Contacts of the helix formed by residues 9 - 22 (chain Y) in PDB entry 3J45
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 LYS 9 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7Y ARG 5.6 0.4 - - - +
8Y GLU* 1.4 74.7 - - - +
10Y SER* 1.3 62.9 + - - +
11Y VAL* 4.4 14.6 - - + +
12Y GLU* 3.3 43.8 + - + +
13Y GLU* 3.0 32.3 + - - +
62Y GLY* 5.4 2.0 - - - -
63Y ALA* 4.6 5.8 - - - +
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Residues in contact with SER 10 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9Y LYS* 1.3 73.0 - - - +
11Y VAL* 1.4 65.4 + - - +
13Y GLU* 3.3 23.1 + - - +
14Y LEU* 3.5 11.4 + - - +
57Y LEU* 5.0 8.3 - - - +
61Y ALA 3.2 25.1 + - - -
62Y GLY* 4.1 4.8 - - - +
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Residues in contact with VAL 11 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9Y LYS* 3.6 14.1 - - + +
10Y SER* 1.4 80.3 - - - +
12Y GLU* 1.3 63.6 + - - +
14Y LEU* 3.6 14.2 - - + +
15Y ASN* 3.4 28.6 + - - +
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Residues in contact with GLU 12 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7Y ARG* 4.5 9.3 - - - +
8Y GLU* 4.0 23.4 - - + +
9Y LYS* 3.3 43.6 + - + +
11Y VAL* 1.3 72.6 - - - +
13Y GLU* 1.3 69.3 + - - +
15Y ASN* 2.9 20.4 + - - +
16Y THR* 3.3 18.5 + - - +
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Residues in contact with GLU 13 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8Y GLU* 3.7 31.7 + - - +
9Y LYS 3.0 30.6 + - - +
10Y SER* 3.3 12.8 + - - +
12Y GLU* 1.3 78.3 - - - +
14Y LEU* 1.3 64.2 + - - +
16Y THR* 3.3 3.5 + - - -
17Y GLU* 3.3 25.5 + - - +
53Y VAL* 3.1 43.0 - - + +
56Y LEU* 3.6 23.1 - - - +
57Y LEU* 3.9 14.8 - - + +
62Y GLY* 3.8 13.0 - - - -
63Y ALA 4.4 0.3 + - - -
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Residues in contact with LEU 14 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10Y SER 3.5 10.9 + - - +
11Y VAL* 3.6 15.9 - - + +
13Y GLU* 1.3 84.6 - - - +
15Y ASN* 1.4 69.3 + - - +
16Y THR 3.4 0.2 + - - -
17Y GLU* 3.6 26.6 + - + +
18Y LEU* 3.7 20.1 - - + +
53Y VAL* 5.3 0.2 - - - -
57Y LEU* 5.9 9.2 - - + -
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Residues in contact with ASN 15 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11Y VAL* 3.4 27.6 + - - +
12Y GLU* 2.9 12.9 + - - +
14Y LEU* 1.4 83.0 - - - +
16Y THR* 1.3 63.3 + - - +
17Y GLU 3.4 0.6 + - - -
18Y LEU* 4.2 18.8 - - + +
19Y LEU* 4.0 17.5 - - - +
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Residues in contact with THR 16 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8Y GLU* 4.3 12.4 + - - +
12Y GLU* 3.3 18.0 + - - +
13Y GLU* 3.3 12.9 + - - -
15Y ASN* 1.3 79.8 - - - +
17Y GLU* 1.3 62.0 + - - +
18Y LEU 3.5 0.2 - - - -
19Y LEU* 3.6 13.3 - - + +
20Y ASN* 3.1 34.1 + - - +
53Y VAL* 6.1 0.7 - - - -
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Residues in contact with GLU 17 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5T GLU* 5.6 4.9 - - - +
13Y GLU 3.3 10.8 + - - +
14Y LEU* 4.0 24.2 - - + +
15Y ASN 3.4 0.8 - - - -
16Y THR* 1.3 75.1 - - - +
18Y LEU* 1.4 64.7 + - + +
19Y LEU 3.1 2.5 - - - -
20Y ASN* 3.5 13.0 - - - +
21Y LEU* 3.0 32.6 + - + +
50Y VAL* 3.7 17.3 - - + +
53Y VAL* 3.7 29.2 - - + +
54Y LYS* 3.5 29.3 + - - +
57Y LEU* 4.2 13.7 - - - +
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Residues in contact with LEU 18 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5T GLU* 3.7 33.9 - - - +
14Y LEU* 3.7 22.0 - - + +
15Y ASN* 4.2 22.0 - - + +
17Y GLU* 1.4 77.8 - - + +
19Y LEU* 1.4 66.4 + - + +
21Y LEU* 4.6 0.4 - - - +
22Y LEU* 3.2 30.7 + - - +
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Residues in contact with LEU 19 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15Y ASN 4.0 18.6 - - - +
16Y THR* 3.6 11.9 - - + +
18Y LEU* 1.4 80.2 - - + +
20Y ASN* 1.4 65.8 + - - +
22Y LEU 3.0 19.6 - - - +
23Y ARG 3.9 1.0 - - - +
24Y GLU* 3.3 26.2 - - + +
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Residues in contact with ASN 20 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16Y THR* 3.1 30.7 + - - +
17Y GLU* 3.2 15.5 + - - +
19Y LEU* 1.4 77.7 - - - +
21Y LEU* 1.4 63.8 + - - +
24Y GLU* 3.8 23.6 - - - +
25Y GLN* 3.4 24.6 + - - +
46Y VAL* 3.5 11.9 - - + +
49Y ASP* 4.3 11.0 + - - +
50Y VAL* 3.7 32.7 - - + +
53Y VAL* 4.9 5.3 - - - +
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Residues in contact with LEU 21 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5T GLU* 4.0 39.3 - - + +
6T ARG* 5.4 3.4 - - + -
9T LYS* 4.1 27.8 - - + +
17Y GLU* 3.0 18.1 + - + +
18Y LEU 4.6 1.1 - - - +
20Y ASN* 1.4 77.3 - - - +
22Y LEU* 1.4 68.9 + - + +
25Y GLN* 4.0 6.7 - - + +
26Y PHE* 3.4 21.7 + - - +
29Y ARG* 4.6 9.1 + - - +
50Y VAL* 4.0 23.6 - - + -
54Y LYS* 5.0 11.2 - - - +
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Residues in contact with LEU 22 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5T GLU* 4.0 35.7 - - + +
8T LEU* 3.8 27.8 - - + +
9T LYS* 4.9 2.5 - - + -
50T LEU* 4.7 15.0 - - + -
18Y LEU* 3.2 16.7 + - - +
19Y LEU* 3.0 17.0 - - - +
21Y LEU* 1.4 90.8 - - + +
23Y ARG* 1.4 68.3 + - + +
26Y PHE* 3.5 30.3 - - + -
29Y ARG* 5.1 0.2 - - - +
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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