Contacts of the helix formed by residues 17 - 29 (chain D) in PDB entry 2H63
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 GLY 17 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15D GLY 3.4 7.3 + - - -
16D VAL* 1.3 75.9 - - - +
18D ARG* 1.3 63.3 + - - -
19D ALA 3.4 2.2 - - - -
20D GLY 4.1 2.0 - - - +
21D SER* 2.8 30.4 + - - -
74D CYS 4.8 0.2 + - - -
501D NAP 3.3 38.3 + - - -
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Residues in contact with ARG 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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17D GLY* 1.3 73.5 - - - +
19D ALA* 1.3 66.5 + - - +
21D SER* 3.4 4.0 + - - -
22D VAL* 3.3 22.7 + - - +
501D NAP 2.7 45.8 + - - +
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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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18D ARG* 1.3 75.5 - - - +
20D GLY* 1.3 61.9 + - - +
22D VAL* 3.2 4.7 + - - +
23D ARG* 3.2 22.7 + - - +
74D CYS* 4.0 15.5 - - + -
97D GLU* 4.1 13.4 - - + +
251D PHE* 4.7 9.5 - - + -
501D NAP 2.6 57.4 + - + +
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Residues in contact with GLY 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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13D VAL* 4.0 6.5 - - - +
15D GLY 3.5 22.2 + - - -
16D VAL* 4.8 4.0 - - - -
17D GLY 3.5 6.1 + - - +
18D ARG 3.3 0.8 - - - -
19D ALA* 1.3 78.6 - - - +
21D SER* 1.3 62.0 + - - +
23D ARG* 3.4 4.3 + - - +
24D MET* 3.1 28.4 + - - +
74D CYS* 3.7 16.6 - - - +
501D NAP 4.3 0.4 + - - -
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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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16D VAL* 4.0 13.2 + - - +
17D GLY 2.8 23.6 + - - +
18D ARG* 3.8 5.1 - - - -
20D GLY* 1.3 73.4 - - - +
22D VAL* 1.3 66.6 + - - +
24D MET* 3.0 13.7 + - - +
25D ARG* 2.9 25.0 + - - +
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Residues in contact with VAL 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 ARG 3.3 10.7 + - - +
19D ALA* 3.2 9.4 + - - +
21D SER* 1.3 77.7 - - - +
23D ARG* 1.3 64.3 + - - +
25D ARG* 3.3 36.9 + - - +
26D ASP* 2.9 24.4 + - - +
251D PHE* 3.7 43.5 - - + -
501D NAP 6.3 0.7 - - - +
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Residues in contact with ARG 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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13D VAL* 4.3 6.5 - - + -
19D ALA 3.2 14.0 + - - +
20D GLY* 3.6 7.6 - - - +
21D SER 3.2 0.2 - - - -
22D VAL* 1.3 78.1 - - - +
24D MET* 1.3 57.5 + - - +
26D ASP* 3.3 7.1 + - - +
27D LEU* 2.9 33.7 + - - +
72D TYR* 3.7 30.0 - - + -
74D CYS* 4.0 8.1 - - - -
95D LEU* 3.9 16.4 - - - +
97D GLU* 3.1 36.3 + - - +
124D GLU* 3.7 3.0 - - - +
251D PHE* 3.0 49.8 + - - +
252D LEU* 4.9 0.2 - - - +
254D ASP* 3.1 23.8 + - - -
255D GLN* 4.0 18.5 + - - +
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Residues in contact with MET 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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13D VAL* 3.7 17.3 - - + -
16D VAL* 3.7 30.7 - - + -
20D GLY 3.1 13.0 + - - +
21D SER* 3.0 11.4 + - - +
23D ARG* 1.3 79.5 - - - +
25D ARG* 1.3 62.2 + - - +
27D LEU* 3.4 2.0 + - - +
28D ARG* 3.0 34.0 + - - +
39D LEU* 3.7 28.0 - - + +
42D PHE* 4.3 24.5 - - - -
51D ILE* 3.9 23.1 - - + -
52D ASP* 5.9 2.0 - - - +
54D VAL* 4.4 12.6 - - + -
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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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21D SER 2.9 17.1 + - - +
22D VAL* 3.3 34.6 - - - +
24D MET* 1.3 78.4 - - - +
26D ASP* 1.3 80.3 + - - +
28D ARG* 3.4 6.9 + - - +
29D ASN* 3.0 49.0 + - - +
52D ASP* 5.6 4.0 - - - +
249D ASN* 5.1 9.1 + - - +
251D PHE* 5.7 0.4 - - - +
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Residues in contact with ASP 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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22D VAL* 2.9 19.5 + - - +
23D ARG* 3.7 8.7 + - - +
25D ARG* 1.3 104.3 + - - +
27D LEU* 1.3 61.9 + - - +
29D ASN* 3.3 13.8 + - - +
31D HIS* 3.9 10.4 + - - +
34D SER* 2.9 18.7 + - - -
249D ASN* 5.1 4.3 - - - +
251D PHE* 3.7 11.1 - - - +
252D LEU* 3.2 46.7 + - + +
255D GLN* 5.0 6.1 - - - +
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Residues in contact with LEU 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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11D VAL* 4.5 10.3 - - + -
13D VAL* 4.2 13.9 - - + -
23D ARG 2.9 19.6 + - - +
24D MET 3.7 3.6 - - - +
26D ASP* 1.3 76.1 - - - +
28D ARG* 1.3 62.5 + - - +
29D ASN 3.4 7.1 + - - +
34D SER* 3.9 13.9 - - - +
37D LEU* 3.7 31.0 - - + -
38D ASN 5.1 1.1 - - - +
39D LEU* 3.7 46.9 - - + +
72D TYR* 4.2 10.5 - - + +
255D GLN* 3.4 24.4 - - - +
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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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24D MET* 3.0 23.3 + - - +
25D ARG* 3.9 4.7 - - - +
27D LEU* 1.3 77.6 - - - +
29D ASN* 1.3 62.3 + - - +
30D PRO* 4.0 1.9 - - - +
39D LEU* 4.5 8.3 - - + -
52D ASP* 3.5 43.5 - - - -
54D VAL* 3.8 19.3 - - + -
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Residues in contact with ASN 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 ARG* 3.0 41.3 + - - +
26D ASP* 3.3 13.2 + - - +
27D LEU 3.3 6.3 - - - +
28D ARG* 1.3 81.2 - - - +
30D PRO* 1.3 74.8 - - + +
31D HIS* 3.4 24.7 + - + +
34D SER* 3.6 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