Contacts of the helix formed by residues 17 - 25 (chain D) in PDB entry 3ELP
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 HIS 17 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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382C ASP* 2.8 22.9 + - - -
384C GLU* 4.0 4.1 + - - -
385C ASP* 3.0 40.9 + - - +
388C GLU* 5.4 2.6 + - - -
15D PHE 3.7 0.4 + - - -
16D GLN* 1.3 104.7 + - + +
18D PHE* 1.3 62.5 + - - +
20D THR* 2.9 6.6 + - + -
21D GLN* 2.7 45.4 + - + +
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Residues in contact with PHE 18 (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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382C ASP* 3.1 3.4 + - - +
15D PHE* 3.6 20.1 + - + +
16D GLN 2.9 6.8 + - - +
17D HIS* 1.3 74.6 - - - +
19D ALA* 1.3 60.0 + - - +
21D GLN* 3.9 8.3 - - - -
22D ALA* 2.8 31.0 + - + +
78D LEU* 3.2 54.6 - - + +
193D PRO* 3.5 22.7 - - + -
194D TYR* 3.5 52.7 - + + -
197D ARG* 4.1 9.6 - - - +
262D LEU* 3.9 27.6 - - + -
263D HIS* 4.3 7.2 - + + -
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Residues in contact with ALA 19 (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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380C LEU 3.6 21.5 - - - +
381C GLU* 4.0 2.2 - - - +
382C ASP* 3.0 19.9 + - - +
18D PHE* 1.3 80.8 - - - +
20D THR* 1.3 62.7 + - - +
22D ALA* 3.4 2.5 + - - +
23D ILE* 3.1 31.1 + - - +
263D HIS* 3.7 31.2 - - + +
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Residues in contact with THR 20 (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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334C LEU* 3.6 30.5 - - + -
381C GLU* 3.4 13.2 - - + +
382C ASP* 3.1 18.8 + - - +
385C ASP* 2.8 30.5 + - + +
17D HIS* 2.9 9.5 + - + -
19D ALA* 1.3 78.1 - - - +
21D GLN* 1.3 60.0 + - + +
23D ILE 3.3 0.9 + - - -
24D HIS* 2.8 38.3 + - + +
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Residues in contact with GLN 21 (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 GLN 4.2 3.6 + - - +
17D HIS* 2.7 41.3 + - + +
18D PHE* 3.7 12.3 + - - +
20D THR* 1.3 69.4 - - + +
22D ALA* 1.3 64.9 + - - +
23D ILE 3.0 2.0 - - - -
24D HIS* 5.2 0.4 - - - -
25D VAL* 2.8 54.9 + - + +
74D ALA* 4.7 2.1 - - - +
77D ALA* 3.5 38.8 + - + +
78D LEU* 4.1 8.1 + - + +
197D ARG* 4.9 2.6 + - - -
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Residues in contact with ALA 22 (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 PHE* 2.8 26.7 + - + +
19D ALA* 3.7 9.4 - - - +
21D GLN* 1.3 74.5 - - - +
23D ILE* 1.3 59.5 + - + +
25D VAL 5.3 1.7 - - - +
74D ALA* 5.4 4.5 - - - +
78D LEU* 3.8 25.1 - - + +
256D ASN* 4.6 7.3 + - - -
259D LEU* 3.9 22.4 - - + +
260D LYS* 3.1 25.5 + - - +
263D HIS* 5.2 0.9 - - + -
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Residues in contact with ILE 23 (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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344C PHE* 3.7 35.9 - - + +
345C GLU* 4.6 6.4 - - + +
380C LEU* 3.6 37.2 - - + +
381C GLU* 4.0 3.6 - - + +
19D ALA 3.1 18.3 + - - +
20D THR 3.8 2.5 - - - +
21D GLN 3.0 0.6 - - - -
22D ALA* 1.3 81.6 - - - +
24D HIS* 1.3 79.0 + - + +
25D VAL 3.8 0.2 - - - -
27D GLN* 2.9 23.5 - - - +
260D LYS* 3.4 37.3 + - + +
263D HIS* 4.3 0.2 - - - +
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Residues in contact with HIS 24 (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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334C LEU* 4.0 23.2 - - + +
336C THR* 5.0 0.9 - - - -
345C GLU* 3.4 41.0 + - + -
381C GLU* 2.9 34.3 + - + +
20D THR* 2.8 42.2 + - + +
21D GLN* 5.2 0.4 - - - -
23D ILE* 1.3 82.7 + - + +
25D VAL* 1.3 65.2 - - + +
26D GLY 3.1 0.9 + - - -
27D GLN* 2.9 22.9 + - - +
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Residues in contact with VAL 25 (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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21D GLN* 2.8 51.0 + - + +
22D ALA 5.3 0.9 - - - +
23D ILE 5.1 0.2 - - - -
24D HIS* 1.3 71.4 - - + +
26D GLY* 1.3 63.6 + - - +
27D GLN* 3.4 11.1 + - - +
70D CYS 4.6 0.2 - - - +
73D LYS* 3.9 13.9 - - + +
74D ALA* 3.4 43.6 - - - +
77D ALA* 4.4 8.3 - - + -
256D ASN* 5.2 0.3 + - - -
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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