Contacts of the helix formed by residues 156 - 170 (chain B) in PDB entry 2FV7
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 156 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128B ASN 4.3 2.0 + - - -
129B LEU* 3.1 36.8 + - - +
131B LEU 4.7 1.3 + - - -
155B ILE* 1.3 76.8 - - - +
157B PRO* 1.4 78.6 - - + +
158B ALA* 3.9 19.3 - - + +
159B THR* 2.9 26.5 + - - +
160B SER 3.3 8.7 + - - -
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Residues in contact with PRO 157 (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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153B LEU* 4.5 7.4 - - + -
155B ILE 3.2 8.0 - - - +
156B THR* 1.4 90.1 - - + +
158B ALA* 1.3 56.1 + - - +
160B SER* 3.1 8.5 + - - -
161B LEU* 2.8 30.4 + - - +
182B ILE* 4.5 21.1 - - + -
189B PHE* 3.5 25.7 - - + -
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Residues in contact with ALA 158 (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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133B THR* 4.5 7.8 - - + +
156B THR* 3.2 13.1 - - + +
157B PRO* 1.3 79.7 - - - +
159B THR* 1.3 57.8 + - - +
161B LEU* 3.6 9.1 + - - +
162B GLU* 3.1 27.0 + - - +
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Residues in contact with THR 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B VAL* 4.7 0.2 - - + -
131B LEU* 2.8 35.8 + - + +
132B ASN* 3.7 15.5 - - - +
133B THR* 4.2 4.5 + - - +
136B LEU* 3.0 39.5 - - + +
155B ILE* 4.0 16.8 - - + -
156B THR* 2.9 18.3 + - - +
158B ALA* 1.3 75.9 - - - +
160B SER* 1.3 60.0 + - - +
162B GLU* 3.2 1.4 + - - -
163B ALA* 2.9 25.7 + - - +
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Residues in contact with SER 160 (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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151B CYS* 3.9 14.5 - - - -
152B GLN 2.9 15.7 + - - -
153B LEU* 4.9 0.6 - - - -
155B ILE* 3.3 13.7 + - - +
156B THR 3.3 5.0 + - - -
157B PRO* 3.1 11.1 + - - +
159B THR* 1.3 74.9 - - - +
161B LEU* 1.3 62.6 + - - +
163B ALA* 3.3 3.9 + - - +
164B LEU* 3.0 30.0 + - - +
176B PHE* 5.0 0.2 - - - -
189B PHE* 4.0 13.0 - - - -
502B UNX 2.7 26.0 - - - -
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Residues in contact with LEU 161 (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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157B PRO 2.8 17.4 + - - +
158B ALA* 3.8 9.4 - - - +
160B SER* 1.3 77.3 - - - +
162B GLU* 1.3 58.0 + - - +
164B LEU* 3.4 4.6 + - + +
165B THR* 2.8 31.8 + - - +
186B ASP* 4.1 15.5 - - - +
188B GLN* 3.9 22.9 - - + +
189B PHE* 3.6 50.8 - - + +
192B LEU* 3.8 19.0 - - + +
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Residues in contact with GLU 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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133B THR* 4.0 20.9 - - + -
136B LEU* 3.8 10.8 - - + -
137B ARG* 5.0 5.2 + - - +
158B ALA 3.1 17.9 + - - +
159B THR 3.2 4.5 + - - +
161B LEU* 1.3 73.8 - - - +
163B ALA* 1.3 65.6 + - - +
165B THR* 3.3 14.2 + - - +
166B MET* 2.8 62.5 + - + +
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Residues in contact with ALA 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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21B VAL* 4.0 21.8 - - + -
136B LEU* 3.6 13.2 - - + +
143B ILE* 5.2 0.2 - - - -
149B MET* 4.0 14.3 - - + +
151B CYS* 3.8 18.6 - - - -
159B THR 2.9 16.4 + - - +
160B SER 3.6 5.6 - - - +
162B GLU* 1.3 75.9 - - - +
164B LEU* 1.3 61.8 + - - +
166B MET* 3.5 6.3 + - - +
167B ALA* 3.2 24.4 + - - +
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Residues in contact with LEU 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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149B MET* 4.8 3.6 - - + -
151B CYS* 4.1 22.2 - - + -
160B SER 3.0 23.6 + - - +
161B LEU* 3.6 7.6 - - + +
163B ALA* 1.3 78.6 - - - +
165B THR* 1.3 56.6 + - - +
167B ALA* 3.6 0.4 + - - -
168B ARG* 3.0 30.8 + - - +
174B THR* 3.8 33.4 - - + +
175B LEU 5.1 1.6 - - - +
176B PHE* 4.3 23.8 - - + -
189B PHE* 3.7 33.7 - - + +
192B LEU* 3.9 28.2 - - + +
193B SER* 4.7 0.2 - - - +
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Residues in contact with THR 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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161B LEU* 2.8 20.4 + - - +
162B GLU* 3.7 17.9 + - - +
164B LEU* 1.3 73.9 - - - +
166B MET* 1.3 59.7 + - + +
168B ARG* 3.2 4.8 + - - -
169B ARG* 2.8 60.2 + - + +
188B GLN* 5.0 6.1 + - - +
192B LEU* 3.4 19.4 - - + +
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Residues in contact with MET 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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136B LEU* 4.0 21.8 - - + +
137B ARG* 3.7 43.5 - - + +
140B ALA* 5.2 9.0 - - + -
143B ILE* 4.1 23.1 - - + -
162B GLU* 2.8 53.5 + - + +
163B ALA* 3.9 4.5 - - - +
165B THR* 1.3 74.6 - - + +
167B ALA* 1.3 63.5 + - - +
169B ARG* 3.2 6.9 + - - +
170B SER* 3.0 28.3 + - - +
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Residues in contact with ALA 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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143B ILE* 4.0 11.3 - - + +
149B MET* 3.6 33.0 - - + -
163B ALA 3.2 12.6 + - - +
164B LEU 3.9 0.2 - - - +
166B MET* 1.3 78.4 - - - +
168B ARG* 1.3 55.5 + - - +
170B SER* 3.1 2.1 + - - -
171B GLY 3.0 7.6 + - - -
172B VAL* 2.7 47.9 + - + +
174B THR* 3.8 11.2 - - + -
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Residues in contact with ARG 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 LEU 3.0 19.7 + - - +
165B THR* 3.6 6.5 - - - +
167B ALA* 1.3 78.0 - - - +
169B ARG* 1.3 76.8 + - - +
171B GLY* 3.3 12.0 + - - +
172B VAL 4.2 6.0 + - - -
174B THR* 4.3 3.6 + - + +
191B THR 3.0 29.8 + - - -
192B LEU* 3.2 37.6 + - + +
193B SER 3.6 7.7 + - - +
194B ASP* 3.0 33.1 + - - +
228B GLY 5.7 0.4 + - - -
230B GLN* 4.8 6.7 + - - +
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Residues in contact with ARG 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 THR* 2.8 51.7 + - + +
166B MET* 3.2 7.6 + - - +
168B ARG* 1.3 98.5 + - - +
170B SER* 1.3 57.9 + - - +
171B GLY 3.4 1.0 + - - -
192B LEU* 5.6 3.8 - - - +
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Residues in contact with SER 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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143B ILE* 5.3 0.7 - - - +
144B SER* 3.3 45.3 - - - +
166B MET 3.0 17.6 + - - -
167B ALA* 3.1 3.5 + - - -
169B ARG* 1.3 76.8 - - - +
171B GLY* 1.3 62.5 + - - +
172B VAL* 3.3 7.5 + - - +
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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