Contacts of the helix formed by residues 311 - 320 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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286A GLU* 3.3 28.3 - - - -
289A ASP* 2.6 29.8 + - + -
290A PHE* 3.5 28.7 + + + -
293A GLN* 4.4 9.4 - - + -
307A GLU 3.2 7.7 + - - +
308A LEU* 3.0 21.3 + - + +
309A MSE 3.3 0.2 - - - -
310A GLN* 1.3 79.4 - - - +
312A PRO* 1.3 87.4 - - + +
313A PHE* 3.0 26.2 + - - +
314A PHE* 2.8 14.0 + - - +
315A THR* 2.9 12.1 + - - -
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Residues in contact with PRO 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286A GLU* 3.6 24.9 - - + +
310A GLN 3.4 3.5 - - - +
311A HIS* 1.3 101.5 - - + +
313A PHE* 1.3 62.4 + - - +
315A THR* 3.1 9.1 + - - +
316A LEU* 2.9 27.7 + - - +
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Residues in contact with PHE 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152A GLU* 3.6 9.9 - - + -
155A LEU 4.4 1.1 - - - -
156A GLY* 3.7 33.9 - - - -
159A ALA* 3.9 18.4 - - + -
160A VAL* 6.1 0.7 - - + -
286A GLU* 3.7 18.2 - - + +
287A PHE* 3.3 59.9 - + + -
290A PHE* 3.8 22.4 - + + -
311A HIS* 3.0 17.9 + - - +
312A PRO* 1.3 78.5 - - - +
314A PHE* 1.3 63.3 + - - +
316A LEU* 4.8 2.0 - - + -
317A HIS* 3.2 53.1 + + - +
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Residues in contact with PHE 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A ALA 5.4 0.2 - - - -
160A VAL* 3.6 33.2 - - + +
163A VAL* 3.6 37.5 - - + -
164A LYS* 3.9 15.0 - - + -
290A PHE* 4.6 7.6 - + + -
308A LEU 3.3 20.9 - - - +
309A MSE 3.1 58.6 - - + -
311A HIS* 2.8 11.8 + - + +
313A PHE* 1.3 78.3 - - - +
315A THR* 1.3 54.9 + - + +
317A HIS 3.3 0.9 + - - -
318A GLU* 2.7 59.0 + - + +
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Residues in contact with THR 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309A MSE 3.5 22.2 - - - +
310A GLN* 3.7 15.2 + - - +
311A HIS 2.9 16.4 + - - +
312A PRO* 3.1 15.1 + - - +
314A PHE* 1.3 75.9 - - + +
316A LEU* 1.3 65.8 + - - +
318A GLU* 3.6 10.6 + - - +
319A SER* 3.7 15.8 + - - -
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Residues in contact with LEU 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152A GLU* 6.0 0.2 - - - +
286A GLU* 5.8 9.9 - - + +
312A PRO 2.9 19.0 + - - +
313A PHE* 4.0 4.5 - - + +
315A THR* 1.3 80.5 + - - +
317A HIS* 1.3 91.7 + - + +
319A SER* 3.3 2.4 + - - -
320A LYS* 3.3 40.2 + - + +
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Residues in contact with HIS 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152A GLU* 4.4 9.9 - - + -
153A ASP* 3.8 34.2 + - - -
156A GLY* 3.7 27.9 - - - +
157A LYS* 3.0 27.0 + - - +
160A VAL* 4.0 3.6 - - + -
313A PHE* 3.2 54.4 + + - +
316A LEU* 1.3 96.1 - - + +
318A GLU* 1.3 68.3 + - - +
319A SER 3.1 1.5 + - - -
320A LYS* 3.7 24.3 + - + +
322A THR* 5.0 1.6 - - - -
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Residues in contact with GLU 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157A LYS* 3.4 11.1 + - - -
160A VAL* 3.8 15.0 - - + +
164A LYS* 2.7 40.8 + - - +
309A MSE 5.4 0.9 - - - +
314A PHE* 2.7 41.1 + - + +
315A THR* 4.2 8.1 - - - +
316A LEU 3.3 0.6 - - - -
317A HIS* 1.3 76.1 - - - +
319A SER* 1.3 64.5 + - - +
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Residues in contact with SER 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157A LYS* 4.4 0.2 - - - -
315A THR 3.7 13.8 + - - -
316A LEU 3.3 3.0 + - - -
317A HIS 3.1 0.2 - - - -
318A GLU* 1.3 86.8 + - - +
320A LYS* 1.3 65.0 + - - +
321A GLY 3.6 1.0 + - - -
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Residues in contact with LYS 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A ASP* 2.5 36.7 + - - -
157A LYS* 2.7 28.2 + - - -
316A LEU* 3.3 33.8 + - + +
317A HIS* 3.7 19.7 + - + +
318A GLU 3.5 1.6 - - - -
319A SER* 1.3 78.3 - - - +
321A GLY* 1.3 68.2 + - - +
322A THR* 3.1 17.9 + - - +
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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