Contacts of the strand formed by residues 192 - 196 (chain E) in PDB entry 1A81
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 192 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168E TRP* 3.4 33.7 - + + -
182E VAL* 4.7 2.2 - - - -
190E GLY 3.5 10.8 - - - +
191E LYS* 1.3 81.2 - - - +
193E LEU* 1.3 69.4 + - - +
194E ILE* 5.3 0.2 - - + -
205E LEU* 4.2 8.7 - - + -
206E CYS 2.9 13.7 - - - +
207E LEU* 3.6 11.2 - - + -
241E VAL* 4.3 13.7 - - + -
245E SER* 4.7 4.9 - - - -
255E LEU* 4.0 34.8 - - + -
256E THR 3.3 28.9 - - - -
257E VAL 3.0 30.0 + - - -
258E PRO* 3.2 12.8 - - + +
259E CYS* 2.7 31.7 + - - -
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Residues in contact with LEU 193 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168E TRP 3.1 13.5 - - - +
170E HIS* 3.5 46.9 - - + +
173E ILE* 5.9 0.2 - - + -
178E SER* 4.9 5.6 - - - -
181E ILE* 4.1 14.8 - - + -
182E VAL* 4.4 5.4 - - + -
192E PHE* 1.3 84.9 - - - +
194E ILE* 1.3 65.2 + - - +
195E ARG* 4.9 3.8 - - + +
205E LEU* 3.1 17.8 - - - +
206E CYS* 2.8 43.3 + - + +
259E CYS* 3.8 18.4 - - + -
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Residues in contact with ILE 194 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168E TRP* 2.4 60.5 + - + +
169E PHE* 3.2 13.2 - - + -
170E HIS 2.9 23.7 + - - -
192E PHE* 5.3 1.1 - - + -
193E LEU* 1.3 71.0 - - - -
195E ARG* 1.3 61.8 + - - +
203E TYR* 4.6 6.7 - - + -
204E ALA 2.7 30.5 - - - +
205E LEU* 4.2 14.6 - - + +
218E ILE* 3.8 18.6 - - + -
237E LEU* 4.6 15.3 - - + -
240E LEU* 5.1 4.7 - - + -
241E VAL* 3.7 17.3 - - + -
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Residues in contact with ARG 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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169E PHE* 4.8 2.7 - - - -
170E HIS* 3.7 14.4 - - + +
171E GLY 3.5 7.2 - - - +
173E ILE* 3.6 33.9 + - + +
174E SER 4.0 7.3 + - - -
175E ARG* 3.5 27.7 + - - +
178E SER* 4.0 8.2 + - - -
193E LEU* 4.9 2.9 - - + -
194E ILE* 1.3 75.3 - - - +
196E ALA* 1.3 63.4 + - - +
197E ARG* 4.2 5.9 - - - +
203E TYR* 3.6 3.0 - - - +
204E ALA* 3.0 46.6 + - - +
206E CYS* 4.1 21.2 - - - -
215E HIS* 3.9 17.8 + - - +
170F PTR 2.6 44.6 + - - -
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Residues in contact with ALA 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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169E PHE* 4.5 7.0 - - + -
171E GLY 3.0 17.9 + - - +
172E LYS* 3.9 23.5 - - + +
173E ILE 4.1 8.1 + - - +
195E ARG* 1.3 74.6 + - - +
197E ARG* 1.3 73.9 + - - +
198E ASP 3.5 0.7 + - - -
199E ASN 4.9 4.7 - - - +
202E SER 3.8 10.1 - - - +
203E TYR* 4.1 17.5 - - + +
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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
------------------------------------------------------------
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