Contacts of the helix formed by residues 45 - 56 (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 ASP 45 (chain y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72G ASN* 5.4 2.3 - - - +
40y PRO* 5.4 4.1 - - + +
41y ILE 4.4 3.9 - - - +
44y ILE* 1.4 81.6 - - - +
46y ALA* 1.4 64.4 + - - +
47y ALA* 3.5 5.4 - - + +
48y VAL* 3.4 28.5 - - + +
49y LEU* 3.6 5.5 + - - +
75y ALA* 3.7 7.8 - - - +
147y GLY 5.2 0.6 - - - +
148y LEU* 3.1 46.7 + - + +
149y VAL* 3.4 26.4 + - - +
156y PHE* 5.1 1.8 - - - -
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Residues in contact with ALA 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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40y PRO* 4.0 26.5 - - + +
44y ILE 4.4 0.2 + - - -
45y ASP* 1.4 71.7 - - - +
47y ALA* 1.3 58.4 + - - +
49y LEU* 3.3 4.5 + - - +
50y ALA* 2.9 30.8 + - + +
73y SER 4.8 1.0 - - - +
74y ARG* 4.4 16.8 - - + +
75y ALA* 3.7 30.3 + - - +
76y SER* 6.0 0.2 - - - +
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Residues in contact with ALA 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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45y ASP* 3.5 4.8 - - + +
46y ALA* 1.3 76.4 - - + +
48y VAL* 1.3 65.5 + - + +
50y ALA* 3.4 7.0 + - - +
51y LYS* 3.4 21.7 + - - +
148y LEU* 5.7 8.3 - - + -
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Residues in contact with VAL 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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45y ASP* 3.4 23.1 - - + +
47y ALA* 1.3 74.1 - - + +
49y LEU* 1.4 67.9 + - - +
51y LYS* 3.8 3.9 + - - +
52y LEU* 3.3 23.6 + - - +
145y MET* 3.5 29.1 - - + +
146y GLN* 3.3 31.4 + - + +
147y GLY 3.9 9.9 - - - +
148y LEU* 5.3 18.4 - - + -
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Residues in contact with LEU 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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44y ILE* 4.8 6.3 - - + -
45y ASP 3.6 8.9 + - - +
46y ALA 3.3 7.8 + - - +
47y ALA 3.3 0.4 - - - -
48y VAL* 1.4 84.4 - - - +
50y ALA* 1.4 60.8 + - - +
52y LEU* 3.1 13.6 + - + +
53y LEU* 3.1 42.1 + - + +
72y LEU* 3.4 25.4 - - + +
73y SER 4.1 1.6 - - - +
75y ALA* 3.6 32.8 - - + +
135y ILE* 5.5 8.3 - - + -
139y LEU* 3.9 36.1 - - + -
146y GLN* 3.7 6.5 - - - +
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Residues in contact with ALA 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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46y ALA* 2.9 17.6 + - + +
47y ALA* 3.6 10.3 - - - +
48y VAL 3.3 0.4 - - - -
49y LEU* 1.4 76.2 - - - +
51y LYS* 1.4 61.0 + - - +
53y LEU* 3.8 2.7 + - - +
54y GLU* 3.6 25.7 + - - +
73y SER 3.9 15.0 - - - +
74y ARG* 5.6 3.8 - - + -
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Residues in contact with LYS 51 (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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47y ALA 3.4 11.6 + - - +
48y VAL* 4.4 4.3 - - - +
50y ALA* 1.4 77.2 - - - +
52y LEU* 1.3 62.1 + - - +
54y GLU* 3.1 30.0 + - + +
55y GLN* 3.4 42.2 + - + +
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Residues in contact with LEU 52 (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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48y VAL 3.3 17.4 + - - +
49y LEU* 3.1 7.0 + - - +
51y LYS* 1.3 79.1 - - - +
53y LEU* 1.3 61.6 + - + +
55y GLN* 3.5 17.9 + - + +
56y GLN* 3.5 18.8 + - - +
57y ARG* 5.3 10.3 + - + +
139y LEU* 3.7 34.5 - - + +
143y PRO* 3.3 33.2 - - + +
144y GLY* 3.8 13.9 - - - +
146y GLN* 3.4 22.9 - - - +
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Residues in contact with LEU 53 (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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49y LEU* 3.1 38.6 + - + +
50y ALA* 4.3 3.4 - - - +
51y LYS 3.3 0.2 - - - -
52y LEU* 1.3 75.8 - - + +
54y GLU* 1.4 62.8 + - - +
55y GLN 3.4 0.2 - - - -
56y GLN* 3.8 17.7 + - - +
57y ARG* 3.9 25.4 - - - +
61y ILE* 4.3 21.3 - - + +
65y ASN* 4.8 8.7 - - - +
72y LEU* 3.4 33.0 - - + +
73y SER* 3.9 13.2 - - - +
135y ILE* 6.4 1.8 - - + -
139y LEU* 5.0 2.7 - - + -
293y TRP* 5.9 0.2 - - - +
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Residues in contact with GLU 54 (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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50y ALA* 3.6 17.1 + - - +
51y LYS* 3.1 27.9 + - + +
53y LEU* 1.4 76.5 - - - +
55y GLN* 1.3 61.7 + - + +
56y GLN* 3.6 10.9 + - - +
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Residues in contact with GLN 55 (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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51y LYS* 3.4 40.2 + - + +
52y LEU* 3.8 29.9 - - + +
53y LEU 3.4 0.2 - - - -
54y GLU* 1.3 78.6 - - + +
56y GLN* 1.3 73.3 + - - +
143y PRO 4.5 5.3 + - - -
144y GLY* 5.7 0.6 - - - -
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Residues in contact with GLN 56 (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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52y LEU* 3.5 10.4 + - - +
53y LEU* 3.8 14.3 + - - +
54y GLU 3.4 11.9 + - - +
55y GLN* 1.3 88.1 + - - +
57y ARG* 1.4 68.5 + - - +
58y GLY 3.3 22.8 - - - +
59y THR* 3.4 25.7 + - - +
61y ILE* 5.7 2.5 - - + -
62y GLU* 3.8 24.8 + - + +
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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