Contacts of the helix formed by residues 52 - 60 (chain B) in PDB entry 4I6J
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 PRO 52 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B TYR 4.2 4.5 - - - +
51B LEU* 1.3 90.2 - - + +
53B LEU* 1.3 66.7 + - - +
54B LEU* 4.6 3.1 - - + +
55B ASP* 3.2 29.0 + - + +
56B ARG* 3.0 18.9 + - - +
128C LYS* 5.0 9.0 - - + -
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Residues in contact with LEU 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B PRO* 1.3 73.9 - - - +
54B LEU* 1.3 58.8 + - - +
56B ARG* 3.2 27.2 + - - +
57B ALA* 2.9 25.5 + - - +
70B PHE* 4.0 25.4 - - + -
76B TRP* 4.2 16.6 - - + -
79B PHE* 4.5 24.0 - - + -
98B LEU* 5.1 4.9 - - + -
160C CYS* 3.9 32.5 - - + +
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Residues in contact with LEU 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B PRO* 3.3 2.9 - - + +
53B LEU* 1.3 79.3 - - - +
55B ASP* 1.3 58.3 + - - +
57B ALA* 3.4 4.8 + - + +
58B HIS* 3.0 59.8 + - + +
157C ASN 3.9 7.9 - - - +
160C CYS* 3.5 33.2 + - + +
161C GLU* 3.7 30.3 - - + +
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Residues in contact with ASP 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B LEU* 3.9 20.3 - - + +
52B PRO* 3.2 26.1 + - + +
54B LEU* 1.3 77.7 - - - +
56B ARG* 1.3 54.8 + - - +
58B HIS* 3.4 11.4 + - - +
59B ALA* 2.8 35.6 + - - +
127C ILE* 4.5 5.9 - - + +
128C LYS* 3.1 28.0 - - - +
129C GLY* 3.2 26.9 + - - -
130C LYS 4.6 1.0 + - - +
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Residues in contact with ARG 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B PHE* 3.4 45.6 + - + +
49B LYS* 5.0 6.1 + - - +
51B LEU* 2.9 22.8 + - + +
52B PRO* 3.0 24.0 + - - +
53B LEU* 3.5 34.3 - - - +
55B ASP* 1.3 71.8 - - - +
57B ALA* 1.3 56.4 + - - +
59B ALA* 3.2 3.3 - - - +
60B SER* 2.5 38.6 + - - -
70B PHE* 3.9 11.7 - - + -
75B LEU* 4.0 41.0 + - + +
76B TRP* 6.1 0.6 - - - -
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Residues in contact with ALA 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B LEU 2.9 13.2 + - - +
54B LEU* 3.5 14.4 - - + +
55B ASP 3.3 0.2 - - - -
56B ARG* 1.3 76.0 - - - +
58B HIS* 1.3 63.8 + - - +
60B SER* 2.5 18.8 + - - -
61B GLN 3.3 4.0 + - - -
70B PHE* 3.5 14.8 - - + -
157C ASN* 3.2 40.0 + - + +
160C CYS* 4.2 14.4 - - + -
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Residues in contact with HIS 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B LEU* 3.0 50.0 + - + +
55B ASP* 3.8 10.8 - - - +
57B ALA* 1.3 72.9 - - + +
59B ALA* 1.3 59.7 + - - +
61B GLN* 2.7 33.7 + - - +
62B VAL 3.5 2.9 + - - -
129C GLY 5.7 0.9 - - - -
130C LYS 3.7 25.4 - - - +
131C THR* 5.1 1.8 - - - -
132C PRO* 3.8 32.5 - - + +
135C ILE* 4.2 7.1 - - + +
157C ASN* 5.3 7.3 - - + +
161C GLU* 5.0 7.2 - - - -
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Residues in contact with ALA 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B PHE* 3.4 24.0 - - + -
51B LEU* 4.3 9.9 - - + -
55B ASP 2.8 23.5 + - - +
56B ARG* 3.2 7.2 - - - +
58B HIS* 1.3 72.0 - - - +
60B SER* 1.3 58.4 + - - +
61B GLN 2.9 5.9 + - - -
62B VAL* 3.0 22.3 + - - +
66B TRP* 3.6 17.4 - - + +
127C ILE* 4.5 4.7 - - + -
135C ILE* 3.9 13.5 - - - +
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Residues in contact with SER 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B PHE* 3.8 7.3 - - - -
56B ARG 2.5 17.3 + - - -
57B ALA* 2.5 25.6 + - - -
59B ALA* 1.3 71.5 - - - +
61B GLN* 1.3 56.8 + - - +
62B VAL 3.4 0.4 - - - -
63B CYS 4.1 0.3 - - - +
67B ASN* 2.7 56.2 + - - +
70B PHE* 3.5 31.6 - - - -
145C PHE* 4.3 0.3 - - - -
157C ASN* 3.7 6.6 + - - -
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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