Contacts of the helix formed by residues 304 - 309 (chain D) in PDB entry 3ENM
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 THR 304 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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236D VAL* 6.0 3.8 - - + -
237D LYS* 4.0 20.9 - - - +
240D ILE* 4.1 5.4 - - - -
303D PRO* 1.3 77.0 - - - +
305D TYR* 1.3 63.5 + - - +
306D PRO* 3.4 15.4 - - - +
307D GLU* 3.1 36.8 + - - +
308D LEU* 3.1 20.3 + - - +
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Residues in contact with TYR 305 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163D VAL* 4.5 11.9 - - + -
166D LEU* 3.2 48.2 - - + +
167D GLU* 3.5 30.1 - - + -
170D HIS* 4.3 20.6 - - + -
236D VAL* 3.7 27.8 + - + +
239D ASP* 3.4 22.9 + - - +
240D ILE* 3.4 27.6 - - + +
243D LEU* 5.3 1.3 - - + -
304D THR* 1.3 68.9 - - - +
306D PRO* 1.3 77.1 - - + +
307D GLU 3.0 1.8 - - - -
308D LEU* 2.9 24.8 + - + +
309D MSE 2.9 17.1 + - - +
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Residues in contact with PRO 306 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167D GLU* 4.8 8.7 - - + +
304D THR* 3.4 16.6 - - + +
305D TYR* 1.3 93.8 - - + +
307D GLU* 1.3 57.1 + - + +
309D MSE 3.0 27.3 + - + +
310D GLN* 3.2 16.1 + - - +
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Residues in contact with GLU 307 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303D PRO* 3.2 19.2 - - + +
304D THR* 3.1 42.8 + - - +
305D TYR 3.0 0.8 - - - -
306D PRO* 1.3 77.2 - - + +
308D LEU* 1.3 66.8 + - - +
309D MSE 3.0 1.3 - - - -
310D GLN* 2.9 20.7 + - - +
311D HIS* 3.2 10.0 + - - +
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Residues in contact with LEU 308 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163D VAL* 4.3 10.3 - - + -
240D ILE* 4.0 17.5 - - + -
243D LEU* 4.0 26.0 - - + -
290D PHE* 3.7 30.1 - - + -
293D GLN* 4.9 4.0 - - + -
294D CYS* 4.3 9.2 - - - -
303D PRO* 3.1 31.6 - - + -
304D THR 3.1 8.8 + - - +
305D TYR* 2.9 26.8 + - + +
307D GLU* 1.3 78.2 - - - +
309D MSE 1.3 58.3 + - - +
310D GLN 3.1 0.2 - - - -
311D HIS* 3.0 21.9 + - + +
314D PHE* 3.3 17.9 - - - +
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Residues in contact with MSE 309 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163D VAL* 3.9 19.7 - - + -
164D LYS* 4.6 18.8 - - + -
167D GLU* 3.9 35.7 - - - +
305D TYR 2.9 14.9 + - - +
306D PRO* 3.2 14.8 - - + +
307D GLU 3.0 0.2 - - - -
308D LEU* 1.3 79.0 - - - +
310D GLN* 1.3 65.4 + - - +
311D HIS 3.4 0.2 - - - -
314D PHE* 3.4 41.4 - - + -
315D THR* 3.5 10.9 - - - +
318D GLU* 5.4 1.8 - - - +
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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