Contacts of the helix formed by residues 395 - 412 (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 ASP 395 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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392A SER* 2.9 16.7 + - - +
393A ILE 3.5 0.2 - - - -
394A ASN* 1.3 76.2 - - - +
396A GLU* 1.3 60.9 + - - +
397A ALA* 2.9 35.3 + - - +
398A VAL* 3.0 40.7 + - + +
399A ILE* 3.2 16.5 + - - +
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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
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339A ARG* 2.8 45.7 + - - +
394A ASN* 3.3 12.3 + - - +
395A ASP* 1.3 72.5 + - - +
397A ALA* 1.3 58.4 + - - +
399A ILE* 3.6 16.1 - - - +
400A GLU* 3.0 42.5 + - - +
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Residues in contact with ALA 397 (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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395A ASP* 2.9 13.8 + - - +
396A GLU* 1.3 75.8 - - - +
398A VAL* 1.3 63.1 + - + +
400A GLU* 3.6 7.8 + - - +
401A ARG* 3.2 23.9 + - - +
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Residues in contact with VAL 398 (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* 3.7 33.0 - - + +
389A VAL* 4.4 6.3 - - - -
392A SER* 3.8 14.8 - - - +
395A ASP* 3.0 39.4 + - + +
397A ALA* 1.3 75.7 - - + +
399A ILE* 1.3 65.8 + - + +
401A ARG* 3.3 12.5 + - - +
402A ILE* 3.1 35.0 + - + +
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Residues in contact with ILE 399 (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 13.9 - - + +
339A ARG* 3.6 53.8 - - + +
340A ALA* 3.9 8.7 - - + +
389A VAL* 4.1 17.3 - - + -
392A SER 4.9 3.8 - - - +
393A ILE 4.0 13.5 - - - +
395A ASP 3.2 10.0 + - - +
396A GLU* 3.6 33.2 - - - +
398A VAL* 1.3 77.4 - - + +
400A GLU* 1.3 64.6 + - + +
402A ILE* 3.3 7.7 + - - +
403A LYS* 3.0 20.1 + - - +
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Residues in contact with GLU 400 (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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396A GLU* 3.0 31.5 + - + +
397A ALA* 3.9 7.7 - - - +
398A VAL 3.3 0.2 - - - -
399A ILE* 1.3 78.0 - - + +
401A ARG* 1.3 62.4 + - - +
403A LYS* 3.1 18.4 + - + +
404A GLY* 3.1 10.4 + - - -
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Residues in contact with ARG 401 (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* 4.7 14.6 + - - +
397A ALA 3.2 15.3 + - - +
398A VAL* 3.3 11.2 + - - +
400A GLU* 1.3 76.9 - - - +
402A ILE* 1.3 69.9 + - - +
404A GLY* 3.2 3.9 + - - -
405A LYS* 3.2 54.9 + - + +
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Residues in contact with ILE 402 (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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340A ALA* 4.1 7.2 - - + -
342A ILE* 4.0 20.4 - - + -
385A TRP* 3.7 44.4 - - + +
388A ASP* 4.0 18.6 - - + +
389A VAL* 3.9 20.2 - - + -
398A VAL* 3.1 20.9 + - + +
399A ILE 3.7 6.5 - - - +
400A GLU 3.2 0.2 - - - -
401A ARG* 1.3 85.9 - - - +
403A LYS* 1.3 59.7 + - - +
405A LYS* 3.2 11.8 + - + +
406A VAL* 3.0 26.9 + - + +
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Residues in contact with LYS 403 (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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339A ARG 3.6 17.0 + - - +
340A ALA* 3.7 9.6 + - - -
341A ASN* 3.4 31.3 + - - +
399A ILE 3.0 13.2 + - - +
400A GLU* 3.1 12.5 + - + +
402A ILE* 1.3 74.9 - - - +
404A GLY* 1.3 62.7 + - - +
406A VAL* 2.9 23.7 - - - +
407A LEU* 3.1 34.1 + - + +
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Residues in contact with GLY 404 (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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400A GLU 3.1 11.9 + - - -
401A ARG* 3.2 3.8 + - - -
402A ILE 3.2 0.4 - - - -
403A LYS* 1.3 78.7 - - - +
405A LYS* 1.3 60.5 + - - +
407A LEU* 3.6 9.5 + - - +
408A ASP* 3.1 23.6 + - - +
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Residues in contact with LYS 405 (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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381A GLU* 5.4 3.0 + - - -
385A TRP* 3.3 55.0 - - + +
401A ARG* 3.2 46.9 + - + +
402A ILE* 3.5 18.4 - - + +
404A GLY* 1.3 76.0 - - - +
406A VAL* 1.3 59.1 - - - +
408A ASP* 3.3 7.0 + - - +
409A ILE* 3.0 27.2 + - - +
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Residues in contact with VAL 406 (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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28A GLU 5.0 0.4 - - - +
30A ILE* 4.1 16.4 - - + -
340A ALA 3.2 26.7 - - - +
341A ASN* 3.5 16.2 - - + +
342A ILE* 3.8 20.6 - - + -
382A LEU* 5.0 0.2 - - + -
385A TRP* 4.0 17.9 - - + -
402A ILE 3.0 15.6 + - - +
403A LYS* 2.9 26.0 - - - +
405A LYS* 1.3 73.3 - - - +
407A LEU* 1.3 64.6 + - + +
409A ILE* 3.2 9.6 + - - +
410A CYS* 2.7 36.2 + - - +
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Residues in contact with LEU 407 (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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28A GLU* 3.9 29.4 - - + +
341A ASN* 3.7 24.5 - - - +
403A LYS* 3.1 43.4 + - + +
404A GLY* 3.9 8.3 - - - +
406A VAL* 1.3 82.7 - - + +
408A ASP* 1.3 58.3 + - - +
410A CYS* 3.5 6.2 - - - +
411A ALA* 3.0 28.4 + - - +
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Residues in contact with ASP 408 (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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404A GLY 3.1 16.5 + - - +
405A LYS* 3.5 7.9 - - - +
406A VAL 3.1 0.4 - - - -
407A LEU* 1.3 77.2 - - - +
409A ILE* 1.3 67.7 + - - +
411A ALA* 3.2 16.2 + - - +
412A ARG* 3.1 38.4 + - - +
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Residues in contact with ILE 409 (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* 4.0 6.5 - - + -
374A PHE* 3.7 35.9 - - + -
378A GLU* 3.8 29.2 - - + +
381A GLU* 4.8 6.7 - - - +
385A TRP* 4.0 24.2 - - + -
405A LYS 3.0 16.5 + - - +
406A VAL* 3.3 15.0 - - - +
408A ASP* 1.3 80.3 + - - +
410A CYS* 1.3 63.4 + - - +
411A ALA 3.3 0.2 - - - -
412A ARG* 3.3 21.7 + - - +
413A TYR* 3.1 42.3 + - + +
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Residues in contact with CYS 410 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27A GLU* 3.5 24.1 - - - +
28A GLU* 3.9 19.7 - - - -
29A HIS 4.0 2.7 - - - -
30A ILE* 3.7 26.5 - - - -
372A ARG* 3.5 20.5 + - - +
374A PHE* 5.7 0.4 - - - -
406A VAL 2.7 22.1 + - - +
407A LEU* 3.5 8.3 - - - +
409A ILE* 1.3 76.8 - - - +
411A ALA* 1.3 62.0 + - - +
413A TYR* 3.3 21.9 + - - +
414A PRO* 3.7 3.3 - - - +
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Residues in contact with ALA 411 (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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407A LEU 3.0 14.3 + - - +
408A ASP* 3.2 10.3 + - - +
410A CYS* 1.3 77.8 - - - +
412A ARG* 1.3 62.8 + - + +
413A TYR 3.3 0.2 - - - -
414A PRO* 3.9 11.9 - - - +
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Residues in contact with ARG 412 (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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378A GLU* 5.1 4.9 + - - +
381A GLU* 5.9 1.0 + - - -
408A ASP* 3.1 34.7 + - - +
409A ILE* 3.3 26.6 + - - +
410A CYS 3.2 0.8 - - - -
411A ALA* 1.3 80.7 - - + +
413A TYR* 1.3 99.5 + - + +
414A PRO* 3.6 6.1 - - - +
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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