Contacts of the helix formed by residues 17 - 30 (chain F) in PDB entry 5L5H
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 17 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7F SER 4.5 1.4 - - - +
8F ASN* 3.4 16.2 + - - +
9F SER* 3.5 28.3 + - - +
10F VAL 3.8 11.1 + - - +
11F PHE* 5.6 6.5 - - + -
16F ARG* 1.3 71.9 - - - +
18F PHE* 1.3 64.7 + - - +
19F GLN* 3.7 8.5 + - - +
20F VAL* 3.0 41.6 + - + +
21F GLU* 3.3 13.9 + - - +
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Residues in contact with PHE 18 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4F TYR* 4.7 5.0 + - + +
5F ASP* 3.5 33.4 - - + -
10F VAL 4.7 2.4 + - - -
12F SER* 3.5 35.7 - - - -
14F ASP* 4.1 6.3 - - - -
16F ARG* 3.5 40.3 + - + -
17F ASN* 1.3 72.8 + - - +
19F GLN* 1.3 57.2 + - - +
21F GLU* 3.1 13.3 + - - +
22F TYR* 2.8 59.3 + + + -
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Residues in contact with GLN 19 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10E VAL 4.1 6.9 + - - -
11E THR* 3.8 14.4 - - - +
12E PHE* 3.2 54.7 - - - +
4F TYR 5.6 0.4 + - - -
5F ASP* 3.0 25.4 - - - +
6F LEU 4.8 0.9 - - - -
7F SER 3.7 6.0 + - - +
8F ASN* 3.6 38.7 - - + +
17F ASN* 3.2 10.8 + - - +
18F PHE* 1.3 78.8 - - - +
20F VAL* 1.3 56.6 + - - +
22F TYR* 3.4 8.6 + - - +
23F ALA* 3.0 25.5 + - - +
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Residues in contact with VAL 20 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8F ASN* 4.4 6.1 - - - +
17F ASN* 3.0 38.3 + - + +
19F GLN* 1.3 75.8 - - - +
21F GLU* 1.3 64.8 + - + +
23F ALA* 3.2 10.6 + - + +
24F VAL* 3.1 27.5 + - + +
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Residues in contact with GLU 21 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16F ARG* 2.8 60.1 + - - +
17F ASN 3.3 9.2 + - - +
18F PHE* 3.1 19.3 + - - +
20F VAL* 1.3 80.3 - - + +
22F TYR* 1.3 64.8 + - + +
24F VAL* 3.4 23.0 + - + +
25F LYS* 3.5 15.1 + - - +
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Residues in contact with TYR 22 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5E TYR* 4.2 3.1 - + - -
12E PHE* 3.9 8.3 - - + -
13E SER 3.4 25.1 - - - +
14E PRO* 3.7 36.1 - - + +
16E GLY* 3.2 22.6 - - - -
5F ASP* 2.6 51.0 + - + +
18F PHE* 2.8 39.4 + + - +
19F GLN* 3.7 21.1 - - - +
21F GLU* 1.3 78.3 - - + +
23F ALA* 1.3 64.3 + - - +
25F LYS* 3.2 15.6 + - + +
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Residues in contact with ALA 23 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12E PHE* 3.7 30.0 - - + -
19F GLN 3.0 13.6 + - - +
20F VAL* 3.2 15.2 + - + +
22F TYR* 1.3 74.1 - - - +
24F VAL* 1.3 63.7 + - + +
26F ALA* 3.2 14.6 + - - +
27F VAL* 3.3 16.2 + - + +
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Residues in contact with VAL 24 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20F VAL* 3.1 20.4 + - + +
21F GLU* 3.4 15.0 - - + +
22F TYR 3.2 0.2 - - - -
23F ALA* 1.3 76.8 - - + +
25F LYS* 1.3 58.3 + - + +
27F VAL* 3.0 14.3 + - + +
28F GLU* 2.9 50.1 + - + +
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Residues in contact with LYS 25 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14E PRO 3.6 19.5 - - - +
15E THR* 3.7 24.6 - - - +
21F GLU 3.5 15.7 + - - +
22F TYR* 3.4 11.4 - - + +
23F ALA 3.2 0.8 - - - -
24F VAL* 1.3 78.3 - - + +
26F ALA* 1.3 57.1 + - - +
28F GLU* 3.4 26.3 + - - +
29F ASN* 3.1 26.7 + - - +
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Residues in contact with ALA 26 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12E PHE* 4.1 16.6 - - + -
15E THR 5.0 0.4 - - - -
16E GLY* 3.4 25.5 - - - +
22F TYR 3.6 2.2 + - - -
23F ALA 3.2 11.7 + - - +
25F LYS* 1.3 75.0 - - - +
27F VAL* 1.3 64.2 + - + +
29F ASN* 3.4 14.8 + - - +
30F GLY* 3.5 8.7 + - - -
76F GLY* 3.6 12.2 - - - -
77F LEU* 4.4 18.4 - - + +
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Residues in contact with VAL 27 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23F ALA 3.5 15.0 - - - +
24F VAL* 3.0 16.3 + - + +
26F ALA* 1.3 75.4 - - + +
28F GLU* 1.3 67.7 + - + +
29F ASN 3.1 0.2 - - - -
30F GLY* 3.0 17.3 + - - +
75F SER* 3.7 30.9 - - - +
76F GLY* 4.0 8.1 - - - -
77F LEU 6.0 0.2 - - - +
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Residues in contact with GLU 28 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24F VAL* 2.9 37.1 + - + +
25F LYS* 3.8 32.0 + - - +
26F ALA 3.4 0.2 - - - -
27F VAL* 1.3 78.7 - - + +
29F ASN* 1.3 60.4 + - - +
30F GLY 3.6 5.2 + - - +
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Residues in contact with ASN 29 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15E THR 5.7 2.9 - - - +
25F LYS 3.1 16.7 + - - +
26F ALA* 3.5 10.5 - - - +
27F VAL 3.1 0.4 - - - -
28F GLU* 1.3 77.4 - - - +
30F GLY* 1.3 61.5 + - - +
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Residues in contact with GLY 30 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26F ALA 3.5 2.8 + - - -
27F VAL 3.0 14.9 + - - +
28F GLU 3.9 6.1 - - - +
29F ASN* 1.3 83.6 - - - +
31F THR* 1.3 69.0 + - - +
32F THR* 5.3 0.3 + - - -
76F GLY* 4.0 20.6 - - - -
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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