Contacts of the helix formed by residues 377 - 388 (chain A) in PDB entry 3EQR
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 377 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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244A GLU* 3.8 22.2 - - - +
313A THR* 4.6 1.3 - - - -
375A ARG 5.3 1.1 - - - +
376A PRO* 1.3 77.2 - - - +
378A PHE* 1.3 59.9 + - - +
379A VAL* 3.6 8.3 + - - +
380A ALA* 3.2 21.3 + - - +
381A LEU* 2.8 27.0 + - - +
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Residues in contact with PHE 378 (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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237A ALA* 3.7 17.5 - - - +
240A MET* 3.3 46.2 - - + -
241A GLY* 3.6 18.8 - - - +
244A GLU* 3.1 32.2 + - + +
309A HIS* 4.0 6.1 - - - -
312A ASP* 3.6 40.8 - - + -
313A THR* 3.6 11.9 - - - -
316A PHE* 3.7 26.0 - + + -
377A THR* 1.3 70.5 - - - +
379A VAL* 1.3 60.0 + - - +
381A LEU* 3.6 16.7 - - + +
382A ARG* 2.8 29.5 + - - +
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Residues in contact with VAL 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A GLY* 5.2 12.6 - - - +
244A GLU* 4.4 3.0 + - - +
377A THR* 3.4 7.9 + - - +
378A PHE* 1.3 75.9 - - - +
380A ALA* 1.3 63.6 + - - +
382A ARG* 3.2 31.0 + - - +
383A ASP* 3.3 19.0 + - - +
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Residues in contact with ALA 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376A PRO* 3.9 16.6 - - + -
377A THR* 3.2 21.1 + - + +
379A VAL* 1.3 79.3 - - - +
381A LEU* 1.3 62.1 + - - +
383A ASP* 3.1 10.0 + - - +
384A PHE* 3.0 36.8 + - + -
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Residues in contact with LEU 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A ALA* 4.4 8.5 - - + -
313A THR* 3.9 21.3 - - + +
316A PHE* 3.9 21.5 - - + -
363A VAL* 3.7 21.8 - - + -
366A GLN* 5.8 0.2 - - + -
367A CYS* 3.7 17.7 - - - -
376A PRO* 3.6 20.2 - - + -
377A THR 2.8 21.0 + - - +
378A PHE* 3.3 34.1 + - + +
380A ALA* 1.3 72.3 - - - +
382A ARG* 1.3 62.8 + - - +
384A PHE* 3.8 5.7 - - + +
385A LEU* 2.9 30.8 + - + +
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Residues in contact with ARG 382 (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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234A VAL* 4.1 14.3 - - + +
237A ALA* 4.1 10.7 - - + +
238A GLU* 3.5 46.5 + - + +
378A PHE 2.8 16.8 + - - +
379A VAL* 3.4 24.3 + - - +
380A ALA 3.2 0.2 - - - -
381A LEU* 1.3 75.3 - - - +
383A ASP* 1.3 86.1 + - - +
385A LEU* 3.9 3.1 - - - +
386A LEU* 3.0 45.2 + - - +
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Residues in contact with ASP 383 (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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379A VAL* 3.3 17.9 + - - +
380A ALA* 3.1 8.8 + - - +
382A ARG* 1.3 103.3 + - - +
384A PHE* 1.3 65.2 + - + +
386A LEU* 3.3 8.9 + - - +
387A GLU* 3.0 42.8 + - - +
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Residues in contact with PHE 384 (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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363A VAL* 3.9 21.4 - - + +
366A GLN* 3.5 31.0 - - - -
376A PRO* 4.3 10.1 - - + -
380A ALA* 3.0 43.4 + - + +
381A LEU* 3.3 11.0 + - + +
383A ASP* 1.3 76.5 - - + +
385A LEU* 1.3 58.2 + - - +
387A GLU* 3.5 15.8 + - - +
388A ALA* 3.1 28.9 + - - +
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Residues in contact with LEU 385 (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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230A SER* 4.9 6.1 - - - +
233A ALA* 3.7 22.9 - - + +
234A VAL* 3.9 16.4 - - + +
237A ALA* 4.2 6.5 - - + -
316A PHE* 3.4 36.3 - - + -
320A LEU* 4.1 17.7 - - + -
324A PHE* 6.0 0.7 - - + -
360A ILE* 5.0 14.1 - - + +
363A VAL* 3.9 26.5 - - + -
381A LEU* 2.9 20.2 + - + +
382A ARG 3.9 1.3 - - - +
384A PHE* 1.3 76.2 - - - +
386A LEU* 1.3 64.8 + - - +
388A ALA* 3.2 6.0 + - + +
389A GLN* 3.2 21.3 + - - +
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Residues in contact with LEU 386 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A VAL* 4.0 15.9 - - + +
238A GLU* 5.4 0.7 - - - +
382A ARG* 3.0 45.5 + - - +
383A ASP* 3.8 9.0 - - - +
385A LEU* 1.3 73.7 - - - +
387A GLU* 1.3 60.0 + - + +
389A GLN* 3.0 50.1 + - - +
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Residues in contact with GLU 387 (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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359A ASP* 3.6 9.0 - - - +
383A ASP* 3.0 33.1 + - - +
384A PHE* 3.7 22.1 - - - +
386A LEU* 1.3 78.7 - - + +
388A ALA* 1.3 57.6 + - - +
389A GLN 3.3 2.1 + - - +
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Residues in contact with ALA 388 (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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357A PRO* 5.4 1.6 - - - +
359A ASP* 3.2 43.4 - - + +
360A ILE* 3.6 27.7 - - + +
363A VAL* 4.8 1.6 - - + -
384A PHE 3.1 17.1 + - - +
385A LEU* 3.6 7.9 - - - +
386A LEU 3.2 0.4 - - - -
387A GLU* 1.3 74.6 - - - +
389A GLN* 1.3 59.2 + - - +
390A PRO* 3.4 9.2 - - - +
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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