Contacts of the helix formed by residues 375 - 392 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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290D GLN* 3.6 23.6 - - + +
294D ASN* 3.0 11.7 - - - -
373D GLY 3.7 9.9 - - - +
374D PHE* 1.3 79.5 - - - +
376D GLU* 1.3 76.0 + - - +
377D ALA* 3.0 4.8 + - + +
378D GLU* 2.9 16.7 + - - +
379D ALA* 2.9 19.8 + - - +
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Residues in contact with GLU 376 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290D GLN* 3.2 20.8 + - - +
293D LYS* 3.2 40.9 - - + +
294D ASN* 2.9 10.0 + - - +
297D ALA* 4.2 18.2 - - + -
375D LYS* 1.3 74.9 - - - +
377D ALA* 1.3 56.9 + - - +
379D ALA* 3.7 4.6 - - - +
380D LYS* 2.8 44.3 + - - +
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Residues in contact with ALA 377 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375D LYS* 3.0 3.1 + - + +
376D GLU* 1.3 78.1 - - - +
378D GLU* 1.3 77.4 + - - +
380D LYS* 3.8 7.1 - - - +
381D GLU* 3.2 24.1 + - - +
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Residues in contact with GLU 378 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373D GLY 4.5 0.7 - - - +
374D PHE* 3.6 27.5 - - + -
375D LYS* 2.9 38.7 + - - +
377D ALA* 1.3 87.2 - - - +
379D ALA* 1.3 58.6 + - - +
381D GLU* 3.3 9.6 + - - +
382D LEU* 2.9 28.9 + - - +
385D TRP* 5.9 0.3 - - - -
409D ILE* 3.9 23.4 - - + +
412D ARG* 5.5 3.3 + - - +
413D TYR* 3.8 27.1 + - + +
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Residues in contact with ALA 379 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294D ASN* 4.1 25.4 - - + +
297D ALA* 4.5 1.8 - - + -
298D MET* 3.5 27.3 - - + +
369D ILE* 4.6 6.5 - - + -
374D PHE* 4.4 4.8 - - + -
375D LYS 2.9 15.5 + - - +
376D GLU* 3.7 4.9 - - - +
378D GLU* 1.3 75.5 - - - +
380D LYS* 1.3 65.2 + - - +
382D LEU* 3.3 6.0 + - - +
383D ALA* 2.9 24.1 + - - +
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Residues in contact with LYS 380 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297D ALA* 3.8 32.5 - - + +
300D GLU* 3.9 24.1 + - - -
301D VAL* 3.8 22.5 - - + +
376D GLU* 2.8 30.5 + - + +
377D ALA* 3.8 6.1 - - - +
379D ALA* 1.3 75.7 - - - +
381D GLU* 1.3 58.1 + - - +
383D ALA* 3.4 3.6 + - - +
384D GLY* 3.0 23.7 + - - -
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Residues in contact with GLU 381 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377D ALA 3.2 16.1 + - - +
378D GLU* 3.5 10.1 - - - +
379D ALA 3.2 0.2 - - - -
380D LYS* 1.3 77.3 - - - +
382D LEU* 1.3 63.0 + - - +
384D GLY* 3.2 2.9 + - - -
385D TRP* 3.1 61.0 + - + +
409D ILE* 5.0 5.5 - - - +
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Residues in contact with LEU 382 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30D ILE* 3.3 37.9 - - + -
32D LEU* 4.0 12.8 - - + -
298D MET* 3.8 19.3 - - + -
342D ILE* 4.0 21.5 - - + -
369D ILE* 4.2 12.3 - - + -
374D PHE* 4.2 11.0 - - + -
378D GLU 2.9 17.4 + - - +
379D ALA* 3.7 4.5 - - - +
380D LYS 3.3 0.2 - - - -
381D GLU* 1.3 74.9 - - - +
383D ALA* 1.3 66.7 + - - +
385D TRP* 3.1 27.3 + - + +
386D MET* 3.0 28.7 + - + +
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Residues in contact with ALA 383 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298D MET* 3.8 23.3 - - + +
301D VAL* 3.8 20.9 - - + -
302D PHE* 3.8 21.5 - - + -
379D ALA 2.9 17.9 + - - +
380D LYS 3.5 5.4 - - - +
382D LEU* 1.3 76.1 - - - +
384D GLY* 1.3 63.2 + - - +
386D MET* 3.2 6.2 + - - +
387D CYS* 3.1 25.8 + - - -
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Residues in contact with GLY 384 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301D VAL* 3.8 8.9 - - - +
305D ARG* 3.5 19.0 + - - -
380D LYS 3.0 15.1 + - - -
381D GLU* 3.6 4.5 - - - -
382D LEU 3.1 0.4 - - - -
383D ALA* 1.3 76.1 - - - +
385D TRP* 1.3 63.2 + - - +
387D CYS 3.1 2.9 + - - -
388D ASP* 2.9 27.4 + - - -
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Residues in contact with TRP 385 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30D ILE* 5.7 0.2 - - + -
342D ILE* 4.7 2.0 - - + -
374D PHE* 6.0 0.4 - + - -
378D GLU 5.9 0.2 - - - -
381D GLU* 3.1 44.9 + - + +
382D LEU* 3.1 31.2 + - + +
384D GLY* 1.3 74.9 - - - +
386D MET* 1.3 63.3 + - - +
388D ASP* 3.1 16.0 + - - +
389D VAL* 3.0 26.9 + - - +
402D ILE* 3.5 30.9 - - + +
405D LYS* 3.3 52.5 - - + +
406D VAL* 4.3 14.1 - - + -
409D ILE* 3.9 35.2 - - + -
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Residues in contact with MET 386 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32D LEU* 3.5 31.6 - - + -
298D MET* 3.9 20.6 - - - -
302D PHE* 4.0 23.8 - - + -
337D LEU* 3.9 26.9 - - + +
342D ILE* 4.1 18.6 - - + -
344D VAL* 3.8 19.5 - - + -
362D ILE* 4.4 3.1 - - + -
364D VAL* 4.3 11.0 - - + -
382D LEU* 3.0 17.3 + - + +
383D ALA 3.2 8.1 - - - +
385D TRP* 1.3 75.8 - - - +
387D CYS* 1.3 57.7 + - - +
389D VAL* 3.0 6.1 + - - +
390D LEU* 2.9 32.2 + - + +
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Residues in contact with CYS 387 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301D VAL* 4.7 0.7 - - - -
302D PHE* 4.0 27.4 - - - -
305D ARG* 3.4 48.9 - - - +
307D TYR* 3.7 19.4 + - + -
383D ALA 3.1 18.7 + - - -
384D GLY 3.6 3.4 - - - +
386D MET* 1.3 75.8 - - - +
388D ASP* 1.3 57.1 + - - +
390D LEU* 4.4 7.6 - - - -
391D ASP* 2.8 36.2 + - - +
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Residues in contact with ASP 388 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305D ARG* 2.7 30.0 + - - +
384D GLY 2.9 17.8 + - - +
385D TRP* 3.1 21.7 + - - +
387D CYS* 1.3 76.2 - - - +
389D VAL* 1.3 63.0 + - - +
391D ASP* 3.5 4.7 + - - +
392D SER* 3.2 22.9 + - - -
398D VAL* 3.7 14.3 - - + +
402D ILE* 4.0 16.1 - - + +
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Residues in contact with VAL 389 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336D ALA* 4.1 37.0 - - + +
337D LEU* 4.0 15.9 - - + -
340D ALA* 4.3 11.4 - - + -
342D ILE* 5.2 0.7 - - + -
385D TRP 3.0 14.1 + - - +
386D MET 3.0 6.7 + - - +
388D ASP* 1.3 74.3 - - - +
390D LEU* 1.3 67.5 + - + +
392D SER 3.0 4.6 - - - -
393D ILE* 2.9 25.7 + - - -
398D VAL* 4.5 5.4 - - - -
399D ILE* 4.1 18.8 - - + -
402D ILE* 3.9 28.0 - - + -
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Residues in contact with LEU 390 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302D PHE* 4.3 19.7 - - + -
307D TYR* 3.1 42.6 + - + +
321D VAL* 5.1 0.2 - - + -
323D LEU* 4.5 9.4 - - + -
328D LEU* 4.3 20.6 - - + +
333D ALA* 3.8 32.3 - - + +
337D LEU* 4.3 16.8 - - + -
362D ILE* 4.7 9.0 - - + -
386D MET* 2.9 20.3 + - + +
387D CYS* 3.9 2.5 - - - +
389D VAL* 1.3 78.1 - - + +
391D ASP* 1.3 62.9 + - - +
392D SER 3.4 0.2 + - - -
393D ILE* 3.5 18.8 + - + +
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Residues in contact with ASP 391 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305D ARG* 2.9 36.4 + - - +
307D TYR* 2.9 20.6 + - - -
326D LYS* 5.4 2.8 + - - -
387D CYS* 2.8 17.4 + - - +
388D ASP* 3.6 6.3 - - - +
390D LEU* 1.3 79.6 - - - +
392D SER* 1.3 63.2 + - - +
393D ILE* 3.8 1.2 + - - +
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Residues in contact with SER 392 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388D ASP 3.2 10.2 + - - -
389D VAL 3.0 7.9 + - - +
391D ASP* 1.3 83.3 + - - +
393D ILE* 1.3 54.8 + - - +
394D ASN 3.0 6.3 - - - +
395D ASP* 2.9 42.6 + - - +
398D VAL* 3.8 18.8 - - - +
399D ILE* 4.8 2.4 - - - +
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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