Contacts of the strand formed by residues 238 - 243 (chain C) in PDB entry 4UM8
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 ASP 238 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228C VAL* 3.5 9.0 - - - +
229C GLY 2.6 34.1 + - - +
230C ASP* 3.4 1.0 - - - +
231C PHE* 3.0 36.3 + - + +
232C ASN* 3.2 15.5 + - - +
234C ASP* 4.6 0.9 - - - +
236C ILE* 3.6 9.4 - - - +
237C ASP* 1.3 74.1 - - - +
239C PHE* 1.3 65.2 + - - +
240C VAL* 3.8 2.7 + - - +
255C ILE* 4.7 1.3 - - + -
256C TYR 3.2 12.1 - - - +
257C ASP* 2.8 15.9 - - - +
258C GLY* 2.7 26.2 + - - +
264C LEU* 4.0 6.0 - - + +
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Residues in contact with PHE 239 (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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164C THR* 4.1 22.0 - - + -
168C ARG* 4.9 3.4 - - - -
170C LEU* 3.6 35.9 - - + -
183C LEU* 4.7 8.7 - - + -
185C SER* 3.2 28.0 - - - -
208C LEU* 4.6 5.2 - - + -
227C ALA 4.1 1.8 - - - -
228C VAL* 4.8 2.0 - - + -
237C ASP 4.2 7.4 - - - -
238C ASP* 1.3 74.8 - - - +
240C VAL* 1.3 63.0 + - - +
254C TYR 3.7 0.7 - - - +
255C ILE* 3.2 5.9 - - - +
256C TYR* 2.8 47.4 + - + +
257C ASP 4.2 4.5 - - - -
258C GLY* 3.8 27.6 - - - -
261C MET* 3.6 37.7 - - + -
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Residues in contact with VAL 240 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170C LEU* 4.7 0.6 - - - +
226C VAL* 3.3 6.9 - - - +
227C ALA* 3.0 52.5 + - + +
228C VAL 5.4 0.7 - - - -
229C GLY 5.4 0.7 - - - +
231C PHE* 3.6 35.2 - - + -
238C ASP 4.6 1.1 - - - +
239C PHE* 1.3 77.2 - - - +
241C SER* 1.3 65.0 + - - +
253C VAL* 3.8 22.2 - - + -
254C TYR 3.5 3.1 - - - +
255C ILE* 4.0 14.8 - - + -
267C PHE* 6.1 0.4 - - + -
280C VAL* 5.7 8.3 - - - -
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Residues in contact with SER 241 (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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183C LEU* 3.6 31.0 - - - -
222C LEU* 3.4 5.8 - - - +
223C GLY* 3.0 32.1 + - - -
225C SER 3.1 11.8 + - - -
226C VAL* 4.5 1.1 - - - -
239C PHE 4.2 0.2 - - - -
240C VAL* 1.3 76.9 - - - +
242C GLY* 1.3 61.0 + - - +
243C VAL* 3.8 1.4 - - - +
253C VAL* 3.3 7.0 - - - +
254C TYR 2.9 35.5 + - - -
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Residues in contact with GLY 242 (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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221C TYR 3.4 8.8 - - - +
223C GLY 3.6 4.5 + - - -
224C TYR* 3.5 12.0 + - - +
225C SER* 3.2 13.5 + - - -
241C SER* 1.3 73.2 + - - +
243C VAL* 1.3 59.5 + - - -
244C PRO* 3.3 14.2 - - - +
252C MET 3.8 4.0 - - - -
253C VAL* 4.1 5.8 - - - -
277C GLY* 3.5 24.2 - - - -
280C VAL* 6.2 1.0 - - - +
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Residues in contact with VAL 243 (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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220C SER* 3.2 36.3 - - - +
221C TYR 4.0 0.4 - - - -
222C LEU* 3.7 22.7 - - + +
241C SER 3.8 4.0 - - - +
242C GLY* 1.3 75.3 - - - -
244C PRO* 1.3 63.9 - - - +
245C ARG 3.3 0.9 - - - -
246C ALA* 3.1 20.6 + - + +
252C MET 2.6 36.8 + - - +
254C TYR* 3.5 44.6 - - + -
277C GLY* 4.5 0.2 - - - -
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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