Contacts of the strand formed by residues 351 - 357 (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 ARG 351 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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190C TYR* 3.4 46.0 + - + -
191C THR 3.4 13.5 - - - +
192C PRO* 4.6 2.5 - - + -
193C ILE* 3.5 5.7 - - - +
290C GLU* 2.8 50.6 + - + +
346C ASP* 2.9 55.1 + - + +
349C ARG* 3.0 57.5 - - - +
350C LYS* 1.3 78.8 - - - +
352C ILE* 1.3 67.7 + - - +
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Residues in contact with ILE 352 (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 3.5 0.9 - - - +
190C TYR* 3.1 5.0 - - - -
191C THR* 2.8 42.5 + - + +
193C ILE* 3.9 18.8 - - + -
199C TYR* 4.0 26.0 - - + +
201C VAL* 3.8 24.2 - - + -
227C VAL* 4.4 6.1 - - + -
343C VAL* 3.9 9.9 - - + -
344C VAL 3.2 10.8 - - - +
345C PHE* 4.2 13.5 - - + -
351C ARG* 1.3 78.6 - - - +
353C GLY* 1.3 66.2 + - - +
354C PHE* 3.3 33.6 - - + -
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Residues in contact with GLY 353 (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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188C LEU* 4.2 5.4 - - - -
189C TRP 3.3 7.2 - - - -
190C TYR* 3.4 24.4 - - - -
343C VAL* 3.4 6.2 - - - -
344C VAL* 2.9 36.1 + - - -
352C ILE* 1.3 74.8 - - - +
354C PHE* 1.3 68.9 + - - -
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Residues in contact with PHE 354 (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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187C SER 3.4 2.3 - - - +
188C LEU* 3.4 2.8 - - - +
189C TRP 2.8 34.0 + - - +
191C THR* 4.3 4.7 - - + -
201C VAL* 5.8 0.2 - - + -
227C VAL* 4.4 19.5 - - + -
287C LEU* 3.5 29.4 - - + -
296C PHE* 4.1 9.0 - + + -
298C ILE* 4.1 39.9 - - + -
333C MET* 4.5 5.2 - - + -
337C ILE* 4.6 10.1 - - + -
338C MET* 5.7 0.7 - - + -
341C PHE* 4.3 13.0 - + + -
342C TYR 3.5 4.7 - - - -
343C VAL* 4.2 22.9 - - + -
352C ILE* 3.3 32.1 - - + -
353C GLY* 1.3 84.0 - - - -
355C ALA* 1.3 60.4 + - - +
370C VAL* 3.5 9.1 - - + +
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Residues in contact with ALA 355 (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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184C TYR* 3.6 35.0 - - + -
185C THR 4.4 2.2 - - - +
187C SER 3.5 16.6 - - - +
188C LEU* 3.7 12.8 - - + -
341C PHE* 3.3 4.4 - - - -
342C TYR 2.7 34.5 + - - +
354C PHE* 1.3 75.3 - - - +
356C VAL* 1.3 57.9 + - - +
370C VAL* 3.7 8.7 - - - -
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Residues in contact with VAL 356 (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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184C TYR* 3.3 17.8 - - - +
185C THR* 3.0 38.8 + - - +
340C GLY 3.9 8.5 - - - +
341C PHE* 4.1 3.1 - - + -
355C ALA* 1.3 72.6 - - - +
357C SER* 1.3 66.5 + - - +
360C HIS* 5.3 10.8 - - + +
368C ALA* 3.5 27.8 - - + +
369C ALA* 3.8 2.2 - - - -
370C VAL* 3.6 26.5 - - + +
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Residues in contact with SER 357 (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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153C GLN* 3.1 24.9 + - - +
154C LEU 5.9 0.4 - - - -
183C LEU 3.6 6.0 + - - -
184C TYR* 4.5 0.7 - - - -
185C THR* 4.7 2.5 + - - +
339C GLU 4.3 1.8 - - - -
340C GLY 3.2 15.5 + - - -
341C PHE* 3.7 23.8 - - - -
342C TYR 3.8 3.4 - - - +
355C ALA 3.4 1.4 + - - -
356C VAL* 1.3 78.1 - - - +
358C ALA* 1.3 65.6 + - - +
359C CYS* 3.3 23.0 + - - -
360C HIS* 3.1 21.9 + - - +
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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