Contacts of the helix formed by residues 334 - 339 (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 GLY 334 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228C ASP* 3.3 13.0 - - - -
231C THR* 3.2 17.3 - - - -
233C ASN 3.2 12.4 + - - -
332C VAL 3.2 7.4 + - - -
333C MET* 1.3 76.5 - - - +
335C ALA* 1.3 56.3 + - - -
336C VAL 3.1 3.4 - - - -
337C ILE* 2.7 25.4 + - - +
338C MET* 3.0 13.0 + - - -
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Residues in contact with ALA 335 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C TYR* 4.3 7.4 - - + -
154C LEU* 4.8 4.7 - - + -
228C ASP 4.2 1.4 + - - -
229C SER* 4.7 3.6 - - - +
231C THR 2.7 15.1 + - - +
232C THR 3.1 7.3 + - - +
307C ARG* 4.5 2.9 - - - +
334C GLY* 1.3 67.9 - - - -
336C VAL* 1.3 64.7 + - - +
337C ILE 3.1 0.2 - - - -
338C MET* 3.8 10.1 - - - +
339C GLU* 2.9 51.6 + - + +
1000C 757 4.0 21.8 - - + -
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Residues in contact with VAL 336 (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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232C THR 3.0 17.6 + - - +
234C LEU* 3.6 26.0 - - + +
300C ILE* 4.1 12.7 - - + +
304C GLN* 3.2 48.7 - - - +
305C TYR* 3.7 18.4 - - + -
307C ARG* 4.8 4.5 - - - +
323C ALA* 3.4 42.0 - - + +
334C GLY 3.0 0.4 + - - -
335C ALA* 1.3 77.2 - - - +
337C ILE* 1.3 60.2 + - + +
339C GLU* 5.0 0.2 - - - -
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Residues in contact with ILE 337 (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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227C VAL* 6.4 0.2 - - + -
234C LEU* 4.0 24.0 - - + -
283C ILE* 6.4 0.2 - - + -
285C LEU* 4.0 22.2 - - + -
298C ILE* 3.6 15.5 - - + -
300C ILE* 3.6 25.1 - - + -
304C GLN* 3.8 0.3 - - - +
333C MET* 3.6 47.8 - - + +
334C GLY 2.7 9.1 + - - +
336C VAL* 1.3 80.1 - - + +
338C MET* 1.3 67.6 + - + +
339C GLU 3.1 1.6 + - - -
340C GLY 3.3 6.4 + - - -
341C PHE* 3.1 27.3 - - + -
354C PHE* 4.6 5.4 - - + -
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Residues in contact with MET 338 (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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152C LEU* 3.6 41.2 - - + +
154C LEU* 4.0 23.4 + - + +
227C VAL* 3.8 26.7 - - + -
228C ASP 4.2 3.6 - - - +
229C SER* 3.8 29.4 - - - -
333C MET 4.2 3.6 - - - +
334C GLY 3.0 12.2 + - - +
335C ALA* 4.5 1.6 - - - -
337C ILE* 1.3 79.5 - - + +
339C GLU* 1.3 57.5 + - - +
340C GLY 3.4 0.2 - - - -
341C PHE* 2.9 26.1 - - - +
343C VAL* 4.2 19.7 - - + -
345C PHE* 3.9 16.2 - - + -
354C PHE* 5.7 0.7 - - + -
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Residues in contact with GLU 339 (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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14C TYR* 2.6 26.5 + - - +
154C LEU* 3.1 30.8 - - + +
155C CYS* 5.1 0.3 - - - -
156C GLY* 3.8 17.8 - - - +
157C ALA* 4.6 2.6 + - - +
304C GLN* 4.6 13.8 - - + +
307C ARG* 2.6 44.2 + - - -
335C ALA* 2.9 26.6 + - + +
336C VAL 4.9 0.4 - - - +
338C MET* 1.3 77.9 - - - +
340C GLY* 1.3 62.3 + - - +
341C PHE 3.2 1.6 + - - +
357C SER* 4.3 2.1 - - - -
359C CYS 3.8 14.2 - - - +
360C HIS* 5.0 1.4 - - - -
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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