Contacts of the helix formed by residues 395 - 413 (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 ASP 395 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392C SER* 2.9 17.6 + - - +
393C ILE 3.5 0.2 - - - -
394C ASN* 1.3 75.0 - - - +
396C GLU* 1.3 62.0 + - - +
397C ALA* 2.9 35.4 + - - +
398C VAL* 3.0 40.4 + - + +
399C ILE* 3.2 16.7 + - - +
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Residues in contact with GLU 396 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339C ARG* 6.0 3.6 - - - +
394C ASN 3.3 8.4 + - - +
395C ASP* 1.3 70.3 + - - +
397C ALA* 1.3 57.3 + - - +
399C ILE* 3.9 11.2 - - - +
400C GLU* 3.0 33.9 + - + +
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Residues in contact with ALA 397 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395C ASP* 2.9 14.0 + - - +
396C GLU* 1.3 76.7 - - - +
398C VAL* 1.3 64.3 + - + +
400C GLU* 3.6 5.8 + - - +
401C ARG* 3.1 24.8 + - - +
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Residues in contact with VAL 398 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388C ASP* 3.7 36.1 - - + +
389C VAL* 4.5 6.3 - - - +
392C SER* 3.8 15.5 - - - +
395C ASP* 3.0 35.1 + - + +
397C ALA* 1.3 75.4 - - + +
399C ILE* 1.3 66.0 + - - +
401C ARG* 3.3 19.7 + - - +
402C ILE* 3.1 25.7 + - + +
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Residues in contact with ILE 399 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336C ALA* 4.1 11.0 - - + +
339C ARG* 3.6 66.0 - - + +
340C ALA* 3.9 8.2 - - + +
389C VAL* 4.1 21.8 - - + -
392C SER 4.8 4.0 - - - +
393C ILE 4.0 14.6 - - - +
394C ASN 5.6 0.2 - - - -
395C ASP 3.2 15.6 + - - +
396C GLU* 4.0 8.7 - - - +
398C VAL* 1.3 77.0 - - + +
400C GLU* 1.3 63.3 + - + +
402C ILE* 3.3 6.8 + - - +
403C LYS* 3.0 21.0 + - - +
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Residues in contact with GLU 400 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396C GLU* 3.0 22.2 + - + +
397C ALA* 3.8 6.3 - - - +
399C ILE* 1.3 78.2 - - + +
401C ARG* 1.3 63.1 + - - +
403C LYS* 3.3 31.8 + - - +
404C GLY* 3.3 10.4 + - - -
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Residues in contact with ARG 401 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388C ASP* 4.4 17.8 + - - +
397C ALA 3.1 18.8 + - - +
398C VAL* 3.3 20.8 + - - +
400C GLU* 1.3 76.9 - - - +
402C ILE* 1.3 73.5 + - - +
404C GLY* 3.4 3.9 + - - +
405C LYS* 3.3 55.6 + - - +
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Residues in contact with ILE 402 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340C ALA* 4.1 8.5 - - + -
342C ILE* 4.1 11.7 - - + -
385C TRP* 3.5 55.4 - - + +
388C ASP* 4.0 11.7 - - + +
389C VAL* 3.9 15.0 - - + -
398C VAL* 3.1 19.1 + - + +
399C ILE 3.7 6.3 - - - +
401C ARG* 1.3 86.8 - - - +
403C LYS* 1.3 62.0 + - - +
405C LYS* 3.0 9.3 + - + +
406C VAL* 2.8 47.1 + - + +
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Residues in contact with LYS 403 (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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339C ARG* 3.2 19.0 + - - +
340C ALA* 3.8 14.5 + - - -
341C ASN* 3.2 32.5 + - - +
399C ILE 3.0 12.5 + - - +
400C GLU* 3.3 31.0 + - - +
402C ILE* 1.3 76.5 - - - +
404C GLY* 1.3 54.7 + - - +
406C VAL* 2.9 2.6 + - - +
407C LEU* 2.7 54.1 + - + +
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Residues in contact with GLY 404 (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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400C GLU 3.3 9.1 + - - -
401C ARG 3.4 4.2 + - - -
402C ILE 3.1 0.4 - - - -
403C LYS* 1.3 81.2 - - - +
405C LYS* 1.3 62.0 + - - +
407C LEU* 3.4 6.5 + - - +
408C ASP* 3.0 25.7 + - - +
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Residues in contact with LYS 405 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381C GLU* 6.0 0.4 + - - -
385C TRP* 3.5 58.0 - - + +
401C ARG* 3.3 45.0 + - - +
402C ILE* 3.0 11.5 + - + +
404C GLY* 1.3 74.9 - - - +
406C VAL* 1.3 57.3 + - - +
408C ASP* 3.5 6.8 - - - +
409C ILE* 3.1 21.1 + - - +
412C ARG* 5.2 0.5 + - - -
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Residues in contact with VAL 406 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C GLU 4.2 0.9 - - - +
30C ILE* 3.5 26.7 - - + -
340C ALA 3.3 17.7 - - - +
341C ASN* 3.7 23.6 - - + +
342C ILE* 4.0 11.0 - - + -
385C TRP* 4.2 10.5 - - + -
402C ILE* 2.8 31.2 + - + +
403C LYS* 2.9 6.0 + - - +
405C LYS* 1.3 73.8 - - - +
407C LEU* 1.3 64.1 + - - +
408C ASP 2.9 5.6 + - - -
409C ILE* 3.1 7.4 + - - +
410C CYS* 2.9 30.3 + - - +
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Residues in contact with LEU 407 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C GLU* 3.5 36.1 - - + +
341C ASN* 3.3 27.6 - - - +
403C LYS* 2.7 44.7 + - + +
404C GLY* 4.1 5.4 - - - +
406C VAL* 1.3 71.9 - - - +
408C ASP* 1.3 61.6 + - - +
410C CYS* 4.0 5.3 - - + +
411C ALA* 3.6 16.8 + - - +
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Residues in contact with ASP 408 (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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404C GLY 3.0 18.2 + - - +
405C LYS* 3.5 9.3 - - - +
406C VAL 2.9 1.0 + - - -
407C LEU* 1.3 75.4 - - - +
409C ILE* 1.3 66.0 + - - +
410C CYS 3.1 1.8 + - - -
411C ALA* 3.1 16.4 + - - +
412C ARG* 3.5 33.0 + - - -
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Residues in contact with ILE 409 (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* 4.0 11.9 - - + -
374C PHE* 3.7 31.6 - - + -
378C GLU* 4.0 26.0 - - + +
381C GLU* 4.8 7.4 - - + +
385C TRP* 4.2 23.8 - - + -
405C LYS 3.1 13.2 + - - +
406C VAL 3.5 8.5 - - - +
408C ASP* 1.3 80.0 - - - +
410C CYS* 1.3 64.7 + - - +
412C ARG* 3.3 34.2 + - - +
413C TYR* 3.1 32.4 + - + +
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Residues in contact with CYS 410 (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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27C GLU* 3.4 25.1 - - - +
28C GLU* 3.8 21.5 - - - -
29C HIS 4.1 0.2 - - - -
30C ILE* 3.8 26.9 - - - -
372C ARG* 3.6 17.4 + - - +
374C PHE* 5.8 0.7 - - - -
406C VAL* 2.9 22.7 + - - +
407C LEU* 4.0 9.0 - - + +
408C ASP 3.1 0.2 - - - -
409C ILE* 1.3 78.9 - - - +
411C ALA* 1.3 61.9 + - - +
413C TYR* 3.1 23.2 - - - +
414C PRO* 3.5 3.3 - - - +
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Residues in contact with ALA 411 (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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407C LEU 3.6 9.9 + - - +
408C ASP* 3.1 11.9 + - - +
410C CYS* 1.3 79.6 - - - +
412C ARG* 1.3 61.7 + - + +
413C TYR 3.4 0.5 + - - -
414C PRO* 3.5 15.8 - - - +
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Residues in contact with ARG 412 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378C GLU* 5.7 1.6 + - - +
381C GLU* 5.3 4.8 + - - -
385C TRP* 6.0 1.2 - - - -
405C LYS 5.2 0.6 + - - -
408C ASP* 3.5 36.1 + - - +
409C ILE* 3.3 44.2 + - - +
410C CYS 3.2 0.6 - - - -
411C ALA* 1.3 78.6 - - + +
413C TYR* 1.3 81.5 + - + +
414C PRO* 3.4 7.5 - - - +
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Residues in contact with TYR 413 (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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372C ARG* 2.6 47.1 + - + +
373C GLY* 3.8 33.9 - - - -
374C PHE* 3.9 17.3 - + + -
378C GLU* 3.5 31.9 + - + +
409C ILE* 3.1 39.5 + - + +
410C CYS 3.1 5.7 - - - +
412C ARG* 1.3 101.0 + - + +
414C PRO* 1.3 59.1 - - - +
1D MET* 5.3 5.4 - - + -
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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
------------------------------------------------------------
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