Contacts of the helix formed by residues 53 - 61 (chain B) in PDB entry 4IXU
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 GLY 53 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B ARG 3.0 10.1 + - - -
51B GLU 3.1 3.5 - - - -
52B ALA* 1.3 79.8 - - - +
54B LEU* 1.3 66.8 + - - +
55B MET 3.3 2.6 + - - -
56B LYS* 3.4 14.3 + - - +
57B ARG* 3.1 28.5 + - - +
316B VAL* 4.4 0.2 - - - -
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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
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28B VAL* 4.3 14.1 - - + -
49B ILE* 3.6 21.3 + - + +
50B ARG* 3.7 7.8 + - + +
52B ALA 3.6 0.4 - - - -
53B GLY* 1.3 75.9 - - - +
55B MET* 1.3 69.5 + - - +
57B ARG* 3.1 5.1 + - + +
58B LEU* 3.0 37.3 + - + +
114B VAL* 4.9 2.0 - - + -
116B LEU* 3.8 39.7 - - + -
316B VAL* 4.0 22.4 - - + +
319B ILE* 3.7 36.6 - - + -
320B ALA* 5.2 0.4 - - - +
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Residues in contact with MET 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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28B VAL* 3.7 37.2 - - + -
50B ARG* 4.5 19.6 + - + +
53B GLY 3.4 0.8 - - - -
54B LEU* 1.3 84.2 - - + +
56B LYS* 1.3 63.3 + - + +
58B LEU* 3.3 1.7 + - - +
59B SER* 3.0 27.9 + - - -
65B LEU* 3.4 34.5 - - + +
67B ASP* 3.7 33.9 - - + +
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Residues in contact with LYS 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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53B GLY* 3.4 13.7 + - - +
54B LEU 3.4 0.4 - - - -
55B MET* 1.3 77.3 - - + +
57B ARG* 1.3 64.5 + - + +
59B SER* 3.3 6.7 + - - -
60B SER* 3.0 31.0 + - - +
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Residues in contact with ARG 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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52B ALA 5.2 3.8 + - - +
53B GLY* 3.1 17.2 + - - +
54B LEU* 3.5 7.6 - - + +
56B LYS* 1.3 77.8 - - + +
58B LEU* 1.3 64.2 + - + +
60B SER* 3.4 7.3 + - - -
61B LEU* 3.4 25.8 + - - +
313B ASN 5.2 0.8 + - - -
316B VAL* 3.6 24.5 - - + +
317B ASP* 2.7 33.1 + - - +
320B ALA* 3.7 17.5 - - + +
325B GLN* 2.7 39.4 + - - +
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Residues in contact with LEU 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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26B VAL* 4.3 10.1 - - + -
28B VAL* 4.3 14.1 - - + -
54B LEU* 3.0 41.8 + - + +
55B MET* 3.9 3.8 - - - +
57B ARG* 1.3 74.4 - - + +
59B SER* 1.3 64.5 - - - +
61B LEU* 3.1 13.5 + - + +
63B CYS* 3.1 29.5 + - + +
65B LEU* 3.9 26.5 - - + -
114B VAL* 5.0 0.9 - - + -
319B ILE* 4.3 13.9 - - + -
320B ALA* 4.3 14.1 - - - -
323B PHE* 4.1 33.7 - - + -
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Residues in contact with SER 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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55B MET 3.0 19.0 + - - -
56B LYS* 3.7 7.3 - - - -
58B LEU* 1.3 76.2 - - - +
60B SER* 1.3 56.1 + - - +
62B GLY* 2.7 26.7 + - - -
63B CYS 3.9 12.3 + - - +
65B LEU* 3.3 15.0 - - - +
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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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56B LYS* 3.0 19.7 + - - +
57B ARG* 3.7 8.5 - - - -
58B LEU 3.2 0.2 - - - -
59B SER* 1.3 76.5 - - - +
61B LEU* 1.3 61.6 + - - +
62B GLY* 3.2 1.1 + - - -
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Residues in contact with LEU 61 (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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57B ARG 3.4 15.7 + - - +
58B LEU* 3.1 17.0 + - + +
59B SER 3.1 0.6 - - - -
60B SER* 1.3 78.0 - - - +
62B GLY* 1.3 60.0 + - - +
63B CYS* 3.5 5.6 - - - -
320B ALA* 3.3 40.2 - - + +
323B PHE* 3.9 16.4 - - + +
324B GLY 4.0 5.4 - - - +
325B GLN* 3.7 31.4 - - + +
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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