Contacts of the strand formed by residues 182 - 191 (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 182 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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176B TYR* 3.6 4.8 - - - -
177B ASN* 3.0 28.9 + - - -
180B ASN* 2.7 22.1 + - - +
181B GLN* 1.3 78.8 + - - +
183B TYR* 1.3 74.6 + - - +
184B TYR* 3.6 39.4 + - + -
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Residues in contact with TYR 183 (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* 4.6 7.0 - - + -
132B ILE* 3.5 30.3 - - + -
141B ALA* 3.4 20.8 - - + +
149B VAL* 5.5 4.3 - - - +
150B ASN* 4.4 10.1 + - - +
152B PHE* 3.9 27.1 - + - -
174B CYS* 4.2 18.8 - - + -
175B ILE 3.8 0.9 - - - -
176B TYR* 3.4 46.7 - + + +
181B GLN 6.0 0.2 - - - -
182B THR* 1.3 78.0 - - - +
184B TYR* 1.3 60.4 + - - +
185B VAL* 3.4 12.7 + - + +
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Residues in contact with TYR 184 (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* 3.9 32.8 - - + -
174B CYS* 4.1 0.9 - - - -
175B ILE* 2.8 43.0 + - + +
177B ASN* 3.6 25.8 - - + -
180B ASN* 3.1 26.9 + - - +
182B THR* 3.7 31.6 + - + +
183B TYR* 1.3 68.4 - - - +
185B VAL* 1.3 66.9 + - - +
186B LEU* 3.2 5.0 + - - +
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Residues in contact with VAL 185 (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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172B LEU* 3.7 30.7 - - + -
174B CYS* 3.7 14.4 - - - -
183B TYR* 3.4 9.1 + - + +
184B TYR* 1.3 69.5 - - - +
186B LEU* 1.3 59.5 + - - +
187B ASP 3.2 25.4 - - - +
188B VAL* 5.4 0.2 - - + -
208B MET* 3.5 24.9 - - + +
209B HIS* 5.9 0.2 - - - -
212B LEU* 4.4 27.0 - - + +
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Residues in contact with LEU 186 (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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122B VAL* 4.2 28.9 - - + +
124B CYS* 4.4 17.9 - - - -
129B ARG* 3.7 31.4 - - - +
173B ASP* 2.7 39.9 + - - +
174B CYS* 4.5 1.3 - - - -
175B ILE* 4.7 13.7 - - + -
184B TYR 3.2 6.0 + - - +
185B VAL* 1.3 75.4 - - - +
187B ASP* 1.3 64.0 + - + +
205B PHE* 3.4 20.1 - - + -
208B MET* 3.7 5.6 - - - +
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Residues in contact with ASP 187 (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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103B MET* 4.7 9.1 - - - +
172B LEU* 4.1 1.7 - - - +
173B ASP* 3.2 36.2 + - + +
185B VAL* 3.2 18.7 - - - +
186B LEU* 1.3 79.5 - - + +
188B VAL* 1.3 77.7 + - - +
189B MET* 5.0 2.9 - - - -
201B THR* 4.8 0.3 - - - +
204B ARG* 2.8 49.9 + - - +
205B PHE* 3.4 16.8 - - - -
208B MET* 3.5 12.7 - - - -
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Residues in contact with VAL 188 (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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171B ILE 4.0 4.0 - - - -
172B LEU* 3.6 20.2 - - + -
185B VAL* 5.4 0.4 - - + -
187B ASP* 1.3 88.0 + - - +
189B MET* 1.3 63.3 + - - +
190B CYS 3.8 19.5 - - - +
191B TRP* 4.2 17.9 - - + -
196B PHE* 3.5 11.2 - - + +
204B ARG* 3.2 48.6 - - + +
207B TRP* 4.6 14.8 - - + -
208B MET* 3.9 11.0 - - + -
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Residues in contact with MET 189 (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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101B GLN 4.8 6.3 - - - +
102B LEU* 4.0 5.2 - - + -
131B LEU* 3.7 22.7 - - + -
171B ILE* 3.2 20.6 + - + +
172B LEU* 3.4 9.6 - - - +
173B ASP* 3.3 48.7 - - + +
187B ASP* 5.0 3.4 - - - +
188B VAL* 1.3 78.5 - - - +
190B CYS* 1.3 64.1 + - - +
195B PRO* 3.6 0.2 - - - +
196B PHE* 2.8 24.9 + - - -
197B TYR* 3.5 47.3 - - + +
204B ARG* 5.1 1.3 - - - +
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Residues in contact with CYS 190 (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* 4.0 9.2 - - + -
169B TYR* 3.5 44.6 - - - -
170B THR* 3.3 7.4 - - - +
171B ILE* 2.8 50.0 + - + +
188B VAL* 3.6 5.8 - - - +
189B MET* 1.3 82.5 - - - +
191B TRP* 1.3 63.9 + - - +
194B HIS 3.5 24.9 - - - -
195B PRO* 4.3 1.8 - - + -
196B PHE* 4.1 1.1 - - - +
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Residues in contact with TRP 191 (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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156B LEU* 4.4 9.4 - - + -
157B PRO* 3.9 24.8 - - + +
169B TYR 4.2 0.9 - - - -
170B THR* 3.7 24.7 - - + -
172B LEU* 4.2 14.4 - - + -
188B VAL* 4.2 10.1 - - + -
190B CYS* 1.3 73.0 - - - +
192B ARG* 1.3 111.9 + - + +
193B GLY 2.8 4.5 + - - -
194B HIS* 2.8 23.3 + - - +
196B PHE* 4.0 9.5 - - + -
207B TRP* 3.9 34.5 - + - +
211B LYS* 4.1 32.1 - - + +
212B LEU* 4.1 29.2 - - + -
215B GLU* 5.6 7.9 - - + -
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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