Contacts of the helix formed by residues 375 - 392 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290C GLN* 3.6 23.3 - - + +
294C ASN* 3.0 12.6 - - - -
373C GLY 3.7 11.0 - - - +
374C PHE* 1.3 78.8 - - - +
376C GLU* 1.3 74.8 + - - +
377C ALA* 3.0 4.1 + - + +
378C GLU* 2.9 16.8 + - - +
379C ALA* 2.9 19.6 + - - +
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Residues in contact with GLU 376 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290C GLN* 3.2 20.1 + - - +
293C LYS* 3.2 42.1 - - + +
294C ASN* 3.0 9.5 + - - +
297C ALA* 4.3 19.5 - - + -
375C LYS* 1.3 75.0 - - - +
377C ALA* 1.3 57.8 + - - +
379C ALA* 3.8 1.3 - - - +
380C LYS* 2.9 45.4 + - - +
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Residues in contact with ALA 377 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375C LYS* 3.0 2.5 + - + +
376C GLU* 1.3 77.9 - - - +
378C GLU* 1.3 79.1 + - - +
380C LYS* 3.4 7.1 + - - +
381C GLU* 3.2 23.2 + - - +
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Residues in contact with GLU 378 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373C GLY 4.5 0.9 - - - +
374C PHE* 3.5 30.5 - - + -
375C LYS* 2.9 37.8 + - - +
377C ALA* 1.3 86.3 - - - +
379C ALA* 1.3 56.9 + - - +
381C GLU* 3.3 9.5 + - - +
382C LEU* 2.9 29.8 + - - +
385C TRP* 5.8 0.2 - - - -
409C ILE* 4.0 18.5 - - + +
412C ARG* 5.7 1.7 + - - +
413C TYR* 3.5 33.9 + - + +
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Residues in contact with ALA 379 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294C ASN* 4.1 26.9 - - + +
297C ALA* 4.6 1.8 - - + -
298C MET* 3.5 25.2 - - + +
369C ILE* 4.6 7.2 - - + -
374C PHE* 4.4 4.9 - - + -
375C LYS 2.9 14.9 + - - +
376C GLU* 3.8 4.9 - - - +
378C GLU* 1.3 76.2 - - - +
380C LYS* 1.3 60.8 + - - +
382C LEU* 3.3 6.0 + - - +
383C ALA* 2.9 29.3 + - - +
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Residues in contact with LYS 380 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297C ALA* 3.8 31.2 - - + +
300C GLU* 4.0 23.5 + - - -
301C VAL* 3.7 23.1 - - + +
376C GLU* 2.9 31.5 + - - +
377C ALA* 3.8 6.3 - - - +
379C ALA* 1.3 75.8 - - - +
381C GLU* 1.3 59.4 + - - +
383C ALA* 3.4 3.7 + - - +
384C GLY* 3.0 23.7 + - - -
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Residues in contact with GLU 381 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377C ALA 3.2 11.8 + - - +
378C GLU* 3.5 11.1 - - - +
380C LYS* 1.3 79.0 - - - +
382C LEU* 1.3 64.4 + - - +
384C GLY* 3.3 2.2 + - - -
385C TRP* 3.1 59.4 + - + +
405C LYS* 6.0 0.2 + - - -
409C ILE* 4.8 9.1 - - + +
412C ARG* 5.3 4.3 + - - -
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Residues in contact with LEU 382 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C ILE* 3.3 38.4 - - + -
32C LEU* 4.0 12.1 - - + -
298C MET* 3.8 19.5 - - + -
342C ILE* 4.0 22.4 - - + -
369C ILE* 4.2 11.4 - - + -
374C PHE* 4.2 11.0 - - + -
378C GLU 2.9 17.2 + - - +
379C ALA 3.7 4.5 - - - +
381C GLU* 1.3 74.3 - - - +
383C ALA* 1.3 66.4 + - - +
385C TRP* 3.0 27.8 + - + +
386C MET* 3.0 29.3 + - + +
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Residues in contact with ALA 383 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298C MET* 3.7 24.4 - - + +
301C VAL* 3.8 22.2 - - + -
302C PHE* 3.8 20.3 - - + -
379C ALA 2.9 18.1 + - - +
380C LYS 3.6 5.6 - - - +
382C LEU* 1.3 75.5 - - - +
384C GLY* 1.3 62.2 - - - +
386C MET* 3.2 6.1 + - - +
387C CYS* 3.1 26.2 + - - -
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Residues in contact with GLY 384 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301C VAL* 3.9 8.9 - - - +
305C ARG* 3.5 18.3 + - - -
380C LYS 3.0 13.9 + - - -
381C GLU* 3.6 4.0 - - - -
382C LEU 3.1 0.6 - - - -
383C ALA* 1.3 74.8 - - - +
385C TRP* 1.3 64.9 + - - +
387C CYS 3.1 2.6 + - - -
388C ASP* 3.0 28.4 + - - -
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Residues in contact with TRP 385 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C ILE* 5.7 0.7 - - + -
342C ILE* 4.7 2.5 - - + -
374C PHE* 6.0 0.4 - + - -
381C GLU* 3.1 43.5 + - + +
382C LEU* 3.0 32.6 + - + +
384C GLY* 1.3 75.1 - - - +
386C MET* 1.3 63.0 - - - +
388C ASP* 3.1 16.3 + - - +
389C VAL* 3.0 26.5 + - - +
402C ILE* 3.5 29.3 - - + +
405C LYS* 3.5 60.6 - - + +
406C VAL* 4.2 15.3 - - + -
409C ILE* 4.2 30.3 - - + -
412C ARG* 6.0 1.3 - - - -
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Residues in contact with MET 386 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32C LEU* 3.5 22.4 - - + -
298C MET* 4.0 19.3 - - - -
302C PHE* 4.0 24.9 - - + -
337C LEU* 3.9 26.6 - - + +
342C ILE* 4.1 20.0 - - + -
344C VAL* 3.8 28.9 - - + -
362C ILE* 4.4 2.9 - - + -
364C VAL* 4.3 10.1 - - + -
382C LEU* 3.0 16.4 + - + +
383C ALA 3.3 7.2 - - - +
385C TRP* 1.3 77.5 - - - +
387C CYS* 1.3 57.6 + - - +
389C VAL* 3.0 6.6 + - - +
390C LEU* 2.9 32.1 + - + +
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Residues in contact with CYS 387 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301C VAL* 4.6 0.7 - - - -
302C PHE* 4.0 26.7 - - - -
305C ARG* 3.3 49.1 - - - +
307C TYR* 3.7 19.9 + - + -
383C ALA 3.1 19.0 + - - -
384C GLY 3.6 2.7 - - - +
386C MET* 1.3 75.8 - - - +
388C ASP* 1.3 58.4 + - - +
390C LEU* 4.3 8.1 - - - -
391C ASP* 2.8 35.3 + - - +
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Residues in contact with ASP 388 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305C ARG* 2.7 30.2 + - - +
384C GLY 3.0 18.9 + - - +
385C TRP* 3.1 22.9 + - - +
387C CYS* 1.3 78.1 - - - +
389C VAL* 1.3 61.5 + - - +
391C ASP* 3.6 4.2 - - - +
392C SER* 3.2 22.7 + - - -
398C VAL* 3.7 14.0 - - + +
401C ARG* 4.4 12.3 + - - +
402C ILE* 4.0 14.9 - - + +
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Residues in contact with VAL 389 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336C ALA* 4.1 35.9 - - + +
337C LEU* 4.0 15.3 - - + -
340C ALA* 4.3 17.0 - - + -
342C ILE* 5.2 0.4 - - + -
385C TRP 3.0 14.3 + - - +
386C MET 3.0 7.4 + - - +
388C ASP* 1.3 74.3 - - - +
390C LEU* 1.3 65.8 + - + +
392C SER 3.1 4.3 - - - -
393C ILE* 2.9 25.8 + - - -
398C VAL* 4.5 5.6 - - + -
399C ILE* 4.1 19.5 - - + -
402C ILE* 3.9 22.7 - - + -
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Residues in contact with LEU 390 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302C PHE* 4.3 20.0 - - + -
307C TYR* 3.1 41.2 + - + +
323C LEU* 4.5 9.6 - - + -
328C LEU* 4.3 20.1 - - + +
333C ALA* 3.8 33.0 - - + -
336C ALA* 5.7 0.2 - - + -
337C LEU* 4.3 16.6 - - + -
362C ILE* 4.7 9.2 - - + -
386C MET* 2.9 21.9 + - + +
387C CYS* 3.9 2.5 - - - +
389C VAL* 1.3 77.4 - - + +
391C ASP* 1.3 62.0 + - - +
392C SER 3.3 0.2 + - - -
393C ILE* 3.4 18.7 + - + +
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Residues in contact with ASP 391 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305C ARG* 2.8 37.2 + - - +
307C TYR* 2.8 20.4 + - - -
326C LYS* 5.4 2.8 + - - -
387C CYS 2.8 20.3 + - - +
388C ASP* 3.6 6.1 - - - +
390C LEU* 1.3 76.0 - - - +
392C SER* 1.3 62.4 + - - +
393C ILE* 3.8 1.0 + - - +
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Residues in contact with SER 392 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388C ASP 3.2 11.4 + - - -
389C VAL 3.1 5.8 - - - +
391C ASP* 1.3 81.7 + - - +
393C ILE* 1.3 56.6 + - - +
394C ASN 3.0 5.8 - - - -
395C ASP* 2.9 42.9 + - - +
398C VAL* 3.8 17.8 - - - +
399C ILE* 4.8 2.6 - - - +
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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