Contacts of the helix formed by residues 185 - 190 (chain E) in PDB entry 1ZWS
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 ALA 185 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183E PHE 3.8 1.4 + - - -
184E VAL* 1.3 78.1 - - - +
186E PRO* 1.3 77.5 - - + +
187E GLU* 3.4 22.2 - - + +
188E ILE* 3.2 21.6 + - + +
189E VAL* 3.4 6.4 + - - +
198E ALA* 4.3 9.4 - - + +
201E TRP* 3.4 29.4 - - + -
202E SER* 5.4 0.4 + - - -
229E ILE* 4.0 1.6 - - - -
263E ARG* 3.7 4.0 - - - +
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Residues in contact with PRO 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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185E ALA* 1.3 80.6 - - + +
187E GLU* 1.3 57.4 + - - +
188E ILE 2.6 18.1 + - - -
189E VAL* 3.0 2.9 + - + -
190E ASN* 2.4 37.9 + - - +
192E GLU* 4.9 0.4 - - - -
201E TRP* 3.2 43.5 - - + -
229E ILE* 3.6 23.6 - - + +
230E THR* 4.9 2.7 - - - -
232E VAL* 4.8 0.2 - - + -
258E LYS* 4.3 30.3 - - + +
263E ARG* 4.2 1.8 - - - +
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Residues in contact with GLU 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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185E ALA* 3.6 10.1 - - - +
186E PRO* 1.3 72.2 - - - +
188E ILE* 1.3 61.8 + - + +
190E ASN 4.3 0.2 - - - -
192E GLU* 2.8 51.6 + - + +
193E PRO 3.6 18.4 - - - +
194E LEU* 3.4 17.8 - - + +
195E GLY 4.5 0.2 - - - +
197E GLU* 3.7 10.7 - - - +
198E ALA* 3.0 33.7 + - + +
258E LYS 4.3 5.0 + - - +
260E THR* 4.5 13.1 - - + +
263E ARG* 2.8 27.9 + - - -
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Residues in contact with ILE 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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138E PHE* 5.4 0.9 - - + +
176E ASN 3.8 15.7 - - - +
177E ILE* 4.1 13.6 - - + +
178E PHE* 3.8 42.6 - - + +
184E VAL* 3.4 32.3 - - + -
185E ALA 3.4 13.9 - - - +
186E PRO 2.6 5.3 + - - -
187E GLU* 1.3 78.2 - - + +
189E VAL* 1.3 72.6 + - - +
190E ASN 3.1 1.1 - - - -
191E TYR* 2.8 17.7 + - - -
194E LEU* 3.6 23.3 - - + -
198E ALA* 4.8 13.2 - - + -
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Residues in contact with VAL 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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177E ILE* 4.9 2.2 - - - +
184E VAL* 4.4 16.4 - - + -
185E ALA 3.6 13.7 - - - +
186E PRO 3.0 4.0 + - - +
188E ILE* 1.3 81.8 - - - +
190E ASN* 1.3 58.3 + - - +
191E TYR 3.1 4.2 + - - -
226E LEU* 4.1 25.6 - - + -
229E ILE* 3.9 22.2 - - + -
230E THR* 3.3 27.8 - - + -
177F ILE* 3.3 38.9 - - + +
189F VAL 4.6 2.6 - - - +
191F TYR* 3.8 11.8 - - + +
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Residues in contact with ASN 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 PRO* 2.4 39.8 + - - +
187E GLU 4.0 0.9 - - - -
188E ILE 3.5 0.2 - - - -
189E VAL* 1.3 73.9 - - - +
191E TYR* 1.3 68.3 + - - +
192E GLU* 2.6 33.6 + - - +
230E THR* 3.0 31.4 - - - +
258E LYS* 4.9 11.4 - - - +
190F ASN* 5.7 2.7 - - - -
191F TYR* 4.1 17.2 - - + +
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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