Contacts of the strand formed by residues 341 - 346 (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 PHE 341 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152C LEU 3.8 5.9 - - - +
153C GLN* 4.5 3.3 - - - -
154C LEU 4.6 0.3 + - - -
298C ILE* 3.8 18.2 - - + -
299C THR 3.1 28.0 - - - -
300C ILE* 3.3 26.0 - - + -
337C ILE* 3.1 29.8 - - + -
338C MET* 2.9 17.4 + - - +
339C GLU 3.2 3.4 + - - -
340C GLY* 1.3 91.0 - - - +
342C TYR* 1.3 65.2 + - - +
343C VAL* 3.7 12.2 - - + +
354C PHE* 4.3 15.9 - + + -
355C ALA 3.3 10.1 - - - +
356C VAL* 4.1 3.4 - - + -
357C SER* 3.7 9.9 - - - +
368C ALA* 4.3 9.6 - - + -
369C ALA 3.9 15.5 - - - -
370C VAL* 3.8 18.8 - - + -
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Residues in contact with TYR 342 (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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151C SER* 2.6 38.9 + - - -
152C LEU 4.0 5.6 - - - -
153C GLN* 3.8 21.3 - - + +
175C ILE* 3.7 5.1 - - + +
179C ILE* 3.4 13.7 - - + -
180C ASP 2.9 32.1 + - - -
183C LEU* 3.7 27.6 - - + +
184C TYR* 3.2 45.8 - + + -
188C LEU* 4.4 9.0 - - + +
341C PHE* 1.3 70.7 - - - +
343C VAL* 1.3 64.6 + - - +
344C VAL* 4.1 4.4 + - + -
353C GLY 3.7 0.7 - - - +
354C PHE* 3.5 6.1 - - - -
355C ALA* 2.7 36.1 + - + +
357C SER* 3.8 4.1 - - - -
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Residues in contact with VAL 343 (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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151C SER* 3.4 1.1 - - - -
152C LEU 2.9 38.2 + - - +
227C VAL* 4.5 4.5 - - + -
338C MET* 4.2 21.1 - - + -
341C PHE* 3.7 17.0 - - + +
342C TYR* 1.3 80.0 - - - +
344C VAL* 1.3 62.9 + - - +
345C PHE* 3.3 34.0 - - + -
352C ILE* 3.9 15.3 - - + -
353C GLY 3.4 9.9 - - - +
354C PHE* 4.2 23.1 - - + -
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Residues in contact with VAL 344 (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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149C LEU* 3.5 32.1 - - + -
150C PHE 3.9 4.0 - - - +
151C SER* 3.9 10.5 - - - -
179C ILE* 3.7 20.0 - - + -
188C LEU* 3.3 41.3 - - + -
190C TYR* 4.6 6.1 - - + +
342C TYR* 4.6 5.4 - - + -
343C VAL* 1.3 73.5 - - - +
345C PHE* 1.3 59.7 + - - +
346C ASP* 3.4 8.5 + - + +
352C ILE* 3.2 12.0 - - - +
353C GLY* 2.9 34.5 + - - +
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Residues in contact with PHE 345 (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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33C THR* 3.9 16.4 - - + -
149C LEU* 3.6 1.2 - - - -
150C PHE* 2.6 66.0 + + + +
152C LEU* 3.9 19.7 - - + -
199C TYR* 3.7 46.2 - + + -
227C VAL* 3.9 18.2 - - + -
338C MET* 3.9 13.2 - - + -
343C VAL* 3.3 39.5 - - + -
344C VAL* 1.3 72.3 - - - +
346C ASP* 1.3 49.1 + - - +
347C ARG* 2.8 22.4 + - - +
351C ARG 3.9 3.8 - - - -
352C ILE* 4.2 9.6 - - + -
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Residues in contact with ASP 346 (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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149C LEU* 4.1 19.9 - - - +
179C ILE* 6.6 0.2 - - - -
190C TYR* 4.1 11.4 + - + -
193C ILE* 4.7 0.4 - - - -
344C VAL* 3.4 6.6 + - + -
345C PHE* 1.3 68.0 - - - +
347C ARG* 1.3 63.5 + - - +
348C ALA* 3.1 15.3 + - - +
349C ARG* 3.2 23.7 + - - +
350C LYS* 3.1 4.2 + - - -
351C ARG* 2.9 78.9 + - + +
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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