Contacts of the helix formed by residues 375 - 392 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290B GLN* 3.6 23.6 - - + +
294B ASN* 3.0 11.9 - - - -
373B GLY 3.7 10.5 - - - +
374B PHE* 1.3 79.3 - - - +
376B GLU* 1.3 76.3 + - - +
377B ALA* 3.2 2.9 - - + +
378B GLU* 2.9 18.1 + - - +
379B ALA* 2.9 19.6 + - - +
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Residues in contact with GLU 376 (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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290B GLN* 3.2 20.2 + - - -
293B LYS* 3.2 41.6 - - + +
294B ASN* 2.9 11.2 + - - +
297B ALA* 4.3 17.0 - - + -
375B LYS* 1.3 75.8 - - - +
377B ALA* 1.3 55.4 + - - +
379B ALA* 3.7 3.7 - - - +
380B LYS* 2.8 44.3 + - + +
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Residues in contact with ALA 377 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375B LYS* 3.0 2.9 + - + +
376B GLU* 1.3 78.1 - - - +
378B GLU* 1.3 78.8 + - - +
380B LYS* 3.4 6.7 + - - +
381B GLU* 3.1 24.2 + - - +
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Residues in contact with GLU 378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373B GLY 4.5 1.2 - - - +
374B PHE* 3.5 29.5 - - + -
375B LYS* 2.9 38.5 + - - +
377B ALA* 1.3 87.4 - - - +
379B ALA* 1.3 57.5 + - - +
381B GLU* 3.4 9.1 + - - +
382B LEU* 2.9 29.6 + - - +
385B TRP* 5.8 0.2 - - - -
409B ILE* 3.9 21.7 - - + +
412B ARG* 5.7 2.0 + - - +
413B TYR* 3.6 30.0 + - + +
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Residues in contact with ALA 379 (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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294B ASN* 4.1 25.8 - - + +
297B ALA* 4.6 1.6 - - + -
298B MET* 3.4 26.4 - - + +
369B ILE* 4.6 7.2 - - + -
374B PHE* 4.4 4.4 - - + -
375B LYS 2.9 15.6 + - - +
376B GLU* 3.7 4.7 - - - +
378B GLU* 1.3 75.8 - - - +
380B LYS* 1.3 59.8 + - - +
382B LEU* 3.7 5.4 - - - +
383B ALA* 2.9 30.1 + - - +
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Residues in contact with LYS 380 (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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297B ALA* 3.8 31.0 - - + +
300B GLU* 3.9 25.1 + - - -
301B VAL* 3.8 22.9 - - + +
376B GLU* 2.8 28.4 + - - +
377B ALA* 3.8 6.3 - - - +
379B ALA* 1.3 75.7 - - - +
381B GLU* 1.3 58.1 + - - +
383B ALA* 3.4 4.1 + - - +
384B GLY* 3.0 24.1 + - - -
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Residues in contact with GLU 381 (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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377B ALA 3.1 14.5 + - - +
378B GLU* 3.6 8.3 - - - +
380B LYS* 1.3 77.2 - - - +
382B LEU* 1.3 64.9 + - - +
384B GLY* 3.2 3.1 + - - -
385B TRP* 3.0 61.8 + - + +
405B LYS* 5.3 3.5 + - - -
409B ILE* 4.8 8.9 - - + +
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Residues in contact with LEU 382 (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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30B ILE* 3.3 37.5 - - + -
32B LEU* 4.0 12.6 - - + -
298B MET* 3.8 19.3 - - + -
342B ILE* 4.1 21.3 - - + -
369B ILE* 4.2 11.9 - - + -
374B PHE* 4.2 11.2 - - + -
378B GLU 2.9 18.3 + - - +
379B ALA* 3.7 4.5 - - - +
380B LYS 3.3 0.2 - - - -
381B GLU* 1.3 72.3 - - - +
383B ALA* 1.3 68.8 + - - +
385B TRP* 3.1 27.6 + - + +
386B MET* 3.0 28.7 + - + +
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Residues in contact with ALA 383 (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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298B MET* 3.8 23.3 - - + +
301B VAL* 3.8 22.4 - - + -
302B PHE* 3.8 20.7 - - + -
379B ALA 2.9 18.5 + - - +
380B LYS 3.5 5.2 - - - +
382B LEU* 1.3 74.6 - - - +
384B GLY* 1.3 64.2 + - - +
386B MET* 3.2 6.2 + - - +
387B CYS* 3.1 25.3 + - - -
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Residues in contact with GLY 384 (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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301B VAL* 3.8 8.9 - - - +
305B ARG* 3.5 18.2 + - - -
380B LYS 3.0 14.3 + - - -
381B GLU* 3.2 5.4 + - - -
382B LEU 3.1 0.4 - - - -
383B ALA* 1.3 73.8 - - - +
385B TRP* 1.3 65.7 + - - +
387B CYS 3.1 2.6 + - - -
388B ASP* 2.9 27.8 + - - -
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Residues in contact with TRP 385 (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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342B ILE* 4.7 2.9 - - + -
374B PHE* 5.9 0.2 - + - -
378B GLU 5.9 0.2 - - - -
381B GLU* 3.0 44.6 + - + +
382B LEU* 3.1 32.5 + - + +
384B GLY* 1.3 74.0 - - - +
386B MET* 1.3 63.8 + - - +
388B ASP* 3.0 16.4 + - - +
389B VAL* 3.0 26.8 + - - +
402B ILE* 3.5 30.0 - - + +
405B LYS* 3.8 60.9 - - + +
406B VAL* 4.2 18.4 - - + -
409B ILE* 4.3 28.0 - - + -
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Residues in contact with MET 386 (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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32B LEU* 3.5 23.1 - - + -
298B MET* 3.9 20.4 - - - -
302B PHE* 4.0 24.0 - - + -
337B LEU* 3.9 26.4 - - + +
342B ILE* 4.1 19.3 - - + -
344B VAL* 3.8 28.9 - - + -
362B ILE* 4.4 3.1 - - + -
364B VAL* 4.3 10.8 - - + -
382B LEU* 3.0 15.9 + - + +
383B ALA 3.2 7.6 - - - +
384B GLY 3.1 0.2 - - - -
385B TRP* 1.3 76.7 - - - +
387B CYS* 1.3 58.0 + - - +
389B VAL* 3.1 5.2 + - - +
390B LEU* 2.9 33.7 + - + +
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Residues in contact with CYS 387 (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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301B VAL* 4.7 0.7 - - - -
302B PHE* 4.0 26.5 - - - -
305B ARG* 3.4 48.9 - - - +
307B TYR* 3.8 20.3 + - + -
383B ALA 3.1 18.5 + - - -
384B GLY 3.1 3.1 + - - +
386B MET* 1.3 72.8 - - - +
388B ASP* 1.3 61.8 + - - +
390B LEU* 4.3 7.2 - - - -
391B ASP* 2.8 36.2 + - - +
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Residues in contact with ASP 388 (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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305B ARG* 2.7 30.5 + - - +
384B GLY 2.9 17.6 + - - +
385B TRP* 3.0 21.5 + - - +
387B CYS* 1.3 78.5 - - - +
389B VAL* 1.3 63.1 + - - +
391B ASP* 3.4 4.4 + - - +
392B SER* 3.2 23.0 + - - -
398B VAL* 3.7 13.8 - - + +
402B ILE* 4.1 16.2 - - + +
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Residues in contact with VAL 389 (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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336B ALA* 4.1 37.9 - - + +
337B LEU* 4.0 14.8 - - + -
340B ALA* 4.3 11.0 - - + -
342B ILE* 5.1 0.2 - - + -
385B TRP 3.0 13.9 + - - +
386B MET* 3.4 6.5 - - - +
388B ASP* 1.3 73.5 - - - +
390B LEU* 1.3 66.7 + - + +
392B SER 3.1 4.3 - - - -
393B ILE* 2.9 26.0 + - - -
398B VAL* 4.4 6.3 - - + -
399B ILE* 4.2 17.5 - - + -
402B ILE* 3.9 28.9 - - + -
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Residues in contact with LEU 390 (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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302B PHE* 4.3 20.0 - - + -
307B TYR* 3.1 39.6 + - + +
323B LEU* 4.5 8.5 - - + -
328B LEU* 4.3 19.9 - - + +
333B ALA* 3.8 32.5 - - + -
336B ALA* 5.8 0.2 - - + -
337B LEU* 4.3 17.3 - - + -
362B ILE* 4.7 9.0 - - + -
386B MET* 2.9 21.3 + - + +
387B CYS* 3.9 2.2 - - - +
389B VAL* 1.3 77.4 - - + +
391B ASP* 1.3 63.4 + - - +
392B SER 3.4 0.2 + - - -
393B ILE* 3.4 18.9 + - + +
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Residues in contact with ASP 391 (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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305B ARG* 2.8 36.7 + - - +
307B TYR* 2.9 21.1 + - - -
326B LYS* 5.4 2.9 + - - -
387B CYS* 2.8 21.5 + - - +
388B ASP* 3.6 6.3 - - - +
390B LEU* 1.3 74.3 - - - +
392B SER* 1.3 63.6 + - - +
393B ILE* 3.8 1.4 + - - +
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Residues in contact with SER 392 (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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388B ASP 3.2 9.9 + - - -
389B VAL 3.1 7.2 + - - +
391B ASP* 1.3 81.5 + - - +
393B ILE* 1.3 56.8 + - - +
394B ASN 3.1 5.6 - - - -
395B ASP* 2.9 42.4 + - - +
398B VAL* 3.8 18.2 - - - +
399B 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
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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