Contacts of the helix formed by residues 376 - 396 (chain A) in PDB entry 1E7E
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 GLU 376 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352A THR* 4.0 15.1 - - + +
356A THR* 3.6 26.7 - - - +
359A LYS* 5.7 0.5 + - - -
372A LYS 4.4 7.2 - - - +
373A VAL* 2.7 16.7 + - + +
375A ASP* 1.3 80.8 - - - +
377A PHE* 1.3 66.4 + - + +
378A LYS 3.5 0.4 - - - -
379A PRO* 3.6 12.1 - - - +
380A LEU* 4.3 14.9 + - - +
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Residues in contact with PHE 377 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A PHE* 3.5 38.1 - + - -
334A TYR* 3.6 28.5 - + - +
349A LEU* 3.8 32.8 - - + -
352A THR* 3.8 23.8 - - + -
353A TYR* 4.3 5.4 - - + -
373A VAL* 3.7 27.1 - - + -
374A PHE* 3.3 34.0 + + + +
376A GLU* 1.3 81.9 - - - +
378A LYS* 1.3 67.0 + - - +
380A LEU* 2.9 16.2 + - + +
381A VAL* 3.0 17.9 + - + +
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Residues in contact with LYS 378 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A PHE 3.8 8.9 + - - +
375A ASP* 4.0 11.4 - - - +
377A PHE* 1.3 75.6 - - - +
379A PRO* 1.3 66.3 - - + +
381A VAL* 3.1 6.2 + - - +
382A GLU* 2.8 70.8 + - + +
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Residues in contact with PRO 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A ASP 3.8 10.1 - - - +
376A GLU* 3.6 12.6 - - - +
377A PHE 3.5 3.8 - - - -
378A LYS* 1.3 94.3 - - + +
380A LEU* 1.3 66.0 + - + +
382A GLU* 4.0 8.6 - - + +
383A GLU* 3.1 26.7 + - - +
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Residues in contact with LEU 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A LEU* 3.7 8.6 - - + +
348A ARG* 3.9 27.9 + - + +
349A LEU* 3.8 25.4 - - + -
352A THR* 3.4 29.6 - - + +
376A GLU 4.3 13.9 - - - +
377A PHE 2.9 10.2 + - - +
379A PRO* 1.3 82.9 - - + +
381A VAL* 1.3 58.9 + - - +
383A GLU* 4.1 2.2 - - - +
384A PRO* 3.0 25.1 - - - +
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Residues in contact with VAL 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334A TYR* 5.1 2.5 - - - +
341A TYR* 3.5 36.8 - - + +
345A LEU* 4.3 18.1 - - + +
349A LEU* 4.5 11.0 - - + -
377A PHE* 3.0 18.6 + - + +
378A LYS* 3.7 7.2 - - - +
380A LEU* 1.3 76.9 - - - +
382A GLU* 1.3 66.8 + - + +
383A GLU 3.2 0.2 - - - -
384A PRO* 3.2 15.8 - - - +
385A GLN* 3.3 37.8 + - - +
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Residues in contact with GLU 382 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A LYS* 2.8 62.1 + - - +
379A PRO* 4.0 7.5 - - + +
381A VAL* 1.3 79.9 - - + +
383A GLU* 1.3 56.4 + - - +
385A GLN* 3.7 13.4 - - - +
386A ASN* 2.9 46.6 + - - +
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Residues in contact with GLU 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A ARG* 4.8 1.7 + - - -
379A PRO 3.1 16.3 + - - +
380A LEU* 4.1 2.2 - - - +
382A GLU* 1.3 78.1 - - - +
384A PRO* 1.3 74.1 - - + +
386A ASN* 3.3 4.5 + - - +
387A LEU* 3.0 30.3 + - - +
485A ARG* 2.6 46.1 + - - -
486A PRO* 4.9 7.2 - - - +
489A SER* 4.3 6.6 - - - -
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Residues in contact with PRO 384 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A LEU* 4.2 17.9 - - + -
348A ARG* 4.6 2.7 - - - +
380A LEU 3.0 28.3 - - - +
381A VAL 3.2 13.5 - - - +
383A GLU* 1.3 92.5 - - + +
385A GLN* 1.3 60.4 + - - +
387A LEU* 3.1 10.1 + - + +
388A ILE* 3.0 28.6 + - - +
446A MET* 4.1 10.1 - - - -
485A ARG* 3.8 8.5 - - - +
1003A DKA 3.6 31.6 - - + +
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Residues in contact with GLN 385 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340A ASP* 5.2 3.4 + - - -
341A TYR* 4.1 14.3 + - - -
381A VAL* 3.3 39.3 + - - +
382A GLU* 3.7 14.0 - - - +
383A GLU 3.2 0.4 - - - -
384A PRO* 1.3 79.3 - - - +
386A ASN* 1.3 66.2 + - - +
388A ILE* 3.2 4.8 + - - +
389A LYS* 3.0 21.8 + - - +
442A GLU* 5.8 3.6 - - - +
446A MET* 3.4 24.5 - - + +
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Residues in contact with ASN 386 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382A GLU* 2.9 35.5 + - - +
383A GLU* 3.8 4.6 - - - +
385A GLN* 1.3 78.0 - - - +
387A LEU* 1.3 61.9 + - - +
389A LYS* 3.6 8.4 - - - +
390A GLN* 3.0 28.1 + - + +
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Residues in contact with LEU 387 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A GLU* 3.0 26.8 + - + +
384A PRO* 3.1 13.0 + - + +
386A ASN* 1.3 77.7 - - - +
388A ILE* 1.3 62.3 + - - +
390A GLN* 3.5 3.4 + - + +
391A ASN* 3.0 43.8 + - - +
410A ARG* 6.5 0.2 - - - -
485A ARG* 4.0 12.8 - - - +
489A SER* 4.3 3.6 - - - +
1003A DKA 3.6 35.2 - - + -
1004A DKA 4.0 25.6 - - - +
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Residues in contact with ILE 388 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384A PRO 3.0 15.1 + - - +
385A GLN* 3.5 9.2 - - - +
387A LEU* 1.3 72.8 - - - +
389A LYS* 1.3 68.6 + - - +
391A ASN* 3.3 3.4 + - - +
392A CYS* 2.9 33.7 + - - +
437A CYS* 6.5 0.4 - - + -
442A GLU* 6.5 0.4 - - + -
445A ARG* 3.9 37.7 - - + +
446A MET* 4.5 18.8 - - + +
449A ALA* 4.0 15.0 - - + -
1003A DKA 3.5 37.7 - - + -
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Residues in contact with LYS 389 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385A GLN 3.0 13.0 + - - +
386A ASN* 3.6 15.3 - - - +
388A ILE* 1.3 77.9 - - - +
390A GLN* 1.3 57.9 + - - +
392A CYS* 3.9 2.8 - - - +
393A GLU* 2.9 39.6 + - + +
442A GLU* 5.7 5.8 - - - +
445A ARG* 5.2 5.6 - - - +
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Residues in contact with GLN 390 (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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386A ASN 3.0 13.5 + - - +
387A LEU* 3.9 6.5 - - + +
389A LYS* 1.3 79.3 - - - +
391A ASN* 1.3 66.0 + - - +
393A GLU* 4.1 9.6 - - - +
394A LEU* 3.4 22.9 + - - +
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Residues in contact with ASN 391 (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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387A LEU* 3.0 45.2 + - - +
388A ILE* 4.1 4.0 - - + +
390A GLN* 1.3 80.3 - - - +
392A CYS* 1.3 63.4 + - - +
393A GLU 3.3 0.4 - - - -
394A LEU* 3.9 4.7 - - - -
395A PHE* 3.1 26.3 + - - +
403A PHE* 3.7 26.3 - - + -
407A LEU* 4.4 2.4 - - - +
410A ARG* 3.2 36.5 + - - +
438A CYS* 4.6 1.7 - - - -
1003A DKA 5.3 10.3 - - + -
1004A DKA 5.0 1.6 + - - +
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Residues in contact with CYS 392 (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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388A ILE* 2.9 32.2 + - - +
389A LYS 4.0 0.9 - - - +
391A ASN* 1.3 77.0 - - - +
393A GLU* 1.3 62.9 + - - +
394A LEU 3.2 0.4 - - - -
395A PHE* 3.6 3.0 + - - +
396A GLU* 2.8 32.1 + - + +
437A CYS* 5.0 1.1 - - - -
438A CYS* 2.0 55.9 - - + -
445A ARG* 3.7 26.9 - - - +
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Residues in contact with GLU 393 (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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389A LYS* 2.9 24.1 + - + +
390A GLN* 4.1 10.2 - - - +
392A CYS* 1.3 79.5 - - - +
394A LEU* 1.3 56.8 + - - +
396A GLU* 3.5 13.7 + - - +
397A GLN* 3.2 42.2 + - - +
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Residues in contact with LEU 394 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A GLN 3.4 16.8 + - - +
391A ASN* 4.1 3.8 - - - +
392A CYS 3.2 0.4 - - - -
393A GLU* 1.3 76.7 - - - +
395A PHE* 1.3 60.6 + - - +
396A GLU 2.9 5.6 - - - -
397A GLN* 2.9 35.7 + - - +
398A LEU* 3.1 39.3 + - + +
403A PHE* 4.0 21.1 - - + -
406A ALA* 4.5 12.3 - - + -
410A ARG* 5.0 12.8 - - - +
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Residues in contact with PHE 395 (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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391A ASN 3.1 20.4 + - - +
392A CYS* 3.8 7.4 - - - +
393A GLU 3.5 0.2 - - - -
394A LEU* 1.3 75.9 - - - +
396A GLU* 1.3 68.9 + - - +
398A LEU 2.5 21.2 - - - +
399A GLY* 4.6 0.5 - - - -
400A GLU* 4.1 21.3 - - + -
403A PHE* 3.6 40.8 - + + -
431A GLY 4.5 0.7 - - - -
434A GLY 4.2 6.3 - - - -
435A SER* 3.5 44.6 - - - -
438A CYS* 4.3 18.6 - - + -
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Residues in contact with GLU 396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392A CYS 2.8 24.5 - - - +
393A GLU* 3.6 11.4 - - - +
394A LEU 2.9 0.8 - - - -
395A PHE* 1.3 92.6 - - + +
397A GLN* 1.3 62.6 + - + +
398A LEU 4.4 1.1 - - - -
438A CYS* 4.4 14.4 - - - +
445A ARG* 5.1 4.0 + - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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