Contacts of the helix formed by residues 53 - 61 (chain B) in PDB entry 5IYB
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 MET 53 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49B GLU* 3.0 29.3 + - + +
52B GLN* 1.3 82.2 - - + +
54B SER* 1.3 64.4 + - - +
55B VAL 3.4 1.6 - - - -
56B GLN* 3.3 5.5 + - - +
57B ARG* 2.8 53.8 + - + +
227B ASN* 5.6 5.2 - - - +
537B GLN* 3.1 33.7 - - + +
140T ARG* 3.8 40.8 - - + +
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Residues in contact with SER 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B GLU* 3.4 19.7 + - - -
50B PHE* 3.3 28.1 + - - -
53B MET* 1.3 78.0 - - - +
55B VAL* 1.3 58.7 + - - +
57B ARG* 3.3 5.5 + - - +
58B ILE* 2.9 36.5 + - - +
227B ASN* 4.4 14.6 + - - +
230B ARG* 5.0 3.4 + - - -
397B GLY 5.1 1.6 + - - -
401B ALA* 4.2 16.9 - - - +
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Residues in contact with VAL 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B PHE* 3.0 50.6 + - + +
51B ILE* 4.3 18.8 - - + +
53B MET 3.4 0.4 - - - -
54B SER* 1.3 74.0 - - - +
56B GLN* 1.3 63.7 + - - +
58B ILE* 3.3 10.5 + - - +
59B VAL* 3.4 15.8 + - - +
91B ILE* 3.5 31.0 - - + -
124B LEU* 4.8 7.0 - - + -
152B ILE* 6.3 2.5 - - + -
404B PHE* 4.0 29.3 - - + -
141T LEU* 5.9 0.7 - - + -
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Residues in contact with GLN 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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51B ILE 4.5 2.4 + - - -
53B MET 3.3 7.7 + - - +
55B VAL* 1.3 79.4 - - - +
57B ARG* 1.3 63.6 + - - +
59B VAL* 3.4 9.6 - - - +
60B GLU* 3.1 26.3 + - - +
89B GLU 3.3 21.3 + - - -
90B GLN* 3.6 16.7 + - - +
91B ILE* 3.1 33.1 + - + +
139T VAL 4.4 2.7 - - - +
140T ARG* 3.8 24.7 - - + +
141T LEU* 3.5 30.3 + - + +
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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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53B MET* 2.8 46.2 + - + +
54B SER* 3.5 7.2 - - - +
56B GLN* 1.3 74.8 - - - +
58B ILE* 1.3 64.5 + - + +
60B GLU* 3.9 8.9 + - - +
61B ASP* 2.7 70.1 + - - +
227B ASN* 4.4 28.5 + - - +
228B SER* 6.0 2.2 - - - +
537B GLN* 5.7 0.6 + - - -
140T ARG* 4.8 11.8 - - - +
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Residues in contact with ILE 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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50B PHE* 5.9 0.2 - - + -
54B SER 2.9 24.2 + - - +
55B VAL* 3.8 4.3 - - + +
56B GLN 3.3 0.6 - - - -
57B ARG* 1.3 77.9 - - + +
59B VAL* 1.3 63.3 + - - +
61B ASP* 3.4 19.2 + - - +
63B PRO* 4.4 8.8 - - - +
227B ASN* 5.9 1.1 - - - +
230B ARG* 4.6 16.4 - - - +
401B ALA* 3.6 31.0 - - + +
404B PHE* 4.3 20.0 - - + -
405B ARG* 3.9 39.0 - - + +
408B PHE* 4.4 17.2 - - + -
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Residues in contact with VAL 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 VAL 3.4 12.3 + - - +
56B GLN* 3.4 25.8 - - - +
58B ILE* 1.3 72.7 - - - +
60B GLU* 1.3 65.6 + - - +
61B ASP 3.3 0.4 - - - -
63B PRO* 4.1 10.3 - - - +
88B PHE* 3.6 24.8 + - + +
89B GLU 3.9 10.3 - - - +
91B ILE* 4.3 19.7 - - + -
126B VAL* 4.8 6.7 - - + -
404B PHE* 4.2 11.0 - - + -
408B PHE* 3.4 44.6 - - + -
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Residues in contact with GLU 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 GLN* 3.1 31.5 + - - +
57B ARG* 4.0 9.2 + - - +
59B VAL* 1.3 78.7 - - - +
61B ASP* 1.3 67.2 + - - +
63B PRO* 4.5 1.7 - - - +
64B PRO* 6.0 0.5 - - - +
88B PHE 4.3 11.4 - - - +
89B GLU* 5.5 6.3 - - + -
138T PRO* 5.2 2.1 - - - +
139T VAL 5.1 2.1 - - - +
140T ARG* 2.7 43.5 + - - -
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Residues in contact with ASP 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* 2.7 48.4 + - - +
58B ILE* 3.4 13.0 + - - +
59B VAL 3.3 3.2 + - - -
60B GLU* 1.3 83.3 - - - +
62B ALA* 1.3 68.6 + - - +
63B PRO* 3.6 2.4 - - - +
64B PRO* 4.8 3.8 - - - +
228B SER* 4.3 8.7 - - - +
405B ARG* 4.0 19.4 + - - +
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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