Contacts of the helix formed by residues 172 - 187 (chain E) in PDB entry 2V8W
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 ASN 172 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148E ASP* 3.0 34.8 + - - +
168E THR* 5.2 1.0 - - - +
169E GLU* 3.1 28.8 + - - +
170E CYS 4.6 0.2 - - - -
171E GLU* 1.3 76.8 - - - +
173E ARG* 1.3 55.3 + - - +
174E GLU 3.3 2.7 - - - -
175E ALA* 3.4 9.0 + - + +
176E VAL* 2.8 37.1 + - - +
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Residues in contact with ARG 173 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A PRO* 4.4 8.7 - - - +
191A PRO* 3.2 36.4 - - + +
170E CYS 4.9 0.2 - - - +
171E GLU* 3.0 18.3 + - - +
172E ASN* 1.3 69.3 - - - +
174E GLU* 1.3 63.9 + - - +
176E VAL* 4.3 0.2 - - - +
177E THR* 2.7 31.2 + - - -
215E PHE* 3.4 35.8 - - + -
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Residues in contact with GLU 174 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A LYS* 2.4 47.3 + - + +
185A GLU* 6.1 2.9 - - + -
189A LEU 4.4 2.8 - - - +
190A PRO 4.3 0.9 - - - -
191A PRO* 3.5 24.7 - - + +
217A VAL* 3.4 11.0 - - + +
145E TYR* 3.2 27.6 - - + +
172E ASN 3.3 0.6 - - - -
173E ARG* 1.3 75.8 - - - +
175E ALA* 1.3 60.8 + - - +
177E THR* 3.4 1.9 + - - +
178E HIS* 2.9 36.7 + - - +
181E ARG* 4.4 3.1 + - - -
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Residues in contact with ALA 175 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145E TYR* 3.5 34.7 - - + -
148E ASP* 3.5 33.2 - - + +
172E ASN* 3.4 13.8 + - + +
174E GLU* 1.3 75.2 - - - +
176E VAL* 1.3 65.4 + - - +
178E HIS* 3.4 1.6 + - - +
179E ILE* 3.0 30.4 + - - +
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Residues in contact with VAL 176 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113E TRP* 2.8 30.4 + - + +
148E ASP* 5.4 1.1 - - + +
167E THR* 3.6 24.5 - - - +
169E GLU 3.6 15.0 - - - +
170E CYS* 4.4 0.4 - - - -
172E ASN* 2.8 25.7 + - + +
173E ARG 4.3 1.3 - - - +
175E ALA* 1.3 72.9 - - + +
177E THR* 1.3 61.9 - - - +
179E ILE* 3.4 5.5 + - - +
180E GLY 3.1 6.8 + - - -
197E TYR* 3.5 28.5 - - + +
215E PHE* 3.3 38.8 - - + -
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Residues in contact with THR 177 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A PRO* 3.7 34.3 - - + +
113E TRP* 4.4 7.4 - - - -
173E ARG 2.7 22.9 + - - -
174E GLU* 3.8 5.2 - - - +
176E VAL* 1.3 74.0 - - - +
178E HIS* 1.3 64.6 + - - +
180E GLY* 3.4 1.4 + - - -
181E ARG* 3.0 30.7 + - + +
215E PHE* 3.9 18.7 - - - +
216E VAL 5.6 1.3 - - - +
217E VAL* 4.0 14.2 - - + +
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Residues in contact with HIS 178 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A VAL 4.0 12.9 + - - -
217A VAL* 4.4 13.2 - - + +
141E SER 5.1 0.2 - - - -
142E PHE* 3.4 29.3 + - - +
143E ASP* 4.2 14.6 + - + -
145E TYR* 3.4 33.8 - + + +
174E GLU* 2.9 19.6 + - - +
175E ALA 3.7 2.0 - - - +
177E THR* 1.3 76.5 - - - +
179E ILE* 1.3 62.3 + - - +
181E ARG* 3.1 40.0 + - - +
182E VAL* 3.0 46.0 + - + +
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Residues in contact with ILE 179 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113E TRP* 4.0 16.4 - - + +
142E PHE* 3.6 42.4 - - + -
145E TYR* 3.5 23.6 - - + +
148E ASP* 3.9 13.0 - - + -
149E VAL* 4.0 7.9 - - + -
165E ILE* 4.1 23.6 - - + -
167E THR* 3.9 20.4 - - + -
175E ALA 3.0 21.0 + - - +
176E VAL* 3.7 3.6 - - - +
178E HIS* 1.3 73.6 - - - +
180E GLY* 1.3 58.2 + - - +
182E VAL 3.2 1.6 + - - -
183E TYR* 2.8 31.4 + - + +
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Residues in contact with GLY 180 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113E TRP* 3.4 37.8 - - - +
176E VAL 3.1 10.7 + - - -
177E THR 3.8 0.2 - - - -
179E ILE* 1.3 76.9 - - - +
181E ARG* 1.3 60.6 + - - +
183E TYR* 3.8 4.2 - - - +
184E LYS* 3.1 26.7 + - - +
195E ILE* 4.4 1.8 - - - +
217E VAL* 3.5 10.8 - - - +
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Residues in contact with ARG 181 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A PRO 5.9 0.6 + - - -
194A VAL* 3.6 21.3 - - - +
216A VAL* 3.3 29.2 + - - +
217A VAL* 3.4 22.6 + - - -
174E GLU* 4.4 2.8 + - - -
177E THR* 3.0 23.4 + - + +
178E HIS* 3.1 46.4 + - - +
180E GLY* 1.3 74.9 - - - +
182E VAL* 1.3 72.1 + - - +
184E LYS* 3.6 1.0 + - - +
185E GLU* 2.7 45.4 + - + +
217E VAL* 4.0 14.8 - - + +
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Residues in contact with VAL 182 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141E SER* 3.6 16.2 - - - +
142E PHE* 3.6 26.2 - - + -
178E HIS* 3.0 46.2 + - + +
181E ARG* 1.3 86.0 - - - +
183E TYR* 1.3 55.7 + - - +
185E GLU* 3.1 6.3 + - - +
186E ARG* 2.7 46.2 + - + +
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Residues in contact with TYR 183 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113E TRP* 4.6 17.5 - - + -
115E ILE* 3.9 21.9 - - + +
133E THR* 2.9 34.5 + - + +
136E CYS* 4.6 11.0 - - - -
142E PHE* 3.9 4.4 - - + -
163E ILE* 3.1 21.0 - - - +
165E ILE* 3.4 39.5 - - + -
179E ILE* 2.8 22.3 + - + +
180E GLY* 3.8 4.3 - - - +
182E VAL* 1.3 73.1 - - - +
184E LYS* 1.3 64.7 + - - +
186E ARG* 3.2 4.3 + - - -
187E LEU* 2.8 53.3 + - + +
195E ILE* 4.4 16.4 - - + -
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Residues in contact with LYS 184 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180E GLY 3.1 14.7 + - - +
181E ARG* 3.6 6.3 - - - +
183E TYR* 1.3 79.9 - - - +
185E GLU* 1.3 75.0 + - - +
187E LEU* 3.3 2.5 + - - -
188E GLY 3.2 3.8 + - - -
189E LEU* 3.1 48.9 + - + +
190E PRO 2.9 32.1 + - - -
191E PRO* 3.5 16.5 + - - +
193E ILE* 3.4 12.4 - - - +
195E ILE* 4.6 12.6 - - + -
217E VAL* 2.9 47.6 - - + +
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Residues in contact with GLU 185 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181E ARG* 2.7 38.0 + - + +
182E VAL* 3.1 7.0 + - + +
184E LYS* 1.3 99.6 + - - +
186E ARG* 1.3 66.2 + - - +
188E GLY* 3.0 16.5 + - - +
189E LEU 4.3 9.4 - - - +
191E PRO* 5.2 5.9 - - - +
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Residues in contact with ARG 186 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132E GLU* 2.2 65.9 + - + +
135E LEU* 4.0 14.5 + - - +
136E CYS* 3.3 42.1 - - - +
141E SER* 3.5 20.6 + - - -
182E VAL* 2.7 33.0 + - + +
183E TYR* 3.6 4.9 - - + +
185E GLU* 1.3 73.4 - - - +
187E LEU* 1.3 60.3 + - - +
188E GLY* 3.5 0.5 + - - -
54F TYR 4.7 2.4 + - - -
55F ASP* 4.6 2.4 - - - +
56F ARG* 3.8 35.9 - - - +
59F LEU* 5.1 0.2 - - - +
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Residues in contact with LEU 187 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115E ILE* 3.5 31.2 - - + -
128E ARG* 4.9 5.2 + - - -
129E PHE* 3.6 61.7 - - + +
132E GLU* 3.8 19.1 - - + -
133E THR* 4.4 0.2 - - - +
183E TYR* 2.8 50.6 + - + +
184E LYS 3.8 4.3 - - - +
186E ARG* 1.3 73.2 - - - +
188E GLY* 1.3 61.4 + - - +
189E LEU* 4.0 20.9 - - + -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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