Contacts of the strand formed by residues 179 - 186 (chain A) in PDB entry 1N6U
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 179 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A ILE* 3.4 6.1 - - + -
116A GLY* 2.6 35.0 + - - -
121A ILE* 2.9 54.3 - - + +
145A GLU* 3.7 6.3 - - - -
146A GLN 2.8 6.1 - - - +
147A SER* 3.2 25.6 - - - +
177A THR* 2.8 25.4 - - - -
178A ASN* 1.3 73.2 - - - +
180A CYS* 1.3 54.0 + - - +
181A VAL* 3.4 17.7 - - + -
199A LYS 2.4 23.2 - - - +
200A CYS* 2.8 11.1 - - - -
201A THR* 2.9 37.6 + - + +
203A LEU* 3.5 12.3 - - + -
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Residues in contact with CYS 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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144A GLU 3.7 0.7 - - - +
145A GLU 4.0 0.2 - - - -
146A GLN* 2.8 47.1 + - + +
178A ASN* 5.3 4.7 - - - -
179A TYR* 1.3 69.5 - - - +
181A VAL* 1.3 54.3 + - - +
182A SER 3.6 0.5 + - - -
198A LEU* 2.7 43.8 - - + +
199A LYS 3.0 6.7 - - - -
200A CYS* 2.0 45.1 - - - -
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Residues in contact with VAL 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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112A PHE* 2.9 32.2 - - + -
114A ILE* 3.7 16.2 - - + -
123A VAL* 3.5 31.6 - - + -
143A ILE* 4.1 3.8 - - + -
144A GLU 3.0 12.1 - - - +
145A GLU* 4.2 3.6 - - + -
170A ILE* 3.4 22.4 - - + -
179A TYR* 3.4 29.6 - - + -
180A CYS* 1.3 71.2 - - - +
182A SER* 1.3 68.1 + - - +
183A VAL* 4.9 0.4 - - + -
198A LEU* 3.5 2.0 - - - -
199A LYS 2.7 16.7 + - - +
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Residues in contact with SER 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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112A PHE* 4.5 0.2 - - - -
142A VAL 3.7 0.9 - - - +
143A ILE* 3.8 2.8 - - - -
144A GLU* 3.1 37.1 + - - -
181A VAL* 1.3 77.8 - - - +
183A VAL* 1.3 76.3 + - - +
184A TYR* 4.0 2.4 + - - -
195A LYS* 2.8 33.4 - - - +
196A SER 3.0 13.5 + - - -
198A LEU* 3.3 29.9 - - - +
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Residues in contact with VAL 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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107A PHE* 5.0 4.2 - - - +
108A GLU* 5.8 0.5 - - - -
110A PRO* 6.2 2.0 - - + -
112A PHE* 3.1 45.8 - - + -
125A VAL* 3.3 30.7 - - + -
127A PHE* 5.1 0.9 - - + -
141A LEU* 3.2 27.6 - - + -
142A VAL 3.8 3.8 - - - -
143A ILE* 5.2 0.2 - - - +
181A VAL* 4.4 2.5 - - + +
182A SER* 1.3 85.7 + - - +
184A TYR* 1.3 58.4 + - - +
185A LEU* 4.3 5.9 - - + +
194A ILE 3.6 3.7 - - - +
196A SER* 3.3 19.8 + - - +
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Residues in contact with TYR 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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141A LEU* 4.6 0.2 - - - -
142A VAL* 2.6 78.2 + - + +
144A GLU* 3.3 40.6 - - + -
153A LYS* 3.6 22.2 + - - +
182A SER* 4.5 1.8 - - - -
183A VAL* 1.3 74.8 - - - +
185A LEU* 1.3 71.4 + - - +
186A GLU* 4.5 4.7 - - + -
189A ASP 5.7 1.8 - - - -
190A GLU* 5.5 3.5 - - - +
192A ALA 4.4 0.7 - - - -
193A VAL* 3.0 36.8 - - + +
194A ILE 2.8 35.4 - - - +
195A LYS* 3.2 10.3 - - + +
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Residues in contact with LEU 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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105A MET* 3.0 29.4 - - + +
107A PHE* 3.3 47.6 - - + -
127A PHE* 4.5 4.5 - - + -
139A LEU* 3.3 18.4 - - + -
140A SER 3.1 17.9 - - - +
141A LEU* 4.2 17.0 - - + -
162A MET* 5.6 0.2 - - + -
183A VAL* 4.3 2.7 - - + +
184A TYR* 1.3 88.4 - - - +
186A GLU* 1.3 59.5 + - - +
187A HIS* 5.3 0.9 - - - +
192A ALA* 2.7 30.0 - - + +
194A ILE* 3.3 18.2 - - + -
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Residues in contact with GLU 186 (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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139A LEU* 4.1 2.9 - - - +
140A SER* 3.0 55.2 + - - -
142A VAL* 3.1 28.7 - - + -
155A LYS* 4.6 16.8 - - + +
184A TYR* 4.5 4.0 - - + -
185A LEU* 1.3 73.5 - - - +
187A HIS* 1.3 86.7 + - - +
188A SER* 3.0 22.0 + - - -
189A ASP 4.2 14.8 + - - +
192A ALA* 4.7 2.2 - - - -
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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