Contacts of the helix formed by residues 40 - 50 (chain Y) in PDB entry 2J28
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 40 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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927B A 5.0 10.6 + - - +
1Y ALA* 3.4 22.7 - - + +
38Y GLU* 2.7 32.9 + - + +
39Y ASP* 1.3 73.7 - - - +
41Y PRO* 1.3 68.9 - - - +
42Y ALA* 3.1 14.3 + - - +
43Y ILE* 3.0 2.7 - - + +
44Y ARG* 2.7 36.5 + - - +
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Residues in contact with PRO 41 (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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851B C 4.0 0.7 + - - -
852B U 3.9 25.9 - - - +
39Y ASP 4.6 1.1 - - - +
40Y THR* 1.3 91.6 - - - +
42Y ALA* 1.3 61.6 + - - +
44Y ARG* 3.7 14.7 - - + +
45Y GLY* 3.2 13.0 + - - -
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Residues in contact with ALA 42 (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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851B C 2.6 49.3 + - + +
852B U 3.9 4.6 + - - -
926B G 3.6 10.8 - - - +
927B A 3.5 24.7 - - + +
1Y ALA 4.7 0.2 - - - +
40Y THR* 3.1 9.1 + - - +
41Y PRO* 1.3 74.3 - - - +
43Y ILE* 1.3 55.6 + - - +
45Y GLY 2.7 4.0 + - - -
46Y MET* 2.7 23.2 + - - +
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Residues in contact with ILE 43 (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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927B A 4.7 0.4 - - - -
1Y ALA 2.8 35.6 - - - +
2Y LYS* 3.4 10.1 - - - -
3Y THR* 3.5 22.4 - - + +
6Y ILE* 5.2 1.1 - - + -
26Y LEU* 4.3 7.6 - - + -
38Y GLU 2.8 30.1 - - - +
39Y ASP* 4.1 2.5 - - - +
40Y THR* 3.0 20.0 - - + +
42Y ALA* 1.3 76.9 - - - +
44Y ARG* 1.3 64.8 + - - +
46Y MET* 2.8 20.7 + - - -
47Y ILE* 2.9 40.8 + - + +
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Residues in contact with ARG 44 (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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39Y ASP* 2.8 44.9 + - - -
40Y THR 2.7 20.2 + - - +
41Y PRO* 3.7 16.3 - - + +
42Y ALA 3.1 0.2 - - - -
43Y ILE* 1.3 82.5 - - - +
45Y GLY* 1.3 51.1 + - - +
47Y ILE* 4.2 6.7 + - - +
48Y ASN* 2.6 36.2 + - - +
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Residues in contact with GLY 45 (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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851B C 3.6 18.3 - - - +
852B U 4.7 6.3 - - - -
41Y PRO 3.2 7.9 + - - -
42Y ALA 2.7 8.3 + - - -
44Y ARG* 1.3 76.3 - - - +
46Y MET* 1.3 57.4 + - - +
47Y ILE 3.0 2.0 - - - -
48Y ASN* 2.7 34.4 + - - +
49Y ALA* 2.9 12.8 + - - +
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Residues in contact with MET 46 (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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850B U 3.4 25.1 - - - +
851B C 3.5 32.6 + - - +
927B A 4.4 8.3 - - - +
928B A 3.7 11.9 - - + +
1Y ALA 3.5 14.1 - - - +
22Y THR* 4.3 9.6 - - - +
25Y GLY* 3.5 24.9 - - - +
26Y LEU* 3.3 37.2 - - + +
42Y ALA 2.7 9.7 + - - -
43Y ILE* 3.3 18.6 - - - +
45Y GLY* 1.3 73.7 - - - +
47Y ILE* 1.3 59.2 + - - +
49Y ALA* 3.5 3.4 + - - +
50Y VAL* 3.2 27.2 + - - +
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Residues in contact with ILE 47 (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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3Y THR* 4.0 14.8 - - + -
6Y ILE* 4.6 4.9 - - + -
26Y LEU* 5.7 8.3 - - + -
39Y ASP* 5.9 0.7 - - - +
43Y ILE* 2.9 42.2 + - + +
44Y ARG* 4.2 8.7 - - - +
46Y MET* 1.3 75.6 - - - +
48Y ASN* 1.3 57.6 + - - +
50Y VAL* 3.0 7.1 - - - -
51Y SER* 2.5 39.2 + - - -
54Y VAL* 4.5 26.9 - - + +
56Y VAL* 4.6 24.9 - - + -
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Residues in contact with ASN 48 (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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44Y ARG* 2.6 27.4 + - - +
45Y GLY* 2.7 22.9 + - - +
47Y ILE* 1.3 76.0 - - - +
49Y ALA* 1.3 60.5 + - - +
51Y SER* 3.0 22.7 - - - -
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Residues in contact with ALA 49 (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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82A U 4.6 4.5 + - - -
851B C 4.2 23.8 - - - +
19Y HIS* 4.2 20.8 - - + +
22Y THR* 4.8 7.4 - - + -
45Y GLY 2.9 9.4 + - - +
46Y MET* 3.6 10.3 - - - +
48Y ASN* 1.3 81.8 - - - +
50Y VAL* 1.3 63.1 + - + +
51Y SER* 3.2 2.4 + - - -
52Y PHE 4.9 0.2 + - - -
53Y MET* 4.5 4.3 - - - +
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Residues in contact with VAL 50 (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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19Y HIS* 4.8 9.0 - - + +
22Y THR* 2.9 29.8 - - - +
23Y LEU* 3.7 26.9 - - + -
26Y LEU* 5.3 5.2 - - + -
46Y MET 3.2 17.0 - - - +
47Y ILE* 3.0 7.4 + - - +
49Y ALA* 1.3 75.7 - - + +
51Y SER* 1.3 52.4 + - - +
52Y PHE 2.7 17.4 + - - -
53Y MET* 3.2 31.7 + - + -
54Y VAL* 3.1 32.1 + - + +
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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