Contacts of the helix formed by residues 403 - 418 (chain D) in PDB entry 1EC8
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 403 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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377D ARG* 3.3 26.5 + - - +
378D LEU 2.8 16.8 + - - +
379D THR 4.0 5.2 - - - -
380D LYS* 4.1 18.5 - - + +
401D GLU 3.4 0.4 + - - -
402D ILE* 1.3 70.4 - - - +
404D MET* 1.3 51.3 - - - +
405D ASP* 3.0 14.7 + - - +
406D GLN* 2.7 44.0 + - + +
407D VAL* 2.8 38.5 + - - +
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Residues in contact with MET 404 (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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14D GLN* 5.4 3.1 - - - +
16D ILE* 3.9 17.9 - - + -
42D ILE* 4.4 12.6 - - + -
402D ILE* 3.7 32.1 + - + +
403D ASP* 1.3 71.9 - - - +
405D ASP* 1.3 57.0 + - - +
407D VAL* 3.7 22.2 - - + +
408D MET* 3.0 44.6 + - + +
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Residues in contact with ASP 405 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403D ASP* 3.0 11.6 - - - +
404D MET* 1.3 77.0 - - - +
406D GLN* 1.3 58.4 - - + +
408D MET* 3.3 4.6 + - - +
409D LYS* 2.8 68.5 + - - +
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Residues in contact with GLN 406 (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 ASN 5.6 1.0 + - - -
376D GLN* 4.9 2.4 - - - +
377D ARG* 3.2 64.2 + - - +
378D LEU* 4.2 5.6 - - - +
403D ASP* 2.7 36.6 + - + +
405D ASP* 1.3 74.0 - - + +
407D VAL* 1.3 63.9 + - - +
409D LYS* 3.3 26.0 + - - +
410D ALA* 2.9 23.7 + - - +
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Residues in contact with VAL 407 (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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16D ILE* 3.9 15.7 - - + -
18D VAL* 3.7 8.8 - - + +
40D ILE* 4.8 8.3 - - + -
42D ILE* 5.2 0.2 - - + -
378D LEU* 3.8 19.7 - - + -
402D ILE* 2.9 39.9 - - + -
403D ASP 2.8 15.5 + - - +
404D MET* 3.7 18.6 - - + +
406D GLN* 1.3 76.9 - - - +
408D MET* 1.3 77.5 + - + +
410D ALA* 3.1 4.7 + - - +
411D HIS* 2.8 24.3 + - - +
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Residues in contact with MET 408 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16D ILE* 3.5 23.6 - - + -
404D MET* 3.0 27.4 + - + +
405D ASP* 3.9 4.0 - - - +
407D VAL* 1.3 99.0 - - + +
409D LYS* 1.3 57.2 + - - +
411D HIS* 3.1 29.5 - - + +
412D GLU* 2.7 43.7 + - + +
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Residues in contact with LYS 409 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405D ASP* 2.8 44.7 + - - +
406D GLN* 3.5 26.2 - - - +
408D MET* 1.3 78.5 - - - +
410D ALA* 1.4 56.5 + - - +
412D GLU* 3.3 6.6 + - - +
413D LEU* 3.0 25.8 + - - +
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Residues in contact with ALA 410 (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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18D VAL* 3.6 16.4 - - + -
19D ALA 3.0 32.9 + - - +
344D PHE* 4.8 3.6 - - + -
378D LEU* 4.4 13.7 - - + -
406D GLN 2.9 14.3 + - - +
407D VAL 3.1 7.6 + - - +
409D LYS* 1.4 73.0 - - - +
411D HIS* 1.3 66.8 + - - +
413D LEU* 3.2 5.4 + - - +
414D TYR 3.0 17.8 + - - -
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Residues in contact with HIS 411 (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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16D ILE* 4.0 4.0 - - + -
17D PRO* 2.9 41.1 + - + +
18D VAL* 3.8 0.6 - - - +
407D VAL 2.8 14.0 + - - +
408D MET* 3.1 35.4 - - + +
410D ALA* 1.3 77.1 - - - +
412D GLU* 1.3 86.3 + - - +
414D TYR* 2.9 21.5 - - - +
415D GLN* 2.9 42.0 + - + +
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Residues in contact with GLU 412 (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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408D MET* 2.7 28.9 + - + +
409D LYS* 3.3 6.0 + - - +
410D ALA 3.2 0.2 - - - -
411D HIS* 1.3 93.2 + - - +
413D LEU* 1.3 50.1 + - - +
415D GLN* 3.2 20.8 + - - +
416D LYS* 2.7 37.6 + - - +
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Residues in contact with LEU 413 (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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19D ALA* 3.7 26.5 - - + +
20D GLY* 4.1 1.6 - - - +
21D HIS* 3.6 23.6 - - + +
35D PHE* 3.5 31.0 - - + -
409D LYS 3.0 14.2 + - - +
410D ALA* 3.2 9.6 + - - +
412D GLU* 1.3 74.9 - - - +
414D TYR* 1.4 63.0 + - - +
416D LYS* 3.5 14.5 + - + +
417D HIS* 3.1 59.3 + - + +
419D LEU* 4.0 0.9 - - - +
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Residues in contact with TYR 414 (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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17D PRO* 3.2 42.8 - - + +
18D VAL 3.7 18.2 - - - -
19D ALA* 3.9 6.7 - - - +
37D THR* 4.0 22.2 - - + -
38D ARG 5.5 0.4 - - - -
39D ASN* 5.6 0.3 + - - -
57D GLY* 6.2 0.2 - - - -
58D GLY 4.7 5.0 + - - -
59D GLU* 4.6 20.0 + - - +
62D ARG* 5.2 2.5 - - - -
410D ALA 3.0 11.3 + - - +
411D HIS 2.9 14.1 + - - +
413D LEU* 1.4 74.9 - - - +
415D GLN* 1.3 85.9 + - - +
417D HIS* 3.4 1.0 + - - -
418D GLY* 3.2 18.0 + - - -
419D LEU* 3.0 48.1 + - + +
420D GLY* 3.7 9.2 - - - -
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Residues in contact with GLN 415 (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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17D PRO* 4.1 3.1 - - - +
411D HIS* 2.9 39.9 + - + +
412D GLU* 3.6 22.0 - - - +
414D TYR* 1.3 99.7 + - - +
416D LYS* 1.3 63.2 + - - +
417D HIS 3.2 1.0 + - - -
418D GLY* 3.2 13.7 + - - -
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Residues in contact with LYS 416 (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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412D GLU 2.7 20.2 + - - +
413D LEU* 3.8 14.5 - - + +
414D TYR 3.3 0.4 - - - -
415D GLN* 1.3 72.4 - - - +
417D HIS* 1.3 93.4 + - + +
418D GLY 3.4 0.2 - - - -
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Residues in contact with HIS 417 (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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35D PHE* 3.4 33.7 - + + -
163D PRO* 5.4 4.9 - - + -
413D LEU* 3.1 38.9 + - + +
414D TYR 3.4 0.2 + - - -
415D GLN 3.1 0.2 - - - -
416D LYS* 1.3 118.0 + - + +
418D GLY* 1.3 66.7 - - - +
419D LEU* 3.0 34.2 + - + +
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Residues in contact with GLY 418 (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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414D TYR 3.2 5.8 + - - -
415D GLN* 3.2 13.6 + - - -
416D LYS 3.4 0.6 - - - -
417D HIS* 1.3 78.5 - - - +
419D LEU* 1.3 63.9 + - - +
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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