Contacts of the strand formed by residues 294 - 300 (chain C) in PDB entry 3DM6
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 GLN 294 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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189C TRP* 4.8 13.6 - - + -
288C MET* 5.2 1.6 - - - +
289C GLY* 2.8 29.8 + - - -
290C GLU* 4.8 5.1 - - - +
291C VAL* 3.0 52.7 + - + +
292C THR 3.0 5.5 + - - -
293C ASN* 1.3 77.6 - - - +
295C SER* 1.3 56.8 + - - +
373C PRO* 3.9 28.1 - - + +
374C PHE 3.8 3.1 - - - +
375C VAL* 5.2 0.4 - - - +
376C THR* 4.6 0.3 + - - -
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Residues in contact with SER 295 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189C TRP* 4.5 2.2 - - - -
204C VAL* 4.6 3.7 - - - +
286C TYR* 4.8 3.1 - - - -
287C LEU 3.2 14.6 - - - -
288C MET* 4.4 2.0 - - - -
289C GLY* 3.4 12.1 - - - +
294C GLN* 1.3 79.1 - - - +
296C PHE* 1.3 66.0 + - - +
373C PRO* 3.4 7.1 - - - +
374C PHE* 2.7 48.7 + - - +
376C THR* 3.4 29.6 - - - +
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Residues in contact with PHE 296 (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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189C TRP* 3.4 57.9 - + + -
190C TYR 3.4 28.0 - - - -
191C THR* 3.9 5.4 - - - -
286C TYR* 2.9 8.3 - - - -
287C LEU* 2.6 68.3 + - + -
288C MET 4.2 1.1 - - - -
289C GLY* 4.6 2.5 - - - -
295C SER* 1.3 82.6 + - - +
297C ARG* 1.3 59.5 + - - +
298C ILE* 4.0 18.8 - - + -
354C PHE* 4.1 7.0 - + + -
370C VAL* 3.8 13.5 - - + -
371C GLU 3.1 17.9 - - - +
372C GLY* 4.3 0.2 - - - -
374C PHE* 4.4 3.6 - - - -
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Residues in contact with ARG 297 (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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207C GLU* 4.2 7.5 + - - -
284C SER* 4.2 15.8 + - - -
285C LEU 3.1 8.1 - - - +
286C TYR* 3.1 49.3 + - + -
296C PHE* 1.3 74.2 - - - +
298C ILE* 1.3 61.6 + - - +
299C THR* 4.2 10.0 + - - +
369C ALA 3.7 0.3 - - - +
370C VAL* 3.4 5.7 - - - +
371C GLU* 2.5 77.8 + - + +
374C PHE* 4.0 19.8 - - + -
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Residues in contact with ILE 298 (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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283C ILE 3.6 1.0 - - - +
284C SER* 3.4 2.0 - - - -
285C LEU* 2.6 47.9 + - + +
287C LEU* 4.5 6.3 - - + -
296C PHE* 4.0 21.5 + - + -
297C ARG* 1.3 76.2 - - - +
299C THR* 1.3 60.9 - - - +
300C ILE* 4.1 5.5 - - + +
333C MET* 3.5 31.9 - - + -
337C ILE* 3.6 18.4 - - + -
341C PHE* 3.8 14.8 - - + -
354C PHE* 4.1 22.4 - - + -
369C ALA 3.3 3.6 - - - +
370C VAL* 4.0 15.0 - - + -
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Residues in contact with THR 299 (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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282C VAL* 3.8 29.6 - - + -
283C ILE 3.2 9.4 - - - +
284C SER* 3.3 16.8 + - - +
297C ARG* 4.2 14.2 + - - +
298C ILE* 1.3 73.6 - - - +
300C ILE* 1.3 64.4 + - - +
301C LEU* 4.2 0.7 - - + -
341C PHE* 3.1 19.9 - - - -
367C THR 4.9 7.0 - - - +
368C ALA* 3.8 8.0 - - - +
369C ALA* 2.8 37.1 + - - +
371C GLU* 4.6 0.9 + - - -
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Residues in contact with ILE 300 (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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234C LEU* 5.8 2.2 - - + -
282C VAL* 3.4 7.4 - - - -
283C ILE* 2.7 47.0 + - + +
285C LEU* 5.5 2.2 - - + -
298C ILE* 4.1 13.7 - - + +
299C THR* 1.3 74.1 - - - +
301C LEU* 1.3 71.6 + - - +
304C GLN* 3.9 16.6 - - + +
305C TYR* 3.9 16.7 - - + -
336C VAL* 4.1 20.9 - - + +
337C ILE* 3.6 29.2 - - + -
341C PHE* 3.3 32.1 - - + -
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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