 4.1 21.1 - - + -
172A LEU* 4.2 17.0 - - + -
173A LYS 3.1 11.3 + - - +
174A GLU 3.6 6.7 - - - +
176A GLU* 1.3 74.7 - - - +
178A GLN* 1.3 69.6 + - + +
180A ILE* 2.9 10.9 + - + +
181A LEU* 2.8 36.2 + - + +
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Residues in contact with GLN 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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13A TRP* 5.4 3.6 - - - -
174A GLU* 2.7 54.6 + - + +
175A GLU* 3.7 7.2 - - - +
177A VAL* 1.3 75.2 - - - +
179A ASN* 1.3 54.4 + - - +
181A LEU* 3.1 21.5 + - - +
182A ASN* 2.7 52.7 + - - +
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Residues in contact with ASN 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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175A GLU* 2.6 49.2 + - - +
176A GLU* 3.9 6.3 - - - +
178A GLN* 1.3 73.2 - - - +
180A ILE* 1.3 53.4 + - - +
182A ASN* 3.3 14.3 + - - +
183A GLN* 2.7 38.5 + - - +
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Residues in contact with ILE 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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49A PRO* 4.6 9.9 - - + -
134A ILE* 4.7 0.2 - - + -
135A PHE* 4.1 36.8 - - + -
140A LEU* 4.7 19.5 - - + -
172A LEU* 5.4 6.1 - - + -
176A GLU* 3.0 28.4 + - + +
177A VAL* 2.9 14.2 + - + +
179A ASN* 1.3 75.7 - - - +
181A LEU* 1.3 64.9 + - + +
183A GLN* 3.1 9.0 - - - +
184A ILE* 2.8 43.2 + - + +
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Residues in contact with LEU 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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13A TRP* 5.9 3.6 - - + -
47A ILE* 4.3 27.6 - - + -
49A PRO* 5.4 3.8 - - + -
50A ALA 6.0 1.6 - - - +
140A LEU* 5.2 3.1 - - + -
177A VAL* 2.8 34.5 + - + +
178A GLN* 3.5 24.2 - - - +
180A ILE* 1.3 83.1 - - + +
182A ASN* 1.3 68.1 + - - +
184A ILE* 3.2 19.3 + - + +
185A LYS* 3.2 23.0 + - + +
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Residues in contact with ASN 182 (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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178A GLN* 2.7 42.7 + - - +
179A ASN* 3.7 16.2 + - - +
181A LEU* 1.3 73.9 - - - +
183A GLN* 1.3 64.6 + - - +
185A LYS* 3.3 37.4 + - - +
186A ARG* 3.6 25.9 - - + +
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Residues in contact with GLN 183 (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 ILE* 4.6 14.4 - - + -
179A ASN* 2.7 16.7 + - - +
180A ILE* 3.1 14.4 - - - +
182A ASN* 1.3 76.4 - - - +
184A ILE* 1.3 68.2 + - - +
185A LYS 2.9 1.4 + - - -
186A ARG* 3.7 13.6 + - - +
188A VAL* 5.5 12.6 - - - +
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Residues in contact with ILE 184 (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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49A PRO* 3.7 18.2 - - + -
50A ALA* 3.2 38.1 - - - +
51A GLU* 3.6 10.3 - - + +
132A ASN* 3.1 42.1 + - - +
134A ILE* 3.3 39.9 - - + -
180A ILE* 2.8 23.3 + - + +
181A LEU* 3.3 17.3 - - + +
183A GLN* 1.3 77.2 - - - +
185A LYS* 1.4 60.3 + - + +
186A ARG 4.0 2.1 + - - +
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Residues in contact with LYS 185 (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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51A GLU* 3.7 29.4 - - + +
69A LYS* 4.8 23.1 - - - +
181A LEU* 3.2 14.1 + - - +
182A ASN* 3.5 29.5 + - - +
183A GLN 2.9 1.4 + - - -
184A ILE* 1.4 80.5 - - + +
186A ARG* 1.3 64.6 + - - +
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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