Contacts of the helix formed by residues 13 - 25 (chain D) in PDB entry 2RCY
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 13 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11D GLY 3.7 2.4 - - - -
12D LEU* 1.3 79.6 - - - +
14D GLN* 1.3 58.0 + - - -
15D MSE 3.5 1.8 - - - -
16D GLY* 4.1 5.2 - - - +
17D SER* 2.6 29.6 + - - -
42D LYS* 4.8 4.0 - - - -
65D ALA 5.2 0.4 + - - -
264D NAP 3.2 36.4 + - - -
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Residues in contact with GLN 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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13D GLY* 1.3 73.7 - - - -
15D MSE 1.3 58.7 + - - +
17D SER* 3.5 6.5 + - - -
18D ALA* 3.4 20.3 - - - +
116D THR* 4.1 10.6 - - + +
264D NAP 3.0 37.7 + - - +
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Residues in contact with MSE 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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14D GLN* 1.3 75.2 - - - +
16D GLY* 1.3 67.2 + - - +
17D SER 3.3 0.4 - - - -
18D ALA* 3.4 4.2 + - + -
19D LEU* 3.0 30.2 + - + +
90D ILE* 3.7 20.4 - - + -
114D PRO* 3.9 15.0 - - + -
115D ASN* 3.6 35.7 - - - +
116D THR* 3.8 4.9 - - - -
118D CYS* 3.6 18.4 - - - -
264D NAP 2.8 70.8 + - + +
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Residues in contact with GLY 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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9D PHE* 4.1 5.2 - - - -
11D GLY 3.7 20.4 - - - -
12D LEU* 3.5 11.1 - - - +
13D GLY 4.0 4.4 + - - +
15D MSE 1.3 79.9 - - - +
17D SER* 1.3 55.4 + - - +
19D LEU* 4.0 3.4 - - - +
20D ALA* 3.0 30.5 + - - +
65D ALA* 4.0 16.0 + - - +
90D ILE* 5.1 0.4 - - - -
264D NAP 4.1 2.4 + - - -
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Residues in contact with SER 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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12D LEU* 3.7 28.4 - - - +
13D GLY 2.6 25.3 + - - -
14D GLN* 3.5 7.6 + - - -
16D GLY* 1.3 71.5 - - - +
18D ALA* 1.3 65.1 + - - +
21D HIS* 2.8 52.8 + - - +
42D LYS* 6.0 0.7 - - - -
119D LEU* 4.9 0.7 - - - -
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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 GLN 3.4 18.6 + - - +
15D MSE 3.4 14.3 + - + +
17D SER* 1.3 80.7 + - - +
19D LEU* 1.3 56.5 + - - +
22D GLY 3.2 18.5 + - - -
116D THR* 4.0 26.5 - - + +
118D CYS* 3.4 12.0 - - - -
119D LEU* 3.6 25.5 - - + +
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Residues in contact with LEU 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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9D PHE* 3.7 21.1 - - + -
15D MSE 3.0 20.7 + - + +
16D GLY* 4.0 2.5 - - - +
18D ALA* 1.3 75.2 - - - +
20D ALA* 1.3 64.4 + - - +
22D GLY* 3.2 1.4 + - - -
23D ILE* 3.2 38.0 + - + +
63D VAL* 4.2 15.7 - - + -
90D ILE* 4.2 22.2 - - + -
114D PRO* 4.1 7.0 - - + -
118D CYS* 3.7 11.6 - - + -
125D PHE* 3.8 22.0 - - + -
145D PHE* 3.6 33.4 - - + -
148D CYS* 5.1 0.8 - - - -
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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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9D PHE* 3.7 34.2 - - + -
12D LEU* 4.0 13.7 - - + -
16D GLY 3.0 20.3 + - - +
17D SER 3.9 2.2 - - - +
19D LEU* 1.3 75.7 - - - +
21D HIS* 1.3 65.0 + - + +
23D ILE* 3.6 2.8 + - - +
24D ALA* 3.0 28.3 + - - +
46D LEU* 5.4 8.7 - - + -
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Residues in contact with HIS 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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12D LEU* 4.6 0.8 - - + +
17D SER* 2.8 38.9 + - - +
20D ALA* 1.3 78.8 - - + +
22D GLY* 1.3 58.8 + - - +
23D ILE 3.4 0.2 - - - -
24D ALA* 3.8 8.2 - - + +
25D ASN* 3.1 41.0 + - - +
44D THR* 2.8 41.4 + - - -
45D THR* 4.4 5.5 + - - -
46D LEU* 5.8 0.7 - - + -
119D LEU* 3.7 24.0 - - + +
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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 ALA 3.2 12.6 + - - -
19D LEU 3.2 4.8 + - - -
21D HIS* 1.3 77.5 - - - +
23D ILE* 1.3 59.9 + - - +
25D ASN* 3.8 4.2 + - - +
26D ALA* 3.5 14.7 + - - +
118D CYS 3.3 25.6 - - - -
119D LEU* 4.4 5.4 - - - +
121D GLY* 5.5 1.2 - - - -
148D CYS* 3.4 19.9 - - - +
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Residues in contact with ILE 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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7D LEU* 4.3 18.8 - - + -
9D PHE* 3.7 25.6 - - + -
19D LEU* 3.2 29.5 + - + +
20D ALA 4.1 2.2 - - - +
22D GLY* 1.3 73.9 - - - +
24D ALA* 1.3 64.7 + - - +
26D ALA* 3.2 17.6 + - - +
27D ASN* 3.5 6.2 + - - -
28D ILE* 3.9 30.1 + - + +
29D ILE* 5.2 7.3 + - + +
144D ILE* 3.8 26.2 - - + +
145D PHE* 4.8 2.0 - - + -
148D CYS* 3.9 18.6 - - - -
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Residues in contact with ALA 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 ALA 3.0 19.4 + - - +
21D HIS* 3.9 10.3 - - + +
22D GLY 3.4 0.2 - - - -
23D ILE* 1.3 77.6 - - - +
25D ASN* 1.3 64.2 + - - +
26D ALA 3.2 0.6 + - - -
27D ASN* 3.5 20.1 + - - +
29D ILE 6.0 1.8 - - - -
45D THR* 5.9 7.4 - - - -
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Residues in contact with ASN 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 HIS* 3.1 24.6 + - - +
22D GLY* 4.2 5.4 - - - +
23D ILE 3.3 0.4 - - - -
24D ALA* 1.3 78.4 - - - +
26D ALA* 1.3 60.0 + - - +
27D ASN* 3.4 9.2 + - - +
119D LEU* 4.1 15.9 + - - +
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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