Contacts of the strand formed by residues 166 - 175 (chain B) in PDB entry 3NTV
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 LEU 166 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142B VAL* 4.6 0.7 - - - -
143B TYR* 3.4 17.7 - - - +
144B ASP 3.5 24.5 - - - +
145B MSE 3.6 9.4 - - - +
146B ILE* 3.9 15.9 - - + +
162B TYR 4.0 1.2 + - - -
163B THR* 2.8 13.3 + - + +
164B PRO 4.3 1.6 - - - +
165B LEU* 1.3 79.6 - - - +
167B LYS* 1.3 70.1 + - - +
168B HIS* 3.8 1.0 + - - -
170B GLY* 4.0 7.2 - - - -
171B LEU 3.7 17.7 - - - +
172B VAL* 3.6 30.5 - - + -
214B TYR* 4.5 2.9 - - + +
230B LYS* 2.8 43.3 + - + -
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Residues in contact with LYS 167 (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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70B ASN* 4.7 13.3 + - - -
71B ASN 5.5 1.4 + - - -
142B VAL* 4.0 16.9 - - + +
143B TYR 2.9 19.7 + - - +
144B ASP* 3.3 35.4 + - - +
165B LEU 3.8 1.2 + - - -
166B LEU* 1.3 79.3 - - - +
168B HIS* 1.3 73.4 + - - +
169B GLN* 3.4 5.6 + - - -
170B GLY* 2.9 35.1 + - - +
230B LYS* 3.6 4.1 - - - +
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Residues in contact with HIS 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B LEU 5.2 0.4 + - - -
167B LYS* 1.3 86.1 - - - +
169B GLN* 1.3 71.2 + - + +
170B GLY 3.3 2.3 + - - -
230B LYS* 3.8 29.6 - - + +
231B GLY* 3.9 24.0 + - - -
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Residues in contact with GLN 169 (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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68A ARG 5.0 7.7 + - - -
69A MSE 6.1 0.2 - - - +
71A ASN* 4.9 12.7 + - - +
70B ASN* 5.0 6.6 - - - +
167B LYS* 4.7 7.9 - - - -
168B HIS* 1.3 76.2 - - + +
170B GLY* 1.3 63.0 + - - +
171B LEU* 4.3 6.4 - - - +
229B ILE* 4.0 20.8 - - + +
230B LYS 2.7 27.4 + - - +
231B GLY* 4.3 8.0 - - - -
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Residues in contact with GLY 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B ASP 3.4 13.2 - - - -
166B LEU* 4.0 8.5 - - - -
167B LYS* 2.9 29.3 + - - -
168B HIS 3.1 2.0 + - - -
169B GLN* 1.3 80.9 - - - +
171B LEU* 1.3 60.6 + - - -
229B ILE* 3.5 3.3 - - - -
230B LYS* 2.9 25.1 + - - +
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Residues in contact with LEU 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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69A MSE 4.3 13.0 - - + -
66B LEU* 4.2 11.0 - - + -
70B ASN* 3.4 34.1 - - + +
72B VAL* 5.1 1.6 - - + -
144B ASP 3.1 12.0 + - - +
145B MSE 3.2 27.8 - - + +
146B ILE 2.9 24.8 + - - +
166B LEU* 3.7 5.2 - - - +
169B GLN 4.3 6.3 - - - +
170B GLY* 1.3 81.3 - - - +
172B VAL* 1.3 61.6 + - - +
173B ILE* 4.0 19.7 - - + -
227B ILE* 4.6 4.9 - - + -
228B SER 3.3 4.3 - - - +
229B ILE* 4.0 24.2 - - + -
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Residues in contact with VAL 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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146B ILE* 3.4 13.0 - - + +
148B ILE* 3.9 17.5 - - + -
159B PHE* 3.8 31.2 - - + -
163B THR* 3.7 21.3 - - + -
166B LEU* 3.6 23.3 - - + -
171B LEU* 1.3 71.9 - - - +
173B ILE* 1.3 62.8 + - - +
174B THR* 4.0 12.6 + - - +
214B TYR* 4.1 8.5 - - + -
226B ALA 3.8 1.0 - - - +
227B ILE* 3.7 1.6 - - - -
228B SER* 2.8 40.8 + - - +
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Residues in contact with ILE 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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63B ILE* 3.9 22.4 - - + -
66B LEU* 3.8 25.6 - - + -
145B MSE 3.8 29.8 - - + -
146B ILE 2.8 9.2 + - - +
147B PHE* 3.4 14.6 - - + -
148B ILE* 2.9 26.0 + - - +
171B LEU* 4.0 13.5 - - + -
172B VAL* 1.3 80.1 - - - +
174B THR* 1.3 57.9 + - - +
225B LEU* 3.5 31.4 - - + -
226B ALA 3.4 4.0 - - - +
227B ILE* 3.9 18.6 - - + -
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Residues in contact with THR 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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148B ILE* 3.2 8.3 - - + +
149B ASP 4.4 0.4 - - - -
150B ALA* 3.6 22.2 - - - +
172B VAL* 4.0 10.2 + - - +
173B ILE* 1.3 73.1 - - - +
175B ASP* 1.3 62.3 + - - +
177B VAL* 3.6 17.3 - - + +
204B TYR* 2.8 45.1 + - + +
208B LEU* 4.4 5.5 - - - +
225B LEU* 3.4 6.7 - - - +
226B ALA* 2.9 43.4 + - - +
228B SER* 5.4 0.5 + - - -
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Residues in contact with ASP 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B VAL* 4.0 29.6 - - - +
56B ASP* 4.9 2.3 + - - +
59B THR* 4.0 22.6 + - - +
147B PHE* 3.9 18.2 - - + -
148B ILE 2.8 10.5 + - - +
149B ASP* 3.5 9.9 - - + +
150B ALA 3.0 25.6 + - - -
173B ILE 4.1 0.8 + - - -
174B THR* 1.3 74.8 - - - +
176B ASN* 1.3 78.2 + - + +
177B VAL 3.3 2.1 + - - -
222B ASP* 6.0 0.3 - - - +
223B ASP* 4.9 7.1 + - - +
224B GLY 3.3 10.1 - - - +
225B LEU* 3.9 3.0 - - + +
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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