Contacts of the helix formed by residues 284 - 293 (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 PRO 284 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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206C TYR* 4.0 11.0 - - - +
282C TYR 4.2 4.5 - - - +
283C ARG* 1.3 85.0 - - + +
285C LYS* 1.3 66.8 + - - +
286C GLU* 4.5 6.3 - - + +
287C GLU* 3.1 39.2 + - + +
288C VAL* 3.3 11.4 + - - +
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Residues in contact with LYS 285 (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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280C SER* 6.4 1.8 - - - -
283C ARG 3.4 5.0 + - - +
284C PRO* 1.3 71.9 - - - +
286C GLU* 1.3 65.4 + - + +
288C VAL* 3.3 8.0 + - - +
289C ALA* 2.9 26.3 + - - +
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Residues in contact with GLU 286 (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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284C PRO* 3.2 6.0 - - + -
285C LYS* 1.3 78.7 - - + +
287C GLU* 1.3 58.1 + - - +
289C ALA* 3.8 5.0 - - - +
290C PHE* 2.8 32.2 + - - +
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Residues in contact with GLU 287 (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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205C PHE* 6.4 0.2 - - - -
206C TYR* 2.6 34.5 + - - -
268C TYR* 2.7 26.1 + - - +
283C ARG* 4.2 1.4 - - - +
284C PRO* 3.1 28.5 + - + +
286C GLU* 1.3 79.9 - - - +
288C VAL* 1.3 57.0 + - - +
290C PHE* 3.2 5.8 + - - +
291C TRP* 2.9 49.8 + - + +
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Residues in contact with VAL 288 (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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268C TYR* 3.5 30.0 - - + +
270C TYR* 4.9 12.7 - - + +
283C ARG* 4.1 29.8 - - + +
284C PRO 3.3 14.7 + - - +
285C LYS* 3.3 8.5 + - - +
287C GLU* 1.3 75.0 - - - +
289C ALA* 1.3 58.4 + - - +
291C TRP* 3.3 2.3 + - - +
292C ARG* 2.9 33.3 + - + +
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Residues in contact with ALA 289 (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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285C LYS 2.9 18.2 + - - +
286C GLU* 3.8 5.4 - - - +
288C VAL* 1.3 77.4 - - - +
290C PHE* 1.3 64.8 + - - +
292C ARG* 3.2 16.1 + - - +
293C LYS* 3.5 13.2 + - - +
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Residues in contact with PHE 290 (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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286C GLU 2.8 20.8 + - - +
287C GLU* 3.2 6.5 + - - +
289C ALA* 1.3 77.8 - - - +
291C TRP* 1.3 85.1 + + - +
293C LYS* 3.4 20.4 + - + +
294C LYS* 3.2 39.2 - - - +
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Residues in contact with TRP 291 (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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205C PHE* 3.7 29.5 - + - -
236C ASP* 6.0 0.7 - - - -
238C MET* 4.3 18.8 - - + -
266C ARG* 4.5 19.5 - - + -
267C VAL* 4.2 10.8 - - - -
268C TYR* 3.4 55.1 - + + -
270C TYR* 2.7 24.8 + - - -
287C GLU* 2.9 36.3 + - + +
288C VAL 4.0 1.1 - - - +
290C PHE* 1.3 93.6 - + - +
292C ARG* 1.3 55.5 + - - +
293C LYS 3.0 2.5 - - - -
294C LYS* 2.8 49.0 + - + +
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Residues in contact with ARG 292 (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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49C ARG* 4.3 17.4 - - - +
53C GLU* 5.7 2.2 + - - -
71C ALA* 5.2 4.8 - - - +
270C TYR* 2.9 61.0 + - - +
288C VAL* 2.9 20.7 + - + +
289C ALA* 3.2 10.7 + - - +
291C TRP* 1.3 77.7 - - - +
293C LYS* 1.3 59.3 + - - +
294C LYS 3.1 0.9 + - - -
295C ASP* 3.4 22.4 + - - +
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Residues in contact with LYS 293 (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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289C ALA 3.5 8.1 + - - +
290C PHE* 3.4 16.3 + - + +
291C TRP 3.0 0.4 - - - -
292C ARG* 1.3 78.9 - - - +
294C LYS* 1.3 58.9 + - + +
295C ASP* 3.4 2.2 - - - +
302C ARG* 5.1 8.3 + - - -
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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