Contacts of the strand formed by residues 196 - 199 (chain E) in PDB entry 1LE9
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 ILE 196 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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195E LYS* 1.3 75.2 - - - +
197E CYS* 1.3 62.5 + - - +
198E ARG* 4.4 1.7 - - - +
199E VAL* 4.0 26.9 - - + -
214E LEU* 4.0 14.8 - - + -
215E LEU 4.2 2.0 - - - -
216E CYS* 4.4 1.6 - - - -
270E MET* 3.6 27.4 - - + +
271E GLN* 3.7 6.1 - - - -
272E LEU* 3.8 13.0 - - + +
281E SER* 3.5 24.7 - - - +
282E GLU* 2.6 34.0 + - - +
284E MET* 4.1 22.0 - - + +
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Residues in contact with CYS 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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195E LYS* 3.6 28.6 + - - -
196E ILE* 1.3 74.5 - - - +
198E ARG* 1.3 67.3 + - + +
215E LEU* 3.2 11.9 + - + +
217E ASP* 3.7 17.0 - - - -
284E MET* 5.9 0.2 - - - -
304F HIS* 4.0 21.1 - - + +
305F ARG* 3.9 10.3 - - - -
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Residues in contact with ARG 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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196E ILE* 3.5 3.4 + - - +
197E CYS* 1.3 83.7 - - + +
199E VAL* 1.3 66.2 - - - +
215E LEU* 2.7 48.4 + - + +
284E MET* 5.0 6.7 - - - -
265F GLU* 4.3 7.9 + - - -
267F TYR* 3.0 22.7 + - + +
301F THR 5.2 0.2 + - - -
302F ASP* 3.5 37.4 + - - +
310F VAL* 3.3 40.6 - - - +
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Residues in contact with VAL 199 (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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196E ILE* 4.0 11.0 - - + -
198E ARG* 1.3 84.2 - - - +
200E ASN* 1.3 63.7 + - - +
201E ARG 3.1 20.6 - - - +
202E ASN* 4.6 4.4 + - - +
212E ILE* 4.3 6.5 - - + -
213E PHE 3.2 10.3 - - - +
214E LEU* 3.6 34.5 - - + -
270E MET* 4.4 15.0 - - + -
284E MET* 3.1 27.4 - - + +
265F GLU* 5.6 0.2 - - - +
267F TYR* 3.3 10.3 + - - -
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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