Contacts of the strand formed by residues 46 - 52 (chain T) in PDB entry 4IBL
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 LYS 46 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94L GLU* 3.7 29.5 + - + +
37T GLN* 3.1 4.2 - - - -
38T ILE* 2.9 47.9 + - + +
39T SER* 5.7 0.4 - - - +
44T ASP* 3.7 28.7 + - + +
45T TRP* 1.3 79.1 - - - +
47T SER* 1.3 66.3 + - - +
48T LYS* 5.2 0.2 - - + -
62T GLU* 3.7 31.2 - - - +
65T LYS* 5.0 7.2 - - - +
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Residues in contact with SER 47 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129H PHE* 5.6 0.9 - - - -
92L VAL* 3.8 15.6 + - - +
93L ASN* 4.5 5.5 - - - +
94L GLU* 4.4 7.4 + - - +
35T THR* 4.3 7.8 - - - +
36T VAL 3.3 7.4 - - - -
37T GLN* 3.4 24.7 + - - +
45T TRP 4.1 1.3 + - - -
46T LYS* 1.3 75.2 - - - +
48T LYS* 1.3 73.2 + - - +
50T PHE* 3.4 32.5 - - - -
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Residues in contact with LYS 48 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77L GLU* 2.8 37.4 + - - -
85L LYS* 4.6 2.4 - - - +
35T THR* 3.7 2.8 - - - +
36T VAL* 2.7 30.1 + - + +
38T ILE* 4.4 12.6 - - + -
46T LYS* 4.4 1.3 - - + +
47T SER* 1.3 86.7 - - - +
49T CYS* 1.3 71.8 + - - +
50T PHE* 3.3 10.4 + - + -
57T CYS* 3.7 16.4 - - - -
58T ASP 4.1 10.8 - - - -
59T LEU* 3.6 19.7 - - + +
61T ASP* 4.6 7.6 - - - +
62T GLU* 4.0 30.0 + - + +
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Residues in contact with CYS 49 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34T TYR 3.3 14.2 - - - +
35T THR* 3.7 2.3 - - - -
36T VAL* 4.5 3.4 - - + -
48T LYS* 1.3 76.2 - - - +
50T PHE* 1.4 71.8 + - - +
52T THR* 3.4 25.6 + - + +
56T GLU 4.4 1.8 - - - -
57T CYS* 2.2 55.4 - - + -
58T ASP 4.0 7.0 - - - -
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Residues in contact with PHE 50 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88L GLN* 3.5 29.4 - - + -
90L ILE* 3.9 24.0 - - + -
92L VAL* 3.8 16.4 - - + -
93L ASN* 3.4 42.4 - - + -
35T THR* 3.7 10.3 - - + +
47T SER* 3.4 48.0 - - - -
48T LYS* 3.3 7.4 - - + -
49T CYS* 1.4 71.8 - - - +
51T TYR* 1.3 82.2 + - + +
52T THR* 3.1 2.4 + - - -
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Residues in contact with TYR 51 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90L ILE* 4.9 6.1 - - + -
92L VAL* 3.7 38.6 - - + +
33T VAL* 3.9 32.2 - - + +
34T TYR 2.9 13.9 + - - -
35T THR* 3.0 14.8 + - - -
50T PHE* 1.3 78.9 - - + +
52T THR* 1.3 64.6 + - - +
53T THR* 3.9 2.1 + - - +
78T TYR* 4.1 21.6 - + - -
82T ASN 4.5 16.8 - - - -
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Residues in contact with THR 52 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25T TRP* 4.4 7.9 - - + -
33T VAL* 3.5 3.6 - - - -
34T TYR* 2.8 45.2 + - + +
35T THR* 5.4 0.2 - - - -
36T VAL* 5.8 0.2 - - + -
49T CYS* 3.5 32.0 - - + +
50T PHE 3.1 3.2 + - - -
51T TYR* 1.3 76.3 - - - +
53T THR* 1.3 61.4 + - - +
54T ASP* 3.1 44.2 + - + +
56T GLU 4.7 0.4 + - - +
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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