Contacts of the strand formed by residues 283 - 286 (chain E) in PDB entry 3ECS
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 LEU 283 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118E PHE* 3.4 39.5 - - + -
226E PHE 3.8 1.2 + - - -
227E TYR* 3.6 20.5 - - + +
228E VAL* 2.9 26.3 + - - +
281E ILE* 3.8 2.0 - - - +
282E THR* 1.3 98.3 - - + +
284E LEU* 1.3 67.4 + - - +
285E PHE* 3.9 9.4 - - + -
290E VAL* 3.8 20.0 - - + -
291E LEU 3.5 17.3 - - - +
292E THR* 4.4 11.9 - - + -
293E PRO* 4.7 0.9 - - - -
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Residues in contact with LEU 284 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200E VAL* 3.5 43.7 - - + -
204E GLY 4.4 11.4 - - - +
206E ILE* 4.8 1.6 - - + -
228E VAL* 3.2 26.9 - - + +
230E ALA* 5.6 2.5 - - + +
235E PHE* 5.1 6.5 - - + -
281E ILE* 3.5 32.3 - - + -
283E LEU* 1.3 72.4 - - - +
285E PHE* 1.3 63.4 + - - +
286E THR* 3.6 5.6 + - - +
289E GLY 3.7 0.3 - - - +
290E VAL* 3.4 4.0 - - - +
291E LEU* 2.8 46.8 + - + +
293E PRO* 4.8 5.2 - - + -
296E VAL* 4.2 12.8 - - + -
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Residues in contact with PHE 285 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111E ILE* 3.4 16.1 - - + +
114E LEU* 4.1 4.9 - - + -
115E CYS* 3.1 32.8 - - + -
118E PHE* 3.4 45.3 - + + -
227E TYR* 3.5 34.3 - + + -
228E VAL 2.6 17.5 + - - -
229E VAL* 3.3 23.0 - - + -
230E ALA 3.1 23.6 + - - +
283E LEU* 3.9 15.7 - - + -
284E LEU* 1.3 72.7 - - - +
286E THR* 1.3 60.0 + - - +
289E GLY 4.3 1.8 - - - -
290E VAL* 3.9 23.1 - - + +
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Residues in contact with THR 286 (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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111E ILE* 3.7 6.1 - - - +
114E LEU* 2.9 26.5 - - - +
230E ALA 3.1 16.8 + - - -
232E SER* 3.8 13.0 + - - -
235E PHE* 3.9 17.1 - - + -
284E LEU* 3.6 7.1 + - - -
285E PHE* 1.3 76.1 - - - +
287E ASP* 1.3 62.2 + - - +
288E LEU* 3.0 28.1 + - + +
289E GLY 2.8 31.0 + - - +
291E LEU* 4.3 16.4 - - + -
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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