Contacts of the helix formed by residues 375 - 392 (chain A) in PDB entry 1EQB
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 LYS 375 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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290A GLN* 3.5 25.4 - - + +
294A ASN* 3.0 12.1 - - - -
373A GLY 3.7 10.5 - - - +
374A PHE* 1.3 79.0 - - - +
376A GLU* 1.3 75.6 + - - +
377A ALA* 3.0 4.9 + - + +
378A GLU* 2.9 17.7 + - - +
379A ALA* 2.9 19.4 + - - +
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Residues in contact with GLU 376 (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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290A GLN* 3.3 19.8 + - - +
293A LYS* 3.2 41.3 - - + +
294A ASN* 3.0 10.8 + - - +
297A ALA* 4.3 17.5 - - + -
375A LYS* 1.3 74.9 - - - +
377A ALA* 1.3 56.9 + - - +
379A ALA* 3.7 3.3 - - - +
380A LYS* 2.9 44.6 + - - +
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Residues in contact with ALA 377 (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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375A LYS* 3.0 2.5 + - + +
376A GLU* 1.3 78.5 - - - +
378A GLU* 1.3 76.5 + - - +
380A LYS* 3.8 7.5 - - - +
381A GLU* 3.2 24.1 + - - +
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Residues in contact with GLU 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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373A GLY 4.6 0.9 - - - +
374A PHE* 3.5 31.3 - - + -
375A LYS* 2.9 37.0 + - - +
377A ALA* 1.3 85.4 - - - +
379A ALA* 1.3 57.6 + - - +
381A GLU* 3.4 10.0 + - - +
382A LEU* 2.9 29.3 + - - +
385A TRP* 5.8 0.2 - - - -
409A ILE* 3.8 24.2 - - + +
412A ARG* 5.1 4.6 + - - +
413A TYR* 4.0 24.7 + - + +
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Residues in contact with ALA 379 (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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294A ASN* 4.1 25.6 - - + +
297A ALA* 4.6 2.2 - - + -
298A MET* 3.5 26.2 - - + +
369A ILE* 4.6 6.3 - - + -
374A PHE* 4.4 4.7 - - + -
375A LYS 2.9 16.0 + - - +
376A GLU* 3.7 4.9 - - - +
378A GLU* 1.3 76.9 - - - +
380A LYS* 1.3 59.0 + - - +
382A LEU* 3.4 5.8 + - - +
383A ALA* 3.0 30.0 + - - +
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Residues in contact with LYS 380 (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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297A ALA* 3.8 32.1 - - + +
300A GLU* 4.0 22.8 + - - -
301A VAL* 3.7 23.2 - - + +
376A GLU* 2.9 30.7 + - + +
377A ALA* 3.8 6.7 - - - +
379A ALA* 1.3 76.7 - - - +
381A GLU* 1.3 57.7 + - - +
383A ALA* 3.5 3.4 + - - +
384A GLY* 3.0 23.6 + - - -
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Residues in contact with GLU 381 (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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377A ALA 3.2 15.5 + - - +
378A GLU* 3.6 7.7 - - - +
380A LYS* 1.3 78.1 - - - +
382A LEU* 1.3 64.8 + - - +
384A GLY* 3.2 2.8 + - - -
385A TRP* 3.0 60.3 + - + +
405A LYS* 5.4 2.8 + - - -
409A ILE* 4.8 8.8 - - - +
412A ARG* 5.9 1.0 + - - -
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Residues in contact with LEU 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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30A ILE* 3.3 39.0 - - + -
32A LEU* 3.9 13.2 - - + -
298A MET* 3.8 18.6 - - + -
342A ILE* 4.1 20.9 - - + -
369A ILE* 4.2 12.6 - - + -
374A PHE* 4.2 10.1 - - + -
378A GLU 2.9 17.6 + - - +
379A ALA 3.7 4.9 - - - +
381A GLU* 1.3 73.0 - - - +
383A ALA* 1.3 67.4 + - - +
385A TRP* 3.0 29.3 + - + +
386A MET* 3.0 27.0 + - + +
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Residues in contact with ALA 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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298A MET* 3.7 22.4 - - + +
301A VAL* 3.8 20.4 - - + -
302A PHE* 3.7 22.8 - - + -
379A ALA 3.0 17.7 + - - +
380A LYS 3.6 4.7 - - - +
382A LEU* 1.3 75.6 - - - +
384A GLY* 1.3 64.0 + - - +
386A MET* 3.2 5.9 + - - +
387A CYS* 3.1 26.2 + - - -
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Residues in contact with GLY 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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301A VAL* 3.9 8.9 - - - +
305A ARG* 3.5 18.9 + - - -
380A LYS 3.0 14.3 + - - -
381A GLU* 3.2 5.6 + - - -
382A LEU 3.1 0.6 - - - -
383A ALA* 1.3 78.0 - - - +
385A TRP* 1.3 62.2 + - - +
387A CYS 3.1 2.8 + - - -
388A ASP* 3.0 27.8 + - - -
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Residues in contact with TRP 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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342A ILE* 4.6 2.9 - - + -
374A PHE* 5.9 0.4 - + - -
378A GLU 5.9 0.2 - - - -
381A GLU* 3.0 43.5 + - + +
382A LEU* 3.0 32.2 + - + +
384A GLY* 1.3 74.8 - - - +
386A MET* 1.3 62.3 + - - +
388A ASP* 3.0 15.9 + - - +
389A VAL* 3.0 26.4 + - - +
402A ILE* 3.7 24.6 - - + +
405A LYS* 3.3 61.3 - - + +
406A VAL* 4.0 17.9 - - + -
409A ILE* 4.0 34.8 - - + -
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Residues in contact with MET 386 (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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32A LEU* 3.5 32.1 - - + -
298A MET* 3.9 19.5 - - - -
302A PHE* 4.0 24.7 - - + -
337A LEU* 3.9 26.6 - - + +
342A ILE* 4.1 19.1 - - + -
344A VAL* 3.8 19.7 - - + -
362A ILE* 4.5 3.4 - - + -
364A VAL* 4.3 10.8 - - + -
382A LEU* 3.0 17.9 + - + +
383A ALA 3.3 7.4 - - - +
385A TRP* 1.3 76.0 - - - +
387A CYS* 1.3 58.8 + - - +
389A VAL* 3.0 5.9 + - - +
390A LEU* 2.9 32.8 + - + +
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Residues in contact with CYS 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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301A VAL* 4.7 0.4 - - - -
302A PHE* 4.1 26.0 - - - -
305A ARG* 3.3 48.2 - - - +
307A TYR* 3.7 20.5 + - + -
383A ALA 3.1 19.4 + - - -
384A GLY 3.1 3.3 + - - +
386A MET* 1.3 76.3 - - - +
388A ASP* 1.3 58.3 + - - +
390A LEU* 4.3 7.2 - - - -
391A ASP* 2.8 35.7 + - - +
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Residues in contact with ASP 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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305A ARG* 2.7 30.8 + - - +
384A GLY 3.0 18.2 + - - +
385A TRP* 3.2 21.2 + - - +
387A CYS* 1.3 77.7 - - - +
389A VAL* 1.3 60.8 + - - +
391A ASP* 3.6 4.7 - - - +
392A SER* 3.2 23.0 + - - -
398A VAL* 3.7 13.4 - - + +
401A ARG* 4.7 10.6 + - - +
402A ILE* 4.0 16.8 - - + +
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Residues in contact with VAL 389 (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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336A ALA* 4.1 37.0 - - + +
337A LEU* 4.0 16.2 - - + -
340A ALA* 4.2 11.4 - - + -
385A TRP 3.0 13.7 + - - +
386A MET 3.0 7.2 + - - +
388A ASP* 1.3 74.7 - - - +
390A LEU* 1.3 66.7 + - + +
392A SER 3.1 4.0 - - - -
393A ILE* 2.9 26.0 + - - -
398A VAL* 4.4 5.4 - - - -
399A ILE* 4.1 17.7 - - + -
402A ILE* 3.9 29.6 - - + -
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Residues in contact with LEU 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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302A PHE* 4.3 19.7 - - + -
307A TYR* 3.1 39.3 - - + +
323A LEU* 4.5 9.6 - - + -
328A LEU* 4.3 20.3 - - + +
333A ALA* 3.8 33.2 - - + +
337A LEU* 4.3 16.4 - - + -
362A ILE* 4.7 9.0 - - + -
386A MET* 2.9 20.7 + - + +
387A CYS* 3.9 2.7 - - - +
389A VAL* 1.3 79.6 - - + +
391A ASP* 1.3 64.2 + - - +
392A SER 3.3 0.2 + - - -
393A ILE* 3.4 19.6 + - + +
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Residues in contact with ASP 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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305A ARG* 2.8 37.6 + - - +
307A TYR* 2.8 21.5 + - - -
326A LYS* 5.5 2.3 + - - -
387A CYS 2.8 20.7 + - - +
388A ASP* 3.6 5.6 - - - +
390A LEU* 1.3 74.8 - - - +
392A SER* 1.3 62.9 + - - +
393A ILE* 3.8 1.4 + - - +
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Residues in contact with SER 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 ASP 3.2 11.5 + - - -
389A VAL 3.1 5.4 - - - +
391A ASP* 1.3 81.3 - - - +
393A ILE* 1.3 55.7 + - - +
394A ASN 3.1 5.8 - - - -
395A ASP* 2.9 43.3 + - - +
398A VAL* 3.8 18.1 - - - +
399A ILE* 4.9 2.3 - - - +
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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
------------------------------------------------------------
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