Contacts of the strand formed by residues 170 - 177 (chain B) in PDB entry 3NC0
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 170 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132B ILE 3.7 0.5 - - - +
133B VAL* 3.6 2.4 - - - +
134B ALA* 2.9 43.3 + - - +
156B LEU* 3.6 17.9 - - + -
157B PRO* 2.9 33.3 + - - +
169B TYR* 1.3 76.1 + - - +
171B ILE* 1.3 70.7 + - - +
172B LEU* 3.6 22.0 - - + -
190B CYS 3.3 13.7 - - - +
191B TRP* 3.7 13.5 - - + -
192B ARG 4.0 2.9 + - - -
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Residues in contact with ILE 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B ALA* 3.7 29.4 - - + +
65B LEU* 3.6 35.0 - - + -
66B ALA* 5.0 1.8 - - + +
131B LEU* 4.2 20.2 - - + -
132B ILE 3.3 8.5 - - - +
133B VAL* 4.6 9.0 - - + -
169B TYR* 4.8 3.1 - - + -
170B THR* 1.3 81.8 - - - +
172B LEU* 1.3 68.4 + - - +
189B MET* 3.2 39.8 + - + +
190B CYS* 2.8 31.9 + - + -
197B TYR* 4.5 2.9 - - - +
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Residues in contact with LEU 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B ALA 3.8 0.2 - - - +
131B LEU* 3.7 2.8 - - - +
132B ILE* 2.9 41.0 + - + +
156B LEU* 3.2 34.3 - - + -
170B THR* 3.6 15.5 - - + -
171B ILE* 1.3 86.2 - - - +
173B ASP* 1.3 59.0 + - - +
174B CYS* 3.6 14.3 + - - -
185B VAL* 3.7 28.5 - - + -
187B ASP 4.1 5.6 - - - +
188B VAL* 3.6 25.1 - - + -
189B MET* 3.4 10.6 - - - +
191B TRP* 4.2 10.1 - - + -
212B LEU* 5.2 2.2 - - + -
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Residues in contact with ASP 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B LEU* 3.4 19.2 - - - +
103B MET* 4.5 9.1 + - - +
129B ARG* 3.1 36.9 + - - -
130B ALA 3.8 2.5 - - - -
172B LEU* 1.3 71.5 - - - +
174B CYS* 1.3 55.7 + - - +
186B LEU* 2.7 49.3 + - - +
187B ASP* 3.2 22.1 + - + +
189B MET* 3.3 24.9 - - + +
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Residues in contact with CYS 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B LYS 4.2 0.2 - - - -
129B ARG* 3.3 7.3 - - - -
130B ALA* 2.8 39.3 + - - +
132B ILE* 3.6 31.0 - - + -
172B LEU* 3.6 18.1 + - - -
173B ASP* 1.3 78.6 + - - +
175B ILE* 1.3 64.3 + - - +
183B TYR* 4.2 17.9 - - + -
184B TYR 3.4 10.3 - - - +
185B VAL* 3.7 26.0 - - - -
186B LEU* 4.9 0.2 - - - -
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Residues in contact with ILE 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B CYS* 4.0 19.5 - - + -
125B PRO* 3.6 47.8 - - + +
126B VAL 4.7 0.4 - - - -
127B GLY* 3.9 8.3 - - - -
128B LYS 3.1 20.4 - - - +
129B ARG* 4.4 19.3 - - + +
174B CYS* 1.3 80.2 - - - +
176B TYR* 1.3 62.4 + - - +
177B ASN* 3.7 2.2 + - + +
183B TYR* 4.6 1.1 - - - -
184B TYR* 2.8 38.9 + - - +
186B LEU* 4.7 18.2 - - + -
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Residues in contact with TYR 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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683A GLU* 3.2 30.0 + - - +
687A GLN* 3.7 6.4 + - - -
127B GLY* 3.2 6.6 - - - -
128B LYS* 2.6 52.5 + - + +
130B ALA* 5.6 0.7 - - + -
149B VAL* 6.5 0.9 - - + -
174B CYS 4.2 0.4 - - - -
175B ILE* 1.3 71.2 - - - +
177B ASN* 1.3 73.4 + - - +
178B GLU* 3.7 25.0 + - + +
181B GLN* 3.6 18.0 - - + +
182B THR 3.6 20.2 - - - -
183B TYR* 3.4 52.7 - + + -
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Residues in contact with ASN 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125B PRO* 4.5 10.4 - - + +
126B VAL* 2.9 30.3 + - - +
127B GLY* 4.6 0.2 - - - -
175B ILE* 3.7 1.0 + - + -
176B TYR* 1.3 78.4 - - - +
178B GLU* 1.3 61.9 + - - +
179B VAL* 3.2 11.3 + - - +
180B ASN* 3.1 31.7 + - + +
181B GLN* 3.2 17.3 + - - -
182B THR 3.0 14.3 + - - +
184B TYR* 3.6 29.6 - - + -
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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