Contacts of the helix formed by residues 15 - 26 (chain B) in PDB entry 1RGQ
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 15 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12B GLN* 4.3 6.7 - - - -
14B ARG* 1.3 76.3 - - - +
16B LEU* 1.3 64.5 + - - +
17B LEU 3.4 2.2 - - - -
18B GLY* 3.3 6.9 + - - +
19B CYS* 3.0 23.2 + - - +
26C VAL* 5.9 0.2 - - - -
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Residues in contact with LEU 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B GLY* 1.3 71.8 - - - +
17B LEU* 1.3 61.0 + - - +
19B CYS* 3.4 7.8 + - + +
20B ILE* 3.2 49.0 + - + +
42B ALA* 4.3 20.0 - - + +
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Residues in contact with LEU 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B GLY 3.4 0.4 - - - -
16B LEU* 1.3 76.9 - - - +
18B GLY* 1.3 63.8 + - - +
20B ILE* 3.4 16.0 + - + +
21B ILE* 3.3 45.1 + - + +
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Residues in contact with GLY 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B ARG* 3.9 13.1 + - - -
15B GLY* 3.3 11.0 + - - -
17B LEU* 1.3 78.5 - - - +
19B CYS* 1.3 53.8 + - - +
21B ILE* 3.7 8.4 + - - +
22B THR* 2.9 34.5 + - - +
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Residues in contact with CYS 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B ARG* 4.0 5.3 - - - +
15B GLY 3.0 17.4 + - - +
16B LEU* 3.4 8.5 - - - +
17B LEU 3.2 0.2 - - - -
18B GLY* 1.3 74.7 - - - +
20B ILE* 1.3 58.6 - - - +
22B THR* 3.5 9.7 - - - +
23B SER* 3.1 28.5 + - - -
40B SER* 3.9 17.7 - - - -
42B ALA* 4.1 16.2 - - - -
24C VAL* 3.4 26.8 - - - +
26C VAL* 3.8 22.2 - - + -
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Residues in contact with ILE 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B LEU* 3.2 36.2 + - + +
17B LEU* 3.8 16.6 - - + +
18B GLY 3.4 0.2 - - - -
19B CYS* 1.3 73.2 - - - +
21B ILE* 1.3 67.3 + - + +
23B SER* 3.2 16.1 + - - -
24B LEU* 3.3 28.4 + - + +
42B ALA* 3.8 23.6 - - + -
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Residues in contact with ILE 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B LEU* 3.3 39.3 + - + +
18B GLY* 4.1 7.0 - - - +
19B CYS 3.4 0.2 - - - -
20B ILE* 1.3 79.1 - - + +
22B THR* 1.3 57.3 + - - +
23B SER 3.2 0.4 + - - -
24B LEU* 3.4 5.1 + - - +
25B THR* 3.1 40.1 + - + +
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Residues in contact with THR 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B ARG* 3.4 27.6 - - - +
18B GLY 2.9 26.2 - - - +
19B CYS* 3.5 8.7 - - - +
21B ILE* 1.3 75.2 - - - +
23B SER* 1.3 58.0 + - - +
24B LEU 3.4 0.2 - - - -
25B THR* 3.5 7.9 - - - -
26B GLY* 3.0 23.9 + - - -
27B ARG 3.1 25.1 + - - -
28B ASP* 3.9 8.1 - - - +
68B ALA* 4.0 0.7 - - - +
24C VAL* 3.5 23.5 - - + +
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Residues in contact with SER 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B CYS 3.1 17.7 + - - -
20B ILE* 3.4 10.3 - - - -
21B ILE 3.2 0.2 - - - -
22B THR* 1.3 78.2 - - - +
24B LEU* 1.3 68.4 + - - +
26B GLY* 3.9 1.6 + - - -
41B THR 4.5 13.3 + - - -
42B ALA* 5.5 1.7 - - - +
21C GLY* 3.8 8.3 - - - -
22C SER* 2.7 59.7 + - - -
24C VAL* 4.1 8.1 - - - -
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Residues in contact with LEU 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B ILE* 3.3 28.1 + - + +
21B ILE* 4.1 4.9 - - - +
23B SER* 1.3 84.4 - - - +
25B THR* 1.3 62.4 + - + +
26B GLY 3.4 0.4 + - - -
21C GLY* 4.6 14.1 - - - -
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Residues in contact with THR 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B ILE* 3.1 29.4 + - + +
22B THR* 3.5 8.1 - - - -
24B LEU* 1.3 77.7 - - + +
26B GLY* 1.3 62.5 + - - +
27B ARG* 3.1 27.2 + - - +
73B PRO* 4.3 10.2 - - - +
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Residues in contact with GLY 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B THR 3.0 16.3 + - - -
23B SER 3.9 0.6 + - - -
24B LEU 3.4 2.2 - - - -
25B THR* 1.3 76.9 - - - +
27B ARG* 1.3 57.2 + - - +
68B ALA* 3.5 17.3 - - - -
69B SER 3.7 0.2 + - - -
72B GLY 3.1 26.5 - - - +
73B PRO* 3.3 17.3 - - - -
22C SER* 4.0 14.6 - - - -
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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