Contacts of the helix formed by residues 12 - 24 (chain B) in PDB entry 1FRP
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 THR 12 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59A ILE* 6.1 2.0 - - + -
10B ILE* 4.0 16.9 + - + +
11B VAL* 1.3 77.8 - - - +
13B LEU* 1.3 64.3 + - - +
14B THR* 3.7 5.4 + - - -
15B ARG* 3.2 23.7 + - - +
16B PHE* 2.9 24.7 + - - +
184B PHE* 4.6 1.3 - - - -
192B GLU* 3.9 33.4 + - + +
193B PHE 3.3 11.0 - - - +
194B ILE* 4.7 8.1 - - + -
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Residues in contact with LEU 13 (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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12B THR* 1.3 71.1 - - - +
14B THR* 1.3 61.6 + - - +
16B PHE* 3.3 1.5 + - + +
17B VAL* 3.0 43.2 + - + +
34B LEU 5.5 2.0 - - - +
38B CYS* 3.7 36.1 - - + -
173B LEU* 4.1 18.6 - - + -
175B LEU* 4.4 11.2 - - + -
184B PHE* 3.8 38.6 - - + -
193B PHE* 3.0 38.3 + - + +
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Residues in contact with THR 14 (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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12B THR* 3.2 6.8 + - - -
13B LEU* 1.3 75.9 - - - +
15B ARG* 1.3 61.2 + - - +
17B VAL* 3.7 1.4 + - - +
18B MET* 3.4 23.6 + - - +
35B ASN* 4.1 26.6 + - - +
38B CYS* 4.9 11.6 - - - -
192B GLU* 3.9 15.9 + - - -
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Residues in contact with ARG 15 (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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9B ASN* 5.5 2.2 - - - +
10B ILE 3.0 27.7 + - - -
11B VAL* 4.0 24.3 - - + +
12B THR* 3.2 19.5 + - - +
14B THR* 1.3 77.9 - - - +
16B PHE* 1.3 60.9 + - - +
18B MET* 3.5 4.9 + - - +
19B GLU* 3.0 43.3 + - + +
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Residues in contact with PHE 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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11B VAL* 3.8 12.8 - - + -
12B THR 2.9 17.5 + - - +
13B LEU* 3.6 6.7 - - + +
15B ARG* 1.3 78.2 - - - +
17B VAL* 1.3 72.9 + - + +
19B GLU* 3.5 6.2 + - - +
20B GLN* 3.0 59.7 + - + +
175B LEU* 4.4 7.6 - - + -
177B MET* 4.0 18.8 - - + -
179B ASN* 4.9 2.7 - - - -
182B ASN* 3.5 33.4 - - - -
184B PHE* 3.8 23.8 - + + -
195B LEU* 4.4 15.0 - - + -
198B ARG* 6.0 1.6 - - + -
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Residues in contact with VAL 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B LEU* 3.0 37.5 + - + +
14B THR 4.2 2.9 - - - +
16B PHE* 1.3 82.9 - - + +
18B MET* 1.3 59.0 + - - +
20B GLN* 3.3 3.0 + - - +
21B GLY 2.9 11.3 + - - -
31B THR* 3.9 19.5 - - + +
34B LEU* 3.9 39.0 - - + -
35B ASN* 4.3 9.2 - - - +
175B LEU* 4.7 4.7 - - + -
177B MET* 5.8 0.9 - - + -
338B AMP 2.8 38.7 + - - +
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Residues in contact with MET 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 THR 3.4 17.0 + - - +
15B ARG* 3.8 4.9 - - - +
16B PHE 3.3 0.2 - - - -
17B VAL* 1.3 75.6 - - - +
19B GLU* 1.3 65.2 + - - +
21B GLY* 3.2 2.5 + - - +
22B ARG* 3.0 58.9 + - + +
31B THR* 4.0 24.2 - - + -
35B ASN* 6.2 0.2 - - - +
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Residues in contact with GLU 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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15B ARG* 3.0 35.9 + - + +
16B PHE* 3.7 7.0 - - - +
18B MET* 1.3 76.5 - - - +
20B GLN* 1.3 56.4 + - + +
22B ARG* 2.9 37.5 + - - +
23B LYS* 3.0 55.8 + - - +
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Residues in contact with GLN 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 PHE* 3.0 51.9 + - + +
17B VAL* 3.6 3.4 - - - +
18B MET 3.2 0.2 - - - -
19B GLU* 1.3 76.4 - - - +
21B GLY* 1.3 63.1 + - - +
23B LYS* 3.4 35.1 + - - +
24B ALA* 3.1 24.8 + - - +
177B MET* 4.4 3.8 - - + -
179B ASN* 3.3 28.2 + - - +
338B AMP 3.1 22.2 + - - +
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Residues in contact with GLY 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 VAL 2.9 11.1 + - - -
18B MET 3.2 3.6 + - - -
20B GLN* 1.3 72.7 - - - +
22B ARG* 1.3 60.3 + - - +
24B ALA 3.6 0.3 + - - -
25B ARG* 3.0 5.4 + - - -
26B GLY* 2.9 31.8 + - - +
28B GLY* 6.5 0.2 - - - -
31B THR* 3.9 6.5 - - - -
338B AMP 3.2 31.8 + - - -
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Residues in contact with ARG 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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18B MET* 3.0 51.3 + - + +
19B GLU* 2.9 32.3 + - - +
20B GLN 3.2 0.2 - - - -
21B GLY* 1.3 74.5 - - - +
23B LYS* 1.3 65.0 + - + +
24B ALA 3.1 1.1 - - - -
25B ARG* 2.9 24.3 + - - +
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Residues in contact with LYS 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 GLU* 3.0 42.8 + - - +
20B GLN* 3.4 34.2 - - - +
22B ARG* 1.3 76.1 - - + +
24B ALA* 1.3 59.3 + - - +
25B ARG* 3.4 17.9 + - - +
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Residues in contact with ALA 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 GLN 3.1 17.0 + - - +
21B GLY 4.0 1.6 - - - +
22B ARG 3.1 0.8 - - - -
23B LYS* 1.3 75.8 - - - +
25B ARG* 1.3 70.5 + - - +
26B GLY* 3.5 0.9 + - - -
338B AMP 3.7 37.8 - - + +
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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