Contacts of the helix formed by residues 15 - 27 (chain D) in PDB entry 2R6C
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 GLU 15 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16D ALA* 1.3 68.5 + - - +
17D GLU* 3.1 10.5 - - - +
18D GLN* 3.2 33.1 + - - +
19D ALA* 3.2 10.4 + - - +
105D TYR* 5.7 0.2 - - - -
534H LEU* 4.8 18.3 - - - +
535H LEU* 4.6 22.2 - - + +
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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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15D GLU* 1.3 77.3 - - - +
17D GLU* 1.3 65.7 + - - +
19D ALA* 3.2 11.5 + - - +
20D VAL* 3.2 19.1 + - - +
105D TYR* 3.6 35.5 - - + +
108D ILE* 3.8 31.0 - - + -
109D VAL* 4.1 4.9 - - + -
535H LEU* 4.8 5.9 - - + +
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Residues in contact with GLU 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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15D GLU 3.1 6.6 - - - +
16D ALA* 1.3 78.7 - - - +
18D GLN* 1.3 61.5 + - - +
20D VAL* 3.3 5.0 + - - +
21D LEU* 3.2 26.0 + - - +
42D ASP 4.3 0.3 - - - +
43D PHE* 3.3 25.6 - - + -
44D TYR* 2.4 37.7 + - - +
45D ARG* 3.6 14.4 + - - +
48D HIS* 2.8 40.4 + - + +
109D VAL* 3.7 22.7 - - + +
116D ARG* 5.4 0.2 + - - -
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Residues in contact with GLN 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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15D GLU* 3.2 25.3 + - - +
17D GLU* 1.3 73.9 - - + +
19D ALA* 1.3 59.2 + - - +
21D LEU* 4.6 1.1 - - - -
22D GLY* 2.8 26.0 + - - -
45D ARG* 4.7 7.5 - - - +
48D HIS* 3.9 9.4 - - + -
88D TYR* 3.2 31.8 + - - +
92D LEU* 3.6 25.6 - - + +
96D VAL* 3.9 4.9 - - - +
456H LEU* 3.3 36.4 - - + +
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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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15D GLU 3.2 10.1 + - - +
16D ALA 3.3 9.9 - - - +
17D GLU 3.2 0.4 - - - -
18D GLN* 1.3 75.1 - - - +
20D VAL* 1.3 59.9 + - - +
22D GLY* 3.6 0.2 - - - -
23D ALA* 2.8 32.8 + - - +
96D VAL* 3.8 15.3 - - + +
102D VAL* 5.9 0.4 - - - -
105D TYR* 3.6 40.6 - - + -
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Residues in contact with VAL 20 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16D ALA 3.2 15.5 + - - +
17D GLU 3.7 5.2 - - - +
19D ALA* 1.3 71.8 - - - +
21D LEU* 1.3 67.6 - - - +
23D ALA* 3.0 13.2 + - - +
24D VAL* 3.0 14.5 + - + +
34D ALA* 3.6 31.6 - - + -
38D LEU* 4.5 11.4 - - + -
43D PHE* 4.4 4.9 - - + -
52D PHE* 4.2 14.4 - - + -
102D VAL* 4.0 14.4 - - + +
105D TYR* 3.8 9.0 - - + +
106D ALA* 3.7 28.9 - - + +
109D VAL* 4.7 2.2 - - + -
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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 GLU 3.2 12.0 + - - +
18D GLN 4.0 3.6 - - - +
20D VAL* 1.3 79.0 - - - +
22D GLY* 1.3 65.3 + - - +
24D VAL* 3.3 10.2 + - - +
25D PHE* 3.4 19.0 + - + -
43D PHE* 4.1 7.4 - - + -
48D HIS* 3.5 48.2 - - + +
51D ILE* 3.8 20.9 - - + -
52D PHE* 4.0 17.7 - - + +
55D MET* 3.7 27.1 - - + +
92D LEU* 4.1 25.6 - - + -
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Residues in contact with GLY 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 GLN 2.8 20.9 + - - -
21D LEU* 1.3 75.2 - - - +
23D ALA* 1.3 56.8 + - - +
25D PHE* 2.9 25.4 + - - +
26D LEU* 3.2 9.9 + - - +
92D LEU* 3.7 20.4 - - - +
93D ALA* 4.7 2.3 - - - -
96D VAL* 3.6 19.5 - - - +
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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 ALA 2.8 20.9 + - - +
20D VAL 3.6 3.6 - - - +
22D GLY* 1.3 68.0 - - - +
24D VAL* 1.3 61.4 + - - +
26D LEU* 3.1 6.6 + - - +
27D ASP 2.9 25.5 + - - -
30D ALA* 3.3 8.8 - - + +
96D VAL* 3.8 9.0 - - + +
98D THR 4.2 5.4 - - - +
99D ALA* 3.7 22.6 - - + +
102D VAL* 3.7 23.1 - - + +
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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 VAL* 3.0 16.5 + - + +
21D LEU 3.5 8.5 - - - +
23D ALA* 1.3 71.8 - - - +
25D PHE* 1.3 63.9 + - + +
26D LEU 3.0 5.1 + - - -
28D PRO* 2.8 34.5 - - + +
30D ALA* 4.0 8.7 - - + -
31D LEU* 3.8 34.3 - - + +
34D ALA* 4.8 6.3 - - + -
55D MET* 3.5 48.2 - - + -
65D VAL* 4.2 14.3 - - + +
102D VAL* 5.4 0.2 - - + -
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Residues in contact with PHE 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 LEU 3.4 19.7 + - - -
22D GLY 2.9 9.2 + - - +
24D VAL* 1.3 78.5 - - + +
26D LEU* 1.3 61.0 + - - +
28D PRO* 5.0 2.1 - - - +
51D ILE* 4.9 7.4 - - + -
55D MET* 5.2 5.4 - - - -
65D VAL 5.6 0.2 - - - -
66D ASP* 4.2 11.1 - - - +
67D LEU* 3.5 43.8 + - + +
70D VAL* 4.0 23.3 - - + -
89D LEU* 3.4 54.3 - - + -
92D LEU* 4.4 8.5 - - + -
93D ALA* 4.0 25.1 - - + -
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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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22D GLY 3.2 5.9 + - - +
23D ALA* 3.1 13.4 + - - +
24D VAL 3.0 2.0 - - - -
25D PHE* 1.3 84.8 - - - +
27D ASP* 1.3 61.7 + - - +
28D PRO* 3.9 1.4 - - - +
93D ALA 5.1 7.4 - - - +
96D VAL* 4.2 21.5 - - + +
97D PRO 4.5 3.1 - - - +
98D THR* 4.1 31.2 - - - +
99D ALA* 4.2 6.1 - - + +
551H HIS* 5.6 4.3 - - + +
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Residues in contact with ASP 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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23D ALA 2.9 9.9 + - - -
26D LEU* 1.3 73.5 - - - +
28D PRO* 1.3 64.0 - - + +
29D ALA* 3.0 15.3 + - - +
30D ALA* 3.7 23.3 + - + +
99D ALA* 3.9 23.8 - - + +
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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