Contacts of the helix formed by residues 182 - 190 (chain E) in PDB entry 3VBB
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 182 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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180E PHE* 3.2 36.2 - - - -
181E GLU* 1.3 73.4 + - - +
183E GLU* 1.3 60.1 + - - +
185E GLY* 3.3 2.3 + - - -
186E ALA* 3.1 27.0 + - - +
193E GLY 3.7 8.2 - - - +
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Residues in contact with GLU 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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181E GLU* 3.2 9.6 + - - +
182E GLY* 1.3 71.6 - - - +
184E LYS* 1.3 64.9 + - + +
185E GLY 3.0 4.4 + - - -
186E ALA* 3.3 13.1 + - - +
187E VAL* 3.3 18.3 + - - +
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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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181E GLU* 3.1 20.6 + - + +
183E GLU* 1.3 76.9 - - + +
185E GLY* 1.3 64.5 + - - +
187E VAL* 3.9 15.6 - - + +
188E VAL* 3.3 28.8 + - - +
195E PHE* 4.2 2.6 - - - -
278F ALA 4.6 6.9 + - - +
279F LEU* 3.5 46.5 + - + +
281F ARG* 3.3 26.1 + - - +
282F ASP* 5.6 0.6 + - - +
283F GLU* 3.7 20.7 + - - +
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Residues in contact with GLY 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 GLU* 3.7 16.5 + - - +
182E GLY 3.3 9.4 + - - -
183E GLU 3.0 1.4 - - - -
184E LYS* 1.3 79.7 - - - +
186E ALA* 1.3 56.0 + - - +
188E VAL* 3.9 1.2 - - - +
189E ALA* 3.0 33.1 + - - +
193E GLY* 3.6 16.7 - - - -
194E TYR* 4.1 4.0 + - - -
195E PHE* 4.1 10.5 - - - -
226F PRO* 4.7 0.9 - - - +
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Residues in contact with ALA 186 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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182E GLY 3.1 15.4 + - - +
183E GLU* 3.3 6.4 + - - +
185E GLY* 1.3 73.9 - - - +
187E VAL* 1.3 62.5 + - + +
190E GLY* 2.9 45.2 + - - +
191E SER* 5.0 1.3 - - - -
192E ARG* 4.8 4.9 - - - +
193E GLY 3.8 6.5 + - - +
230F ARG* 3.5 3.6 + - - -
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Residues in contact with VAL 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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183E GLU 3.3 16.3 + - - +
184E LYS* 3.9 20.0 - - + +
185E GLY 3.4 0.2 - - - -
186E ALA* 1.3 77.7 - - + +
188E VAL* 1.3 61.8 + - + +
230F ARG* 2.8 28.9 + - - +
233F VAL* 3.9 18.5 - - + +
278F ALA* 5.7 3.4 - - + +
281F ARG* 4.7 11.2 - - - +
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Residues in contact with VAL 188 (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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184E LYS 3.3 17.1 + - - +
185E GLY 3.9 2.2 - - - +
186E ALA 3.2 0.4 - - - -
187E VAL* 1.3 81.6 - - + +
189E ALA* 1.3 63.1 + - - +
190E GLY 3.8 0.2 + - - -
195E PHE* 4.3 8.7 - - + -
226F PRO* 4.3 11.0 - - + -
229F MET* 3.4 29.4 - - + -
230F ARG* 3.2 23.1 + - - +
233F VAL* 3.7 10.3 - - + +
275F PRO* 4.2 21.8 - - + +
278F ALA* 3.7 36.1 - - + +
279F LEU* 5.2 0.4 - - - -
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Residues in contact with ALA 189 (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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185E GLY 3.0 18.2 + - - +
188E VAL* 1.3 73.4 - - - +
190E GLY* 1.3 58.7 + - - +
191E SER 5.1 0.9 - - - +
193E GLY* 3.9 13.7 - - - -
319E HIS* 6.0 0.5 - - - -
226F PRO* 3.5 31.4 - - + -
228F PHE* 3.6 29.0 - - + +
229F MET* 4.6 0.2 - - - +
230F ARG* 4.2 4.7 - - - -
266F LYS* 3.6 19.9 + - - -
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Residues in contact with GLY 190 (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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186E ALA* 2.9 37.5 + - - -
188E VAL 3.5 2.0 + - - -
189E ALA* 1.3 78.8 - - - +
191E SER* 1.3 66.2 + - - -
193E GLY 3.3 4.7 + - - -
230F ARG* 3.9 23.2 - - - +
266F LYS* 4.8 4.0 - - - -
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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