Contacts of the helix formed by residues 14 - 22 (chain B) in PDB entry 3FA9
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 ASN 14 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B GLU* 1.3 89.6 + - - +
15B PHE* 1.3 66.4 + - - +
16B GLU 3.4 2.0 - - - -
17B GLU* 3.7 24.9 - - + +
18B LEU* 3.0 22.9 + - - +
128B VAL* 4.6 8.6 - - + +
129B VAL 3.1 27.8 + - - +
130B CYS* 3.7 2.4 - - - +
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Residues in contact with PHE 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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12B SER* 4.5 4.5 - - - +
13B GLU 3.3 2.8 - - - -
14B ASN* 1.3 78.7 - - - +
16B GLU* 1.3 65.5 + - - +
18B LEU* 3.2 15.8 + - + +
19B LEU* 3.3 27.2 + - + +
32B ALA* 4.1 19.1 - - + -
33B VAL* 4.3 11.2 - - + -
36B ALA* 3.9 25.8 - - + -
76B VAL* 4.2 23.6 - - + -
123B MET* 4.4 4.5 - - + -
130B CYS* 3.6 18.6 - - - -
132B LYS* 3.6 18.8 - - - -
138B ACT 3.5 29.6 - - + +
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Residues in contact with GLU 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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14B ASN 3.4 0.2 - - - -
15B PHE* 1.3 82.3 - - - +
17B GLU* 1.3 57.4 + - - +
19B LEU* 3.2 8.8 + - - +
20B LYS* 2.9 26.8 + - + +
26B VAL* 4.3 0.2 - - - +
29B ARG* 2.9 45.4 + - + +
30B LYS* 2.9 41.1 + - - -
33B VAL* 4.0 19.9 - - + +
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Residues in contact with GLU 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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14B ASN* 3.4 27.6 + - - +
15B PHE 3.3 0.6 - - - -
16B GLU* 1.3 77.4 - - - +
18B LEU* 1.3 63.2 + - - +
20B LYS* 3.2 23.0 + - - +
21B VAL* 3.0 42.8 + - + +
128B VAL* 4.0 17.7 - - + +
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Residues in contact with LEU 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 ASN 3.0 13.2 + - - +
15B PHE* 3.2 11.2 - - + +
17B GLU* 1.3 77.9 - - - +
19B LEU* 1.3 61.9 + - - +
21B VAL* 3.3 14.1 - - - +
22B LEU* 3.2 24.2 - - + +
76B VAL* 3.9 21.5 - - + -
123B MET* 3.8 35.0 - - + +
124B THR 4.0 1.8 - - - -
125B ALA* 3.7 39.3 - - + +
128B VAL* 3.8 17.9 - - + +
130B CYS* 3.7 21.3 - - + -
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Residues in contact with LEU 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 PHE* 3.3 26.2 + - + +
16B GLU* 3.2 10.2 + - - +
18B LEU* 1.3 80.2 - - + +
20B LYS* 1.3 63.0 + - - +
22B LEU* 3.1 9.5 + - - +
24B VAL* 3.0 47.4 + - + +
29B ARG* 3.9 21.5 - - + +
32B ALA* 3.6 30.3 - - + -
76B VAL* 3.9 45.1 - - + +
77B ASP* 4.5 1.8 - - + -
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Residues in contact with LYS 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 GLU* 2.9 17.2 + - + +
17B GLU* 3.4 29.8 - - - +
18B LEU 3.2 0.2 - - - -
19B LEU* 1.3 78.4 - - - +
21B VAL* 1.3 58.7 + - + +
23B GLY* 3.2 18.2 + - - -
24B VAL 4.2 1.7 + - - +
29B ARG* 3.5 44.8 + - - +
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Residues in contact with VAL 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 GLU* 3.0 28.5 + - - +
18B LEU* 3.3 15.0 - - - +
20B LYS* 1.3 76.9 - - + +
22B LEU* 1.3 57.2 + - - +
23B GLY 3.3 2.1 + - - -
105B PRO* 5.2 4.9 - - - +
125B ALA* 4.3 18.4 - - + +
126B ASP* 5.4 6.3 - - + +
127B ASP* 5.6 2.5 - - - +
128B VAL* 3.5 37.9 - - + -
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Residues in contact with LEU 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 LEU* 3.2 20.4 + - + +
19B LEU* 3.1 10.6 + - - +
21B VAL* 1.3 77.5 - - - +
23B GLY* 1.3 60.1 + - - +
24B VAL* 3.4 1.2 + - - +
76B VAL* 3.4 32.3 - - + -
77B ASP* 4.1 20.3 - - + +
79B ARG* 3.8 31.0 + - - +
105B PRO* 3.8 27.4 - - + -
107B THR* 4.0 7.2 - - + -
125B ALA* 3.6 30.7 - - + -
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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