Contacts of the strand formed by residues 156 - 163 (chain A) in PDB entry 5N4D
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 PHE 156 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150A PHE* 3.4 11.1 - - - -
151A SER* 2.9 31.9 + - - +
153A ASP* 5.0 0.2 - - - -
154A GLY 3.5 0.2 - - - -
155A LYS* 1.3 109.1 + - + +
157A PHE* 1.4 62.2 + - - +
158A ALA 4.2 0.2 - - - -
173A VAL* 3.9 13.7 - - + -
174A ARG 3.5 16.6 - - - -
175A SER* 4.1 15.5 - - - -
176A THR 4.2 1.6 - - - +
193A LEU* 4.0 21.3 - - + -
207A TRP* 3.7 23.8 - + + -
211A SER 4.8 9.6 - - - -
241A VAL* 4.0 19.3 - - + -
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Residues in contact with PHE 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A LEU* 3.5 29.2 - - + -
131A PHE* 3.8 19.3 - + + -
132A PHE* 3.5 31.4 - + + -
145A MET* 4.0 7.9 - - - -
148A CYS* 3.5 36.1 - - + -
149A LYS 4.0 1.6 - - - -
150A PHE* 3.5 38.6 - + + -
156A PHE* 1.4 74.4 - - - +
158A ALA* 1.3 60.0 + - - +
159A TYR* 3.6 34.5 - + + -
173A VAL* 3.4 3.8 - - - -
174A ARG* 2.9 39.0 + - - +
176A THR 5.2 0.9 - - - +
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Residues in contact with ALA 158 (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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148A CYS* 3.3 5.5 - - - +
149A LYS 2.9 41.1 + - - +
156A PHE 4.2 0.6 - - - -
157A PHE* 1.3 72.2 - - - +
159A TYR* 1.3 62.0 + - - +
171A ILE* 4.2 7.0 - - + -
172A TYR 3.2 9.2 - - - +
173A VAL* 4.4 2.2 - - + +
205A ILE* 4.2 12.6 - - + -
207A TRP* 3.9 20.3 - - + +
214A PHE* 4.1 17.9 - - + -
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Residues in contact with TYR 159 (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 PHE* 3.3 30.0 - + - -
137A LEU* 4.1 8.0 - - + +
145A MET* 4.0 15.3 - - + -
147A LEU 3.5 4.9 - - - -
148A CYS* 4.1 0.7 - - + +
157A PHE* 3.6 30.7 - + + -
158A ALA* 1.3 74.1 - - - +
160A ALA* 1.3 61.5 + - - +
161A VAL* 3.7 22.2 + - + -
170A THR 3.6 1.0 - - - +
171A ILE* 3.4 5.0 - - - +
172A TYR* 2.9 63.3 + + + +
173A VAL 4.1 0.2 - - - -
174A ARG* 3.1 45.3 + - + +
180A LEU* 5.3 0.5 - - - +
190A ASP* 4.2 2.9 + - - -
192A ARG* 3.5 16.6 - - - +
205A ILE* 4.8 0.2 - - - -
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Residues in contact with ALA 160 (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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145A MET* 3.4 7.1 - - - +
146A VAL* 3.0 41.1 + - + -
147A LEU* 2.9 17.6 + - + +
159A TYR* 1.3 71.6 - - - +
161A VAL* 1.3 61.3 + - - +
169A SER* 4.3 1.3 - - - -
170A THR 3.3 7.2 - - - +
171A ILE* 4.2 3.4 - - + +
200A PHE* 3.6 36.6 - - + -
205A ILE* 4.5 2.8 - - + +
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Residues in contact with VAL 161 (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 LEU* 4.0 22.7 - - + -
143A ALA* 4.0 12.3 - - + -
144A GLY 3.3 7.6 - - - +
145A MET* 5.0 0.2 - - - -
159A TYR* 3.7 27.4 - - + -
160A ALA* 1.3 77.0 - - - +
162A SER* 1.3 73.4 + - - +
163A HIS* 3.7 24.1 - - + +
168A TYR 4.5 0.3 - - - +
169A SER* 3.3 4.7 - - - -
170A THR* 2.8 36.3 + - - +
172A TYR* 3.8 22.0 - - + -
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Residues in contact with SER 162 (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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143A ALA* 3.2 4.5 - - - -
144A GLY 2.8 31.8 + - - -
146A VAL* 3.6 6.3 - - - +
160A ALA 4.3 0.2 - - - -
161A VAL* 1.3 74.9 - - - +
163A HIS* 1.3 63.1 + - - +
168A TYR 4.2 6.4 + - - -
169A SER* 2.6 24.0 + - - -
697A GLY* 4.2 0.4 - - - -
698A HIS* 2.6 38.5 + - - +
700A MET* 3.6 18.5 - - - +
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Residues in contact with HIS 163 (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 LEU 5.7 2.0 - - - -
138A ALA* 5.4 3.6 - - + -
142A SER* 3.3 13.0 + - - +
143A ALA* 3.7 23.0 - - + +
161A VAL* 3.7 18.3 - - + +
162A SER* 1.3 78.7 - - - +
164A LEU* 1.3 67.9 + - - +
165A GLY 3.3 0.3 + - - -
166A GLY* 3.0 17.1 + - - -
168A TYR 5.1 2.8 + - - -
170A THR* 5.8 4.9 - - - -
172A TYR* 5.2 7.5 + - - -
697A GLY* 3.5 9.7 - - - -
700A MET* 3.5 5.8 - - - -
223B GLU* 3.4 35.8 + - + +
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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