Contacts of the helix formed by residues 45 - 54 (chain X) 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 GLN 45 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96B C 5.3 4.7 + - - +
97B C 6.4 1.6 - - - -
41X HIS* 2.9 38.8 + - + +
43X LEU* 2.5 41.7 + - - +
44X LYS* 1.3 98.0 + - - +
46X VAL* 1.3 66.8 + - + +
47X ARG 3.6 0.2 - - - -
48X ARG* 3.9 6.8 + - - +
49X ASP* 3.2 25.1 + - - +
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Residues in contact with VAL 46 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17X GLU* 3.9 25.1 - - + +
21X LEU 4.8 6.1 - - - +
22X LEU* 3.8 28.9 - - + -
43X LEU 5.7 1.1 - - - +
44X LYS* 4.3 0.6 - - - +
45X GLN* 1.3 83.5 - - + +
47X ARG* 1.3 62.0 + - + +
48X ARG 3.2 0.2 - - - -
49X ASP* 2.9 11.8 + - + +
50X VAL* 2.8 29.5 + - + +
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Residues in contact with ARG 47 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B U 4.5 1.0 - - - +
73B A 4.1 13.0 + - - +
9T LYS* 3.3 38.0 - - - +
18X LEU* 3.0 34.2 - - - +
22X LEU* 3.1 16.3 - - + +
25X GLN* 3.2 29.1 - - - +
44X LYS* 3.3 44.4 - - + +
45X GLN 3.6 0.4 - - - -
46X VAL* 1.3 74.4 - - + +
48X ARG* 1.3 66.1 + - - +
50X VAL* 3.0 31.5 + - - +
51X ALA 3.9 2.1 + - - -
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Residues in contact with ARG 48 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B G 6.0 0.2 + - - -
61B C 5.4 4.8 + - - -
73B A 4.3 10.5 - - - +
74B A 5.3 12.3 + - - -
75B G 4.4 25.5 + - - +
76B C 4.1 30.6 + - - +
87B U 5.5 4.8 + - - -
104B A 5.7 3.0 + - - -
44X LYS* 3.8 34.0 + - + +
45X GLN* 4.0 9.0 - - - +
46X VAL 3.2 0.2 - - - -
47X ARG* 1.3 79.4 - - - +
49X ASP* 1.3 59.7 + - - +
51X ALA* 3.6 16.1 + - - +
52X ARG* 4.0 11.0 - - - +
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Residues in contact with ASP 49 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1X MET 3.5 24.2 + - - +
6X LEU* 5.8 0.2 - - - +
17X GLU* 4.1 17.4 - - - +
45X GLN 3.2 17.1 + - - +
46X VAL* 2.9 18.6 + - - +
48X ARG* 1.3 75.6 - - - +
50X VAL* 1.3 53.7 + - - +
51X ALA 2.5 25.4 - - - +
52X ARG* 3.8 15.3 - - - +
53X VAL* 3.4 8.1 - - - +
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Residues in contact with VAL 50 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B U 4.9 14.6 - - - -
15X ASN* 4.5 12.0 - - - +
17X GLU* 4.4 11.2 - - + -
18X LEU* 4.3 18.8 - - + -
46X VAL* 2.8 22.4 + - + +
47X ARG* 3.0 39.9 + - - +
49X ASP* 1.3 73.0 + - - +
51X ALA* 1.3 66.1 + - - +
53X VAL* 2.9 16.5 - - - +
54X LYS* 2.9 24.5 - - + +
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Residues in contact with ALA 51 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B U 3.3 41.2 + - - +
73B A 5.3 0.9 - - - +
76B C 3.8 12.3 - - - +
47X ARG 3.9 1.6 + - - -
48X ARG 3.6 12.2 + - - +
49X ASP 2.5 20.5 - - - +
50X VAL* 1.3 79.3 - - - +
52X ARG* 1.3 57.5 + - - +
53X VAL 2.3 21.7 + - - -
54X LYS* 3.3 13.0 - - - -
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Residues in contact with ARG 52 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B C 3.3 33.4 + - - +
77B G 2.6 37.5 + - - -
1X MET 5.1 1.1 - - - -
2X LYS 2.8 29.5 + - - -
3X ALA* 3.6 17.4 - - - +
6X LEU* 3.7 13.6 - - + +
48X ARG* 4.0 11.3 + - - +
49X ASP* 3.8 27.6 - - - +
51X ALA* 1.3 73.9 - - - +
53X VAL* 1.3 56.9 + - - +
54X LYS 3.1 0.4 - - - -
55X THR* 2.7 48.4 + - - +
56X LEU* 3.0 13.5 - - - +
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Residues in contact with VAL 53 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1X MET 4.7 3.8 - - - +
6X LEU* 3.6 24.0 - - + +
14X LEU* 4.7 17.0 - - + -
15X ASN* 4.1 32.1 - - + +
17X GLU* 4.4 11.0 - - - +
49X ASP* 3.4 13.9 - - - +
50X VAL* 2.9 28.5 - - - +
51X ALA 2.3 21.1 + - - +
52X ARG* 1.3 67.0 - - - +
54X LYS* 1.3 53.4 + - - +
55X THR 2.7 20.1 - - - +
56X LEU* 4.3 3.0 - - - +
57X LEU* 4.4 5.5 + - - +
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Residues in contact with LYS 54 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B U 3.4 63.9 + - + +
4T GLU* 6.0 1.1 + - - -
15X ASN* 4.5 21.8 - - - +
50X VAL* 2.9 25.1 - - + +
51X ALA* 3.4 11.7 - - - -
53X VAL* 1.3 81.9 - - - +
55X THR* 1.3 58.5 + - - +
57X LEU* 3.9 21.2 - - - +
58X ASN 5.4 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