Contacts of the helix formed by residues 19 - 29 (chain D) in PDB entry 3G4C
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 ASN 19 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D GLY* 1.3 75.4 - - - +
20D ASP* 1.3 66.8 + - - +
21D LEU* 3.0 30.8 + - - +
22D SER* 2.9 21.9 + - - -
60D ILE* 3.4 12.7 - - - +
197D LYS 4.0 17.9 - - - +
198D CYS* 4.2 7.2 - - - -
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Residues in contact with ASP 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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19D ASN* 1.3 75.2 - - - +
21D LEU* 1.3 64.6 + - - +
22D SER 3.2 1.2 + - - -
23D ALA* 3.2 15.8 + - - +
24D VAL* 3.4 12.5 + - - +
45D ILE* 3.9 7.4 - - + +
60D ILE* 4.6 2.5 - - - -
197D LYS 4.8 0.3 - - - +
198D CYS* 3.2 17.3 - - - +
199D PRO* 3.3 15.6 - - - +
200D TRP* 3.1 51.6 + - + +
201D THR* 2.7 34.4 + - - -
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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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19D ASN* 3.0 17.4 + - - +
20D ASP* 1.3 77.7 - - + +
22D SER* 1.3 53.0 + - - +
23D ALA 3.2 0.2 - - - -
24D VAL* 3.5 8.5 - - + +
25D ARG* 2.7 47.9 + - + +
41D ASP* 3.5 28.7 - - + +
200D TRP* 3.8 26.7 - - + -
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Residues in contact with SER 22 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C ASP* 4.6 3.6 + - - -
159C PHE* 5.0 2.4 - - - -
18D GLY* 3.0 25.6 - - - -
19D ASN* 2.9 18.9 + - - -
21D LEU* 1.3 78.3 - - - +
23D ALA* 1.3 55.8 + - - +
25D ARG* 3.8 11.9 + - - +
26D ALA* 3.3 25.1 + - - +
56D PRO 4.8 0.7 - - - -
59D HIS* 4.0 19.2 - - - +
60D ILE* 3.9 11.4 - - - -
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Residues in contact with ALA 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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19D ASN 3.9 0.6 + - - -
20D ASP* 3.2 10.9 + - - +
22D SER* 1.3 79.4 - - - +
24D VAL* 1.3 61.3 + - + +
26D ALA* 3.4 0.5 + - - +
27D ALA* 3.0 30.1 + - - +
45D ILE* 5.2 2.0 - - + -
48D LEU* 5.0 2.7 - - + -
56D PRO* 3.5 25.1 - - + +
57D PHE* 3.7 35.2 - - + -
60D ILE* 3.8 10.0 - - + +
201D THR* 5.1 0.2 - - - +
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Residues in contact with VAL 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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20D ASP 3.4 12.5 + - - +
21D LEU* 3.2 14.3 + - + +
23D ALA* 1.3 75.7 - - - +
25D ARG* 1.3 69.9 + - + +
27D ALA* 3.3 2.4 + - - +
28D ARG* 3.2 50.9 + - - +
41D ASP* 3.7 38.6 - - + +
44D LEU* 3.9 17.7 - - + -
45D ILE* 3.7 17.7 - - + -
48D LEU* 5.4 1.1 - - + -
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Residues in contact with ARG 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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14C VAL* 3.6 31.7 + - - +
15C ASP* 5.8 2.6 + - - +
159C PHE* 4.1 11.0 - - + -
21D LEU* 2.7 33.0 + - + +
22D SER* 4.0 10.6 + - - +
24D VAL* 1.3 75.9 - - + +
26D ALA* 1.3 50.0 + - - +
28D ARG* 3.2 3.0 + - - +
29D VAL* 2.7 31.9 + - - -
30D SER* 3.2 23.7 + - - +
31D PHE* 3.2 44.8 + - + +
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Residues in contact with ALA 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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85C ASN* 3.4 20.9 - - - +
159C PHE* 3.7 18.1 - - + +
22D SER 3.3 14.3 + - - +
23D ALA 3.6 4.9 - - - +
24D VAL 3.2 0.8 - - - -
25D ARG* 1.3 77.6 - - - +
27D ALA* 1.3 62.1 + - - +
29D VAL* 3.1 14.2 + - - +
56D PRO* 4.1 3.1 - - + +
59D HIS* 3.3 40.6 - - + +
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Residues in contact with ALA 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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85C ASN* 4.4 4.9 + - - +
23D ALA 3.0 17.2 + - - +
24D VAL 3.9 4.0 - - - +
26D ALA* 1.3 75.2 - - - +
28D ARG* 1.3 58.9 + - - +
29D VAL* 4.5 4.0 - - - +
44D LEU* 4.4 10.1 - - + -
48D LEU* 3.6 32.3 - - + -
56D PRO* 3.8 15.4 - - + +
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Residues in contact with ARG 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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157C ARG* 5.2 1.9 + - - -
24D VAL* 3.2 24.8 + - - +
25D ARG* 3.8 3.4 - - - +
26D ALA 3.1 0.4 - - - -
27D ALA* 1.3 77.3 - - - +
29D VAL* 1.3 72.3 + - - +
30D SER* 4.2 15.2 - - - +
40D ARG* 3.9 20.8 + - - +
41D ASP* 2.9 28.5 + - - +
44D LEU* 3.5 29.2 - - + +
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Residues in contact with VAL 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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65C HIS* 3.7 10.4 + - - +
85C ASN* 3.7 14.1 - - + +
86C GLU 3.9 4.9 - - - +
87C LEU* 3.9 23.3 - - + +
157C ARG* 2.7 52.8 + - + +
158C PHE* 3.7 26.5 - - - -
159C PHE* 3.9 15.5 - - + -
25D ARG 2.7 10.4 + - - -
26D ALA 3.1 14.5 + - - +
27D ALA 4.5 4.3 - - - +
28D ARG* 1.3 82.8 - - - +
30D SER* 1.3 55.7 + - - +
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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