Contacts of the helix formed by residues 13 - 21 (chain D) in PDB entry 3DOY
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 PHE 13 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114A THR* 5.7 1.6 - - - -
115A PRO 6.2 0.2 - - - +
9D GLN* 5.9 0.2 - - - -
11D GLN* 3.7 37.5 - - + -
12D PHE* 1.3 77.3 - - - +
14D ILE* 1.3 58.1 - - + +
15D GLU* 3.1 26.7 - - - +
16D HIS* 2.7 44.7 + + - +
17D ILE* 3.0 11.7 + - - +
31D ASP 4.1 4.0 - - - -
32D ARG* 3.6 42.8 - - - +
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Residues in contact with ILE 14 (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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50A PHE* 3.6 44.9 - - + -
63A PRO* 3.7 23.1 - - + +
114A THR* 5.0 5.2 - - - +
115A PRO* 4.1 25.2 + - + +
13D PHE* 1.3 74.5 - - + +
15D GLU* 1.3 71.9 + - - +
17D ILE* 4.3 6.1 - - + -
18D LEU* 3.0 38.9 + - + +
28D LEU* 4.2 4.5 - - + -
30D VAL 4.0 18.2 - - - +
31D ASP* 3.4 18.5 + - - +
32D ARG* 5.7 0.2 - - - +
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Residues in contact with GLU 15 (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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61A ASN 5.1 9.2 - - - +
62A LYS* 5.5 12.2 + - - +
63A PRO* 5.5 2.4 - - + +
114A THR* 5.7 3.3 + - - +
13D PHE* 3.0 26.2 + - - +
14D ILE* 1.3 91.3 - - + +
16D HIS* 1.3 78.7 + - + +
18D LEU* 3.8 12.4 - - - +
19D GLN* 2.8 34.5 + - - +
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Residues in contact with HIS 16 (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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9D GLN* 4.4 18.0 + - - -
12D PHE* 3.6 22.5 - + + -
13D PHE* 2.7 48.6 + + - +
15D GLU* 1.3 86.8 - - + +
17D ILE* 1.3 65.0 + - - +
18D LEU 3.1 0.2 - - - -
19D GLN* 3.0 14.8 + - - -
20D ILE* 3.3 10.5 + - - +
80D PHE* 4.7 1.1 - - - -
89D PHE* 3.5 43.4 - + + -
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Residues in contact with ILE 17 (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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12D PHE* 4.5 1.3 - - + +
13D PHE 3.0 14.8 + - - +
14D ILE* 3.8 7.9 - - + +
16D HIS* 1.3 76.2 - - - +
18D LEU* 1.3 57.7 + - - +
20D ILE 3.2 0.2 + - - -
21D LEU* 2.9 55.8 + - + +
28D LEU* 4.0 18.8 - - + +
30D VAL* 3.9 13.2 - - + +
31D ASP 3.5 35.2 - - - +
32D ARG* 3.6 10.5 - - - +
33D ILE* 3.9 28.9 - - + -
80D PHE* 4.0 13.0 - - + -
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Residues in contact with LEU 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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50A PHE* 3.9 23.6 - - + -
61A ASN* 4.3 28.7 - - - +
63A PRO* 4.3 16.6 - - + -
14D ILE* 3.0 23.2 + - + +
15D GLU* 3.8 11.2 - - - +
17D ILE* 1.3 77.6 - - - +
19D GLN* 1.3 61.3 + - + +
20D ILE 3.2 1.0 + - - -
21D LEU 3.5 6.4 - - - +
24D ARG* 2.8 43.1 + - - +
28D LEU* 3.3 31.2 - - + -
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Residues in contact with GLN 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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15D GLU* 2.8 28.6 + - - +
16D HIS* 3.0 13.0 + - - +
18D LEU* 1.3 78.0 - - + +
20D ILE* 1.3 59.4 + - - +
89D PHE* 3.7 24.3 - - + -
91D PRO* 3.5 37.0 - - + +
94D ALA* 3.4 17.2 - - - +
95D LYS 5.2 0.2 + - - -
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Residues in contact with ILE 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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16D HIS 3.5 13.5 - - - +
17D ILE 3.2 1.4 + - - +
19D GLN* 1.3 87.8 - - - +
21D LEU* 1.3 71.0 + - + +
22D PRO* 3.8 4.3 - - - +
80D PHE* 3.7 33.9 - - + -
83D PHE* 3.6 40.5 - - + -
84D THR* 4.5 4.7 - - + -
88D GLY 4.7 0.2 - - - +
89D PHE* 3.6 30.3 - - + -
90D ASP 4.0 20.4 - - - +
91D PRO 4.4 0.7 - - - -
94D ALA* 3.6 19.8 - - + +
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Residues in contact with LEU 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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17D ILE* 2.9 29.7 + - + +
18D LEU 3.5 7.3 - - - +
20D ILE* 1.3 79.1 - - + +
22D PRO* 1.3 71.5 - - + +
23D HIS* 3.9 14.4 - - + +
24D ARG* 2.9 21.8 + - - -
28D LEU* 3.9 25.1 - - + -
30D VAL* 4.7 4.0 - - + -
76D GLN* 3.9 41.7 - - + +
79D GLY* 4.3 6.5 - - - -
80D PHE* 3.9 27.4 - - + +
83D PHE* 6.2 0.4 - - + -
99D VAL* 5.4 4.3 - - + -
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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