Contacts of the helix formed by residues 311 - 319 (chain B) 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 HIS 311 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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286B GLU* 3.2 31.0 - - + -
289B ASP* 3.0 26.9 + - + -
290B PHE* 3.4 33.1 - + + -
293B GLN* 4.6 11.2 - - + -
307B GLU 3.3 5.8 + - - +
308B LEU* 2.9 20.8 + - + +
310B GLN* 1.3 77.7 - - - +
312B PRO* 1.3 68.1 - - + +
313B PHE 3.1 21.8 + - - -
314B PHE* 2.8 6.9 + - - +
315B THR* 2.8 30.7 + - - +
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Residues in contact with PRO 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286B GLU* 4.1 21.1 - - + -
310B GLN 3.7 4.0 - - - +
311B HIS* 1.3 97.7 - - + +
313B PHE* 1.3 58.2 + - - +
315B THR* 3.4 12.5 + - - +
316B LEU* 2.9 32.7 + - - +
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Residues in contact with PHE 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152B GLU* 4.1 10.1 - - - -
155B LEU 4.4 0.4 - - - -
156B GLY* 3.6 33.4 - - - -
159B ALA* 4.0 16.4 - - + -
160B VAL* 6.3 0.2 - - + -
284B SER* 4.6 2.2 - - - -
286B GLU* 3.8 17.6 - - + +
287B PHE* 3.3 59.9 - + + -
290B PHE* 3.8 24.5 - + + -
311B HIS* 3.1 18.2 + - - +
312B PRO* 1.3 78.3 - - - +
314B PHE* 1.3 64.2 + - - +
316B LEU* 4.6 3.1 - - + -
317B HIS* 3.2 53.3 + + - +
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Residues in contact with PHE 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159B ALA* 5.4 0.7 - - + -
160B VAL* 4.0 31.9 - - + +
163B VAL* 3.8 34.5 - - + -
164B LYS* 4.3 3.1 - - - -
290B PHE* 4.3 11.4 - + + -
308B LEU 3.5 13.7 - - - +
309B MSE 3.2 59.0 - - + -
311B HIS* 2.8 9.4 + - - +
313B PHE* 1.3 84.7 - - - +
315B THR* 1.3 60.9 + - + +
317B HIS 3.1 1.6 + - - -
318B GLU* 2.8 66.6 + - + +
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Residues in contact with THR 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309B MSE 3.6 21.3 - - - +
310B GLN* 3.7 17.5 - - - +
311B HIS 2.8 20.0 + - - +
312B PRO* 3.4 14.6 + - - +
314B PHE* 1.3 75.8 - - + +
316B LEU* 1.3 65.8 + - - +
318B GLU* 3.9 4.3 - - - +
319B SER* 3.7 19.4 + - - -
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Residues in contact with LEU 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286B GLU* 5.4 14.1 - - + +
312B PRO 2.9 22.8 + - - +
313B PHE* 3.9 4.7 - - + +
315B THR* 1.3 80.9 + - - +
317B HIS* 1.3 83.6 + - + +
319B SER* 3.7 4.3 + - - -
320B LYS* 3.4 36.6 + - + +
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Residues in contact with HIS 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152B GLU* 4.0 12.0 - - + +
153B ASP* 3.8 31.3 + - + +
156B GLY* 3.7 28.3 - - - +
157B LYS* 3.0 29.1 + - + +
160B VAL* 4.3 3.4 - - + -
313B PHE* 3.2 52.0 + + - +
314B PHE 3.1 3.4 + - - +
316B LEU* 1.3 93.5 - - + +
318B GLU* 1.3 66.5 + - - +
319B SER 3.1 2.7 + - - -
320B LYS* 3.3 27.4 + - + +
322B THR* 5.0 0.9 - - - -
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Residues in contact with GLU 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157B LYS* 3.6 11.2 + - - +
160B VAL* 3.7 25.3 - - + +
164B LYS* 3.2 24.6 + - - -
309B MSE 5.3 2.9 - - - +
314B PHE* 2.8 46.8 + - + +
315B THR* 3.9 7.2 - - - +
317B HIS* 1.3 78.6 - - - +
319B SER* 1.3 58.6 + - - +
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Residues in contact with SER 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157B LYS* 4.5 0.2 - - - -
315B THR 3.7 13.4 + - - -
316B LEU* 3.7 5.0 + - - -
317B HIS 3.1 0.4 - - - -
318B GLU* 1.3 79.6 - - - +
320B LYS* 1.3 65.1 + - - +
321B GLY 3.5 1.6 + - - -
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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