Contacts of the helix formed by residues 18 - 29 (chain D) in PDB entry 2DFD
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 ILE 18 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17D GLY* 1.3 74.9 - - - +
19D GLY* 1.3 67.3 + - - +
20D GLN 3.2 1.1 + - - -
21D PRO* 3.2 3.5 - - - +
22D LEU* 2.9 38.4 + - + +
81D PRO* 3.9 15.3 - - + -
122D ILE* 3.9 8.7 - - + -
229D ALA 3.8 14.4 - - - +
230D THR* 4.0 11.0 - - - -
233D MET* 3.8 24.9 - - + -
234D ALA* 4.3 7.4 - - - +
3004D NAD 2.9 68.8 + - + +
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Residues in contact with GLY 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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11D VAL* 4.4 2.4 - - - +
13D GLY 3.5 23.6 + - - -
14D ALA* 3.1 13.0 - - - -
16D GLY 3.4 4.7 + - - -
18D ILE* 1.3 77.1 - - - +
20D GLN* 1.3 55.7 + - - +
22D LEU* 3.8 2.2 - - - +
23D SER* 2.8 34.1 + - - -
81D PRO* 4.1 13.2 - - - +
3004D NAD 4.3 1.2 + - - -
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Residues in contact with GLN 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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223C LYS* 5.0 4.2 + - - -
230C THR* 4.3 7.1 + - - -
231C LEU* 3.7 35.4 - - + +
14D ALA 3.3 15.3 - - - +
15D SER* 2.9 22.9 + - - +
16D GLY 3.1 12.7 + - - +
19D GLY* 1.3 73.3 - - - +
21D PRO* 1.3 64.4 - - + +
23D SER* 3.2 5.5 + - - -
24D LEU* 2.9 26.5 + - - +
42D HIS* 5.7 1.4 - - - +
46D VAL* 3.7 25.5 - - + +
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Residues in contact with PRO 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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21C PRO* 5.2 6.7 - - + -
24C LEU* 3.8 16.3 - - + +
231C LEU* 4.6 4.9 - - + -
17D GLY 3.0 28.7 - - - +
18D ILE* 3.2 10.1 - - - +
20D GLN* 1.3 88.9 - - + +
22D LEU* 1.3 62.8 + - - +
24D LEU* 3.3 10.9 + - + +
25D LEU* 3.0 26.9 + - - +
230D THR 4.2 1.8 - - - +
231D LEU* 4.1 19.5 - - + -
234D ALA* 3.7 18.4 - - + -
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Residues in contact with LEU 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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11D VAL* 4.3 17.7 - - + -
18D ILE* 2.9 29.8 + - + +
19D GLY 3.8 2.7 - - - +
21D PRO* 1.3 76.1 - - - +
23D SER* 1.3 58.7 + - - +
25D LEU* 3.1 3.6 + - - -
26D LEU* 3.0 46.6 + - + +
79D VAL* 3.9 29.6 - - + -
81D PRO* 4.4 2.9 - - + -
122D ILE* 4.2 13.7 - - + -
234D ALA* 3.6 14.3 - - - +
237D GLY* 4.0 4.3 - - - -
238D ALA* 3.6 33.9 - - + +
241D VAL* 5.5 0.9 - - + -
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Residues in contact with SER 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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11D VAL* 3.8 12.5 - - - +
14D ALA* 4.0 4.0 - - - +
19D GLY 2.8 24.7 + - - -
20D GLN* 3.6 3.4 - - - -
22D LEU* 1.3 78.1 - - - +
24D LEU* 1.3 55.6 + - - +
26D LEU* 4.4 6.3 - - - -
27D LYS* 2.9 25.8 + - - +
35D LEU* 3.3 11.9 - - - +
37D LEU* 3.3 26.6 - - - +
46D VAL* 5.4 0.4 - - - -
50D LEU* 3.5 22.9 - - - -
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Residues in contact with LEU 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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21C PRO* 3.8 29.6 - - + +
24C LEU* 5.6 1.6 - - + -
25C LEU* 4.1 23.6 - - + -
231C LEU* 3.5 22.9 - - + +
234C ALA* 4.2 0.2 - - + -
235C TYR* 4.3 4.5 - - + -
20D GLN 2.9 13.3 + - - +
21D PRO* 3.4 12.6 - - + +
22D LEU 3.2 0.2 - - - -
23D SER* 1.3 73.7 - - - +
25D LEU* 1.3 65.4 + - + +
27D LYS* 3.3 1.2 + - - +
28D ASN* 2.9 45.3 + - - +
50D LEU* 3.6 14.6 - - + +
53D ILE* 3.5 31.9 - - + -
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Residues in contact with LEU 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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24C LEU* 4.1 15.7 - - + -
25C LEU* 3.7 30.5 - - + -
28C ASN* 3.7 18.4 - - - +
21D PRO 3.0 15.4 + - - +
22D LEU 3.1 7.1 + - - +
24D LEU* 1.3 78.7 - - + +
26D LEU* 1.3 62.6 + - - +
28D ASN* 3.5 13.6 + - + +
29D SER* 3.5 7.6 + - - -
234D ALA* 3.5 26.7 - - + +
235D TYR* 3.6 19.1 - - + +
238D ALA* 3.8 16.6 - - + -
242D PHE* 3.7 14.4 - - + -
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Residues in contact with LEU 26 (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* 3.9 15.9 - - + -
11D VAL* 3.5 32.3 - - + -
22D LEU* 3.0 39.5 + - + +
23D SER* 3.7 4.9 - - - +
24D LEU 3.2 0.2 - - - -
25D LEU* 1.3 73.9 - - - +
27D LYS* 1.3 64.4 + - - +
29D SER* 3.0 11.4 + - - -
32D VAL* 3.5 32.6 - - + +
35D LEU* 4.0 12.8 - - + -
79D VAL* 4.9 2.9 - - + -
238D ALA* 4.7 2.2 - - + -
241D VAL* 3.8 30.5 - - + -
242D PHE* 3.9 18.2 - - + -
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Residues in contact with LYS 27 (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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161C THR* 6.0 0.4 - - - +
23D SER 2.9 18.3 + - - +
24D LEU 3.7 3.8 - - - +
26D LEU* 1.3 75.2 - - - +
28D ASN* 1.3 58.7 + - - +
29D SER 3.2 4.2 + - - +
35D LEU* 3.7 11.8 - - + +
50D LEU* 3.5 29.8 - - + +
51D SER* 4.8 3.9 + - - +
53D ILE* 3.3 32.5 + - + -
55D THR* 2.7 63.2 + - - +
57D ALA* 2.5 41.0 + - + +
59D VAL* 3.5 21.2 - - + +
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Residues in contact with ASN 28 (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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25C LEU* 3.8 24.2 - - - +
235C TYR* 3.5 31.0 - - + -
24D LEU* 2.9 42.1 + - - +
25D LEU* 3.7 10.7 - - + +
26D LEU 3.2 0.2 - - - -
27D LYS* 1.3 75.6 - - - +
29D SER* 1.3 58.0 + - - +
30D PRO* 3.9 5.7 - - - +
53D ILE* 3.8 9.0 - - - +
55D THR* 4.1 15.7 - - - +
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Residues in contact with SER 29 (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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25D LEU 3.5 1.7 + - - -
26D LEU 3.0 13.7 + - - +
27D LYS 3.2 4.4 - - - +
28D ASN* 1.3 78.0 - - - +
30D PRO* 1.3 68.4 - - - +
31D LEU* 2.9 28.5 + - - +
32D VAL* 3.2 18.6 + - - +
55D THR* 5.6 2.8 - - - -
57D ALA* 5.2 0.5 + - - +
242D PHE* 3.4 35.6 - - - -
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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