Contacts of the helix formed by residues 189 - 198 (chain E) in PDB entry 1R4N
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 PHE 189 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184E ARG* 3.7 31.4 - - + +
187E LYS 5.2 0.9 - - - +
188E PRO* 1.3 75.4 - - - +
190E PRO* 1.3 80.7 - - + +
191E GLU* 3.4 18.8 - - + -
192E LEU* 3.2 49.1 + - + +
193E ARG* 2.8 19.6 + - - +
325E VAL* 4.2 9.6 - - + -
345E VAL* 4.0 11.7 - - + -
346E TYR* 4.3 17.9 - + - -
349E LYS* 3.4 53.6 - - + +
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Residues in contact with PRO 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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188E PRO 4.7 0.7 - - - +
189E PHE* 1.3 86.2 - - + -
191E GLU* 1.3 78.1 + - - +
193E ARG* 2.6 25.6 + - + +
194E GLU* 2.6 26.8 + - + +
349E LYS* 5.3 4.0 - - - +
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Residues in contact with GLU 191 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189E PHE* 3.4 22.4 - - + -
190E PRO* 1.3 85.7 - - - +
192E LEU* 1.3 52.5 + - - +
194E GLU* 3.2 14.7 + - - +
195E HIS* 2.7 34.1 + - - +
345E VAL* 4.0 12.4 - - + +
348E GLU* 6.4 1.6 - - + -
349E LYS* 4.2 15.0 + - + +
352E LYS* 3.3 32.8 + - - +
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Residues in contact with LEU 192 (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 LEU 3.9 11.7 - - - +
184E ARG 3.7 23.6 - - - +
185E LEU* 5.0 1.1 - - + -
188E PRO* 3.9 11.0 - - + -
189E PHE* 3.2 34.2 + - + +
190E PRO 2.9 1.6 + - - -
191E GLU* 1.3 75.4 - - - +
193E ARG* 1.3 57.1 + - - +
195E HIS* 2.8 23.4 + - + +
196E PHE* 2.9 52.9 + - + -
342E LEU* 4.4 2.9 - - + -
345E VAL* 3.6 14.4 - - + -
346E TYR* 3.6 29.4 - - + +
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Residues in contact with ARG 193 (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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188E PRO* 5.0 13.2 - - + +
189E PHE 2.8 12.0 + - - +
190E PRO* 2.6 18.6 + - + +
192E LEU* 1.3 72.6 - - - +
194E GLU* 1.3 64.8 + - - +
196E PHE* 3.0 16.1 + - + +
197E GLN* 2.9 46.1 + - + +
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Residues in contact with GLU 194 (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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190E PRO* 2.6 23.1 + - + +
191E GLU* 3.5 21.0 + - - +
193E ARG* 1.3 74.8 - - + +
195E HIS* 1.3 62.2 + - - +
197E GLN* 3.4 24.1 + - - +
198E SER* 3.3 17.5 + - - -
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Residues in contact with HIS 195 (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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191E GLU 2.7 13.1 + - - +
192E LEU* 2.8 17.6 + - + +
194E GLU* 1.3 76.9 - - - +
196E PHE* 1.3 74.4 + + - +
198E SER* 2.9 25.0 + - - -
199E TYR* 3.8 33.4 + + - -
216E VAL* 4.7 2.7 - - + +
338E LYS 5.2 0.2 - - - -
341E LYS* 3.9 38.9 - - + -
342E LEU* 3.8 37.7 - - + +
345E VAL* 3.7 21.2 - - + +
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Residues in contact with PHE 196 (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 LEU* 3.7 21.3 - - + -
188E PRO* 5.0 4.5 - - + -
192E LEU* 2.9 57.3 + - + -
193E ARG* 3.4 11.2 - - + +
195E HIS* 1.3 86.5 - + - +
197E GLN* 1.3 56.5 + - - +
198E SER 2.9 1.4 + - - -
199E TYR* 2.9 14.6 + - - +
215E ILE* 3.6 28.3 - - + -
216E VAL* 4.2 20.0 - - + -
219E ALA* 3.7 23.8 - - + -
220E LYS* 2.7 31.7 + - + +
342E LEU* 4.8 2.2 - - + -
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Residues in contact with GLN 197 (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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193E ARG* 2.9 49.1 + - + +
194E GLU* 3.6 24.7 + - - +
195E HIS 3.3 0.2 - - - -
196E PHE* 1.3 75.5 - - - +
198E SER* 1.3 56.7 + - - +
199E TYR 3.1 9.5 + - - +
220E LYS* 3.8 11.5 + - - +
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Residues in contact with SER 198 (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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194E GLU 3.3 8.3 + - - -
195E HIS* 2.9 20.7 + - - -
197E GLN* 1.3 78.5 - - - +
199E TYR* 1.3 66.8 + - - +
341E LYS* 4.6 14.1 + - - -
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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