Contacts of the helix formed by residues 11 - 21 (chain D) in PDB entry 3H90
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 ARG 11 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D SER* 1.3 79.2 + - - +
12D ALA* 1.3 57.9 + - - +
13D ALA* 3.1 8.3 - - - +
14D ILE* 3.4 40.3 - - - +
15D ALA 4.1 0.2 + - - -
64D LEU* 4.3 21.9 - - + +
79D GLU* 2.5 32.9 + - - -
142D THR* 2.8 24.6 + - - +
143D GLN 4.4 2.0 - - - +
144D SER* 3.3 36.1 - - - +
240D GLY 4.7 1.6 - - - -
241D PRO* 3.6 40.9 - - + +
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Residues in contact with ALA 12 (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 VAL* 4.9 11.7 - - + -
10D SER* 3.2 12.4 + - - +
11D ARG* 1.3 73.4 - - - +
13D ALA* 1.3 58.3 + - - +
14D ILE 3.1 2.5 - - - -
15D ALA* 3.1 13.2 + - + +
16D ALA* 2.9 29.8 + - - +
64D LEU* 5.9 0.2 - - - -
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Residues in contact with ALA 13 (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 VAL* 5.2 10.7 - - + +
10D SER 3.5 17.6 + - - +
11D ARG 3.1 0.4 - - - -
12D ALA* 1.3 78.3 - - - +
14D ILE* 1.3 58.0 + - - +
16D ALA* 3.5 14.7 - - - +
17D THR* 3.4 6.6 - - - +
134D PHE* 5.0 0.2 - - - -
137D TRP* 5.5 9.2 - - + -
138D VAL* 3.3 24.1 - - + +
141D ARG* 5.7 6.7 - - + -
142D THR* 4.1 18.4 - - + -
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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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11D ARG* 3.4 36.5 + - - +
12D ALA 3.1 1.0 - - - -
13D ALA* 1.3 73.2 - - - +
15D ALA* 1.3 70.0 + - - +
16D ALA 3.0 1.6 - - - -
17D THR* 3.2 12.1 - - - +
18D ALA* 3.1 21.3 + - - +
60D VAL* 3.6 37.1 - - + +
63D SER* 5.3 0.2 - - - +
64D LEU* 4.0 11.9 - - + -
79D GLU* 4.7 4.3 - - - +
138D VAL* 4.0 2.5 - - + -
142D THR* 3.6 34.1 - - + +
144D SER* 3.7 21.5 - - - +
147D VAL* 3.7 12.5 - - + +
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Residues in contact with ALA 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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12D ALA* 3.1 18.7 + - + +
14D ILE* 1.3 85.8 - - + +
16D ALA* 1.3 61.9 + - - +
18D ALA* 3.3 14.4 - - - +
19D MET* 3.0 22.9 - - - +
57D LEU* 4.2 1.3 - - + +
60D VAL* 4.6 7.6 - - + -
61D ARG* 5.1 18.6 - - + +
64D LEU* 4.8 12.1 - - + -
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Residues in contact with ALA 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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12D ALA 2.9 12.1 + - - +
13D ALA* 3.5 15.0 - - - +
14D ILE 3.0 0.2 - - - -
15D ALA* 1.3 72.8 - - - +
17D THR* 1.3 58.5 + - - +
18D ALA 3.0 3.6 - - - -
19D MET* 2.8 30.4 + - - +
20D ALA* 2.9 10.1 + - - +
134D PHE* 4.3 15.7 - - + -
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Residues in contact with THR 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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13D ALA 3.4 13.0 + - - +
14D ILE* 3.2 18.4 - - - +
16D ALA* 1.3 75.2 - - - +
18D ALA* 1.3 60.9 + - - +
20D ALA* 3.4 11.7 - - - +
21D SER* 3.5 19.6 + - - -
134D PHE* 3.9 8.7 - - - -
135D GLN* 3.2 29.1 + - - +
138D VAL* 3.5 32.1 - - + -
147D VAL* 3.7 17.4 - - + +
150D ASP* 4.7 1.7 - - - +
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Residues in contact with ALA 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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14D ILE 3.1 11.3 + - - +
15D ALA 3.3 13.2 - - - +
16D ALA 2.9 0.6 + - - -
17D THR* 1.3 78.5 - - - +
19D MET* 1.3 60.9 + - - +
21D SER* 3.4 8.8 + - - -
22D LEU* 3.3 21.0 - - - +
53D SER 4.3 5.1 - - - +
56D ASN* 5.1 3.8 - - - +
57D LEU* 3.5 39.3 - - + +
60D VAL* 4.2 9.0 - - + -
147D VAL* 5.5 1.5 - - + +
150D ASP* 5.5 3.1 - - - -
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Residues in contact with MET 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 ALA* 3.0 27.6 - - + +
16D ALA* 2.8 11.8 + - - +
18D ALA* 1.3 71.0 - - - +
20D ALA* 1.3 58.8 + - - +
21D SER 3.0 2.2 - - - -
22D LEU* 2.6 44.2 + - + +
23D LEU 3.5 0.2 + - - -
57D LEU* 4.3 14.6 - - + -
61D ARG* 3.4 41.1 - - - +
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Residues in contact with ALA 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 ALA 2.9 4.8 + - - +
17D THR* 3.4 24.7 - - - +
19D MET* 1.3 78.2 - - - +
21D SER* 1.3 55.4 + - - +
23D LEU* 3.1 29.0 - - - +
131D LEU* 3.3 16.7 - - + +
134D PHE* 3.5 26.9 - - + -
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Residues in contact with SER 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 THR 3.5 2.4 + - - -
18D ALA 3.4 9.1 + - - -
19D MET 3.0 1.0 - - - -
20D ALA* 1.3 73.6 - - - +
22D LEU* 1.3 59.5 + - - +
23D LEU* 3.0 5.3 - - - +
24D LEU* 3.2 24.8 + - - +
49D ASP 5.2 1.0 - - - +
50D ILE* 5.7 0.5 - - - -
53D SER* 3.5 28.0 - - - -
131D LEU* 3.8 8.8 - - - +
135D GLN* 3.0 28.8 + - - -
150D ASP* 3.2 9.8 + - - -
154D TYR* 3.3 14.1 + - - -
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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