Contacts of the strand formed by residues 138 - 148 (chain A) in PDB entry 3NFP
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 138 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A GLY* 1.3 73.2 + - - -
139A ALA* 1.3 71.3 + - - +
186A THR* 4.4 16.6 - - + -
187A VAL 3.9 11.7 - - - +
188A PRO* 5.0 3.6 - - - +
189A SER* 4.3 1.8 - - - +
115B PHE* 3.9 20.4 - - + -
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Residues in contact with ALA 139 (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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129A PRO* 4.3 20.0 - - + -
133A SER* 5.3 7.2 - - - +
138A THR* 1.3 74.5 - - - +
140A ALA* 1.3 58.4 + - - +
186A THR* 3.4 5.5 - - - -
187A VAL* 2.8 44.7 + - + +
189A SER* 3.8 17.6 + - - +
192A LEU* 4.5 14.8 - - + -
115B PHE* 4.3 4.3 - - - -
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Residues in contact with ALA 140 (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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129A PRO* 3.3 24.8 - - - +
139A ALA* 1.3 76.2 - - - +
141A LEU* 1.3 63.7 + - - +
184A VAL* 5.9 0.4 - - + -
185A VAL 3.3 12.3 - - - +
186A THR* 3.7 15.0 - - + -
187A VAL* 4.8 0.4 - - - +
115B PHE* 3.7 30.1 - - + -
117B PHE* 3.5 16.4 - - + -
134B LEU* 4.5 7.6 - - + -
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Residues in contact with LEU 141 (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 3.4 15.7 - - - +
129A PRO* 3.9 28.5 - - + -
140A ALA* 1.3 75.1 - - - +
142A GLY* 1.3 59.8 + - - +
157A TRP* 4.2 16.6 - - + -
184A VAL* 3.6 6.6 - - - +
185A VAL* 2.9 54.4 + - + +
187A VAL* 4.7 9.0 - - + -
192A LEU* 4.1 17.3 - - + -
197A TYR* 4.3 25.6 - - + -
214A VAL* 4.5 17.3 - - + +
215A GLU* 5.8 1.3 - - - +
216A PRO* 6.4 0.2 - - + -
117B PHE* 4.0 4.9 - - - -
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Residues in contact with GLY 142 (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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126A PRO* 3.7 2.4 - - - +
127A LEU* 2.8 46.7 + - - +
141A LEU* 1.3 78.1 - - - +
143A CYS* 1.3 59.8 + - - -
157A TRP* 3.7 16.2 - - - -
183A SER 3.1 14.6 - - - -
184A VAL* 4.2 0.9 - - - -
214A VAL* 4.3 4.3 - - - +
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Residues in contact with CYS 143 (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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124A VAL* 4.3 14.4 - - + -
125A PHE 3.7 4.5 - - - +
126A PRO* 5.1 1.6 - - - -
127A LEU* 3.8 2.8 - - - +
142A GLY* 1.3 77.5 - - - -
144A LEU* 1.3 60.4 + - - +
145A VAL* 5.0 7.0 - - + +
155A VAL* 5.4 1.1 - - + -
157A TRP* 4.1 3.3 - - + -
182A SER* 3.4 4.9 - - - -
183A SER* 2.9 36.6 + - - +
199A CYS* 2.0 52.9 - - + -
201A VAL* 5.2 0.9 - - + -
212A LYS* 4.4 5.8 - - - -
214A VAL* 4.4 14.6 - - - -
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Residues in contact with LEU 144 (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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123A SER 3.4 1.6 - - - +
124A VAL* 3.3 6.6 - - - +
125A PHE* 2.7 65.0 + - + +
127A LEU* 4.4 20.4 - - + -
143A CYS* 1.3 74.0 - - - +
145A VAL* 1.3 65.8 + - - +
146A LYS* 4.7 9.2 - - + -
180A SER* 4.4 13.2 - - - +
181A LEU 3.9 7.6 - - - +
182A SER* 3.8 19.1 - - - +
123B GLN* 4.7 5.4 - - - +
130B SER* 4.4 22.7 - - - +
132B VAL* 5.2 9.6 - - + -
177B THR* 5.7 7.2 - - + +
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Residues in contact with VAL 145 (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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122A PRO* 3.6 27.4 - - + -
123A SER 3.6 3.6 - - - +
124A VAL* 4.4 5.6 - - + -
143A CYS* 5.0 5.8 - - + +
144A LEU* 1.3 79.4 - - - +
146A LYS* 1.3 62.3 + - - +
148A TYR* 4.5 7.7 - - + -
153A VAL* 4.7 4.7 - - + -
155A VAL* 4.9 8.3 - - + -
180A SER* 3.4 4.0 + - - -
181A LEU* 2.9 62.7 + - + +
182A SER* 5.7 0.7 - - - -
183A SER* 5.9 1.6 - - - +
201A VAL* 3.9 37.9 - - + -
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Residues in contact with LYS 146 (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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122A PRO* 3.6 2.1 - - - +
123A SER* 2.9 36.7 + - - +
125A PHE* 4.2 13.4 - - + -
144A LEU* 4.7 13.2 - - + -
145A VAL* 1.3 76.8 - - - +
147A ASP* 1.3 101.7 + - - +
148A TYR* 3.7 3.1 - - - -
174A GLN* 4.0 10.5 - - - +
179A TYR 3.8 2.7 - - - -
180A SER* 3.4 22.7 - - - +
123B GLN* 3.8 33.1 + - - +
126B SER* 5.8 1.2 + - - -
128B THR* 4.9 13.3 - - - +
130B SER* 4.2 11.2 - - - +
179B THR* 5.8 3.9 - - + +
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Residues in contact with ASP 147 (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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120A LYS* 3.5 26.7 + - - +
121A GLY 2.9 20.1 - - - +
122A PRO 4.7 0.2 - - - -
123A SER* 5.3 5.8 - - - -
146A LYS* 1.3 104.1 + - - +
148A TYR* 1.3 55.4 + - - +
174A GLN* 3.7 5.2 + - - +
178A LEU* 3.4 27.6 - - + +
179A TYR 3.0 11.8 + - - -
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Residues in contact with TYR 148 (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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120A LYS* 3.5 16.4 - - - +
122A PRO* 3.9 18.4 - - + -
145A VAL* 4.5 9.9 - - + -
146A LYS 4.4 6.1 - - - -
147A ASP* 1.3 77.8 - - - +
149A PHE* 1.3 65.1 + - - +
150A PRO 3.8 13.0 - - - -
151A GLU* 4.4 13.0 + - - +
152A PRO* 5.5 0.2 - - - +
153A VAL* 3.4 33.3 + - + +
171A ALA* 3.4 23.9 - - - +
178A LEU* 3.5 3.2 - - - +
179A TYR* 2.8 72.1 + - + +
180A SER* 3.8 4.5 - - - -
181A LEU* 3.9 15.2 - - + +
203A HIS* 3.7 20.4 - + - +
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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