Contacts of the strand formed by residues 261 - 266 (chain C) in PDB entry 1UMD
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 SER 261 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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197C ALA 3.6 3.6 + - - -
198C VAL* 3.9 4.1 - - - +
199C PHE* 3.0 29.5 + - - +
230C ILE* 4.0 6.3 - - - -
231C PRO* 3.3 21.9 - - - +
233C TYR* 4.2 6.7 - - - -
250C ALA* 3.9 25.0 + - - +
253C ARG* 3.0 30.1 + - - -
259C GLY 4.5 0.5 + - - -
260C PRO* 1.3 73.7 + - - +
262C LEU* 1.3 61.3 + - - +
263C VAL* 4.1 0.7 - - - -
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Residues in contact with LEU 262 (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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173C PHE* 4.0 17.3 - - + -
183C TRP* 4.1 25.4 - - + -
187C ILE* 4.6 2.5 - - + -
199C PHE* 3.3 27.1 - - + +
201C ALA 5.0 0.4 - - - +
221C ILE* 3.4 34.1 - - + +
222C ALA* 4.3 4.5 - - - +
224C LYS* 4.2 0.2 - - + -
225C ALA* 3.8 32.5 - - + +
228C PHE* 4.9 3.1 - - + -
230C ILE* 4.1 7.2 - - + +
231C PRO 3.0 7.1 + - - +
232C GLY* 3.2 3.1 - - - -
233C TYR* 2.9 24.9 + - - +
261C SER* 1.3 74.7 - - - +
263C VAL* 1.3 66.8 + - - +
264C GLU 4.1 0.2 + - - -
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Residues in contact with VAL 263 (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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198C VAL* 4.3 9.6 - - + -
199C PHE 2.8 12.2 + - - +
200C ILE* 3.3 10.6 - - + +
201C ALA* 2.8 26.7 + - - -
233C TYR* 3.8 20.0 - - + +
235C VAL* 4.1 15.0 - - + -
246C VAL* 4.1 11.2 - - + -
247C VAL* 4.1 13.0 - - + -
250C ALA* 4.1 22.9 - - + -
262C LEU* 1.3 81.0 - - - +
264C GLU* 1.3 62.2 + - - +
265C LEU* 3.7 26.2 - - + -
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Residues in contact with GLU 264 (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 ALA* 3.8 5.2 - - + -
203C ASN* 3.0 35.3 + - + -
212C TYR* 5.8 0.2 - - - -
220C THR* 3.5 4.0 - - - +
221C ILE* 2.8 44.6 + - + -
222C ALA* 3.0 14.4 + - - +
233C TYR 2.8 17.3 + - - +
234C LEU* 3.4 26.3 - - + +
235C VAL* 2.9 33.3 + - - +
262C LEU* 4.1 1.0 + - - +
263C VAL* 1.3 71.8 - - - +
265C LEU* 1.3 62.4 + - - +
266C ARG* 3.6 11.8 - - + -
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Residues in contact with LEU 265 (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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76C ALA* 3.6 33.9 - - + +
80C ILE* 4.1 13.0 - - + -
200C ILE* 3.5 28.9 - - + -
201C ALA 2.8 12.6 + - - +
202C GLU* 3.7 4.1 - - + -
203C ASN 3.0 23.2 + - - -
235C VAL* 3.7 25.6 - - + -
237C GLY* 4.1 9.4 - - - -
243C SER* 3.8 21.3 - - - +
246C VAL* 5.8 0.2 - - + -
247C VAL* 4.4 5.6 - - + -
263C VAL* 3.7 14.8 - - + -
264C GLU* 1.3 73.1 - - - +
266C ARG* 1.3 63.6 + - - +
267C VAL* 3.3 2.6 + - - +
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Residues in contact with ARG 266 (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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15C PRO* 4.1 25.8 - - - +
203C ASN* 3.6 6.5 - - - -
205C PHE* 3.6 36.7 - - + -
234C LEU* 3.7 22.0 - - + +
235C VAL 2.9 19.5 + - - +
236C ASP* 3.9 3.0 - - - +
237C GLY* 2.7 26.8 + - - +
238C MET* 3.6 5.9 + - - +
264C GLU* 3.6 25.1 - - + +
265C LEU* 1.3 69.9 - - - +
267C VAL* 1.3 58.5 + - - +
291C TRP* 4.5 19.8 - - + -
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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