Contacts of the strand formed by residues 200 - 204 (chain C) in PDB entry 5E9W
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 THR 200 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195C LYS* 5.1 2.2 + - - -
198C ASP* 4.2 10.0 + - - +
199C ILE* 1.3 74.0 + - - +
201C VAL* 1.3 64.3 + - - +
221C ASN* 5.5 0.5 - - - +
222C LYS* 3.6 24.6 - - + +
224C VAL* 5.8 0.2 - - + -
276C MET* 4.5 11.4 - - + -
277C CYS 3.2 27.5 + - - +
278C PHE* 3.6 15.8 - - + -
279C ASP* 2.8 43.0 + - - +
280C ILE 3.4 4.7 + - - -
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Residues in contact with VAL 201 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188C LEU* 4.8 0.4 - - + -
199C ILE* 4.2 9.4 - - + -
200C THR* 1.3 80.2 - - - +
202C LEU* 1.3 68.9 + - - +
215C TRP* 3.6 49.4 - - + -
220C ILE* 3.9 23.1 - - + -
222C LYS 3.1 5.9 + - - -
223C LEU* 3.5 17.7 - - + +
224C VAL 3.0 24.8 + - - -
278C PHE* 3.5 7.6 - - - -
280C ILE* 3.3 21.8 - - + +
282C SER* 4.8 0.4 - - - -
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Residues in contact with LEU 202 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201C VAL* 1.3 72.4 - - - +
203C ASP* 1.3 54.5 + - - +
204C LEU* 3.6 6.4 + - + +
224C VAL* 3.8 31.0 - - + +
226C THR* 4.1 19.7 - - + -
267C LEU* 4.1 14.8 - - + -
271C PHE* 4.6 2.9 - - + -
278C PHE* 3.4 35.9 - - + -
280C ILE 2.9 11.5 + - - +
281C CYS* 3.2 22.6 - - + -
282C SER 2.8 33.3 + - - +
303C ASN 3.5 24.9 - - - +
304C ALA 4.7 0.9 - - - +
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Residues in contact with ASP 203 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201C VAL 4.0 1.0 - - - -
202C LEU* 1.3 70.6 - - - +
204C LEU* 1.3 61.9 + - - +
205C GLY 3.6 0.2 + - - -
206C CYS* 3.7 30.7 + - + +
209C GLY* 6.2 0.5 - - - -
211C ASP* 4.0 18.0 + - - +
212C LEU* 5.6 0.5 + - - +
215C TRP* 3.8 19.9 + - - +
223C LEU* 4.1 15.9 - - + +
224C VAL 2.9 14.2 + - - +
225C CYS* 4.8 4.3 - - - -
226C THR* 3.2 26.5 + - - +
282C SER* 3.3 20.2 + - - +
284C GLN* 5.0 1.4 + - - +
501C SAH 4.5 7.3 + - - -
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Residues in contact with LEU 204 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202C LEU* 3.6 5.4 + - + -
203C ASP* 1.3 69.7 - - - +
205C GLY* 1.3 66.3 + - - +
226C THR* 3.9 10.5 - - + -
262C SER* 3.6 29.8 - - - +
267C LEU* 4.6 2.0 - - + -
281C CYS* 4.1 9.9 - - - -
282C SER 2.9 13.3 + - - +
283C CYS* 3.7 19.7 - - - -
284C GLN 4.3 0.7 + - - -
286C VAL* 3.5 17.7 - - + +
300C MET* 4.0 31.6 - - + +
303C ASN* 4.1 11.9 - - + +
304C ALA* 3.8 39.9 - - + +
501C SAH 4.4 2.2 - - + -
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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