Contacts of the helix formed by residues 161 - 170 (chain B) in PDB entry 3FUV
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 GLY 161 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159B ALA 3.4 2.6 + - - -
160B TYR* 1.3 76.8 - - - +
162B VAL* 1.3 65.0 + - - -
163B LEU* 3.2 3.3 - - - +
164B THR* 2.9 23.3 + - - -
165B LEU* 3.3 10.5 + - - +
216B PHE* 3.8 24.9 - - - -
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Residues in contact with VAL 162 (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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161B GLY* 1.3 71.2 - - - -
163B LEU* 1.3 65.0 + - - +
165B LEU* 3.1 4.3 + - - +
166B ARG* 2.9 24.3 + - + +
209B PHE* 4.4 8.5 - - + -
212B VAL* 4.0 26.0 - - + -
213B GLU* 3.5 40.8 - - + +
216B PHE* 3.9 25.8 - - + -
217B GLY 5.7 0.2 - - - +
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Residues in contact with LEU 163 (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 THR* 3.6 29.2 - - + +
127B VAL* 5.7 0.7 - - + -
128B THR* 4.0 12.3 - - - +
147B VAL 4.5 1.3 - - - +
150B ARG* 3.6 55.4 - - + +
151B MET* 3.8 29.2 - - + -
161B GLY 3.2 0.8 - - - +
162B VAL* 1.3 81.7 - - - +
164B THR* 1.3 63.5 + - - +
166B ARG* 3.6 8.0 - - + +
167B VAL* 3.1 36.9 + - + +
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Residues in contact with THR 164 (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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150B ARG 2.5 24.8 + - - +
151B MET 4.4 7.5 - - - +
152B THR 4.3 1.8 - - - -
153B ALA* 3.1 36.5 - - + +
159B ALA 3.5 5.2 + - - -
160B TYR* 3.5 15.7 - - + -
161B GLY 2.9 27.5 + - - -
163B LEU* 1.3 79.2 - - - +
165B LEU* 1.3 59.3 + - - +
167B VAL* 3.5 3.1 + - - +
168B ALA* 3.0 28.8 + - + +
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Residues in contact with LEU 165 (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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160B TYR* 3.6 26.9 - - + +
161B GLY 3.3 8.9 + - - +
162B VAL 3.1 6.1 + - - +
164B THR* 1.3 77.1 - - + +
166B ARG* 1.3 57.4 + - - +
168B ALA* 3.7 5.6 - - + +
169B HIS* 2.8 36.6 + - - +
209B PHE* 3.5 13.3 - - + -
212B VAL* 3.8 15.3 - - + -
216B PHE* 3.8 30.1 - - + -
256B ASP 4.1 1.1 - - - -
257B LEU* 3.7 44.5 - - + +
260B PHE* 3.8 15.3 - - + -
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Residues in contact with ARG 166 (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 THR* 4.0 34.0 - - + +
131B LEU* 4.8 3.6 - - + -
132B LYS* 3.4 26.7 - - - +
162B VAL* 2.9 20.6 + - + +
163B LEU* 3.6 12.1 - - + +
165B LEU* 1.3 76.6 - - - +
167B VAL* 1.3 64.1 + - - +
169B HIS* 3.6 0.7 + - - +
170B HIS* 3.0 56.5 + - + -
204B ASP* 2.8 29.5 + - - -
209B PHE* 3.3 52.9 - - + +
213B GLU* 5.5 3.2 + - - -
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Residues in contact with VAL 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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127B VAL* 4.7 3.1 - - + -
131B LEU* 3.9 20.6 - - + -
151B MET* 3.7 27.4 - - + +
163B LEU* 3.1 35.6 + - + +
164B THR 3.8 3.1 - - - +
166B ARG* 1.3 76.9 - - + +
168B ALA* 1.3 58.9 + - - +
170B HIS* 3.2 2.1 + - - +
171B ALA* 2.8 32.5 + - + +
173B ALA* 3.7 29.4 - - + -
197B LEU* 3.7 22.0 - - + -
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Residues in contact with ALA 168 (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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164B THR* 3.0 20.5 + - + +
165B LEU* 3.3 9.8 + - + +
167B VAL* 1.3 76.5 - - - +
169B HIS* 1.3 63.1 + - - +
171B ALA 3.4 18.7 + - - +
173B ALA* 5.9 1.3 - - - -
200B THR* 5.7 0.9 - - - +
257B LEU* 4.1 21.3 - - + +
261B ARG* 5.2 0.2 + - - -
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Residues in contact with HIS 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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165B LEU 2.8 22.3 + - - +
166B ARG 3.8 2.2 - - - +
168B ALA* 1.3 74.7 - - - +
170B HIS* 1.3 75.1 + + - +
200B THR* 4.3 2.4 + - - +
202B ALA* 3.5 20.4 - - + +
203B LEU 2.8 28.1 + - - -
205B ASP* 3.7 31.0 + - + +
208B LEU* 4.1 5.2 - - + +
209B PHE* 3.6 23.3 - + + -
257B LEU* 4.0 5.3 - - + +
261B ARG* 2.8 40.7 + - - +
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Residues in contact with HIS 170 (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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131B LEU* 3.1 48.7 + - + +
132B LYS* 3.9 9.1 - - - +
166B ARG* 3.0 56.8 + - - +
167B VAL 3.2 3.1 + - - +
169B HIS* 1.3 82.5 - + - +
171B ALA* 1.3 59.4 + - - +
199B PRO* 3.3 6.8 - - + +
200B THR* 2.9 27.4 + - - -
201B GLY 4.5 1.4 + - - -
202B ALA* 2.9 24.3 + - - +
203B LEU* 3.6 4.0 - - - -
204B ASP* 3.5 32.1 - - - -
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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