Contacts of the helix formed by residues 101 - 106 (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 THR 101 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67T VAL 4.5 1.3 - - - +
68T LYS* 3.6 17.7 - - - +
69T GLN 3.4 15.0 - - - +
70T THR* 2.7 27.6 + - - +
99T GLU 4.4 0.4 - - - -
100T PHE* 1.3 73.4 - - - +
102T PRO* 1.4 67.8 - - - +
103T TYR* 4.6 0.7 - - + +
104T LEU* 3.0 36.3 + - + +
105T GLU* 2.8 36.2 + - - +
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Residues in contact with PRO 102 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19T PHE* 3.6 24.5 - - + -
63T ILE* 3.8 28.9 - - + -
67T VAL* 3.2 19.7 - - - +
69T GLN 3.3 11.9 - - - +
71T TYR* 3.7 8.7 - - + -
100T PHE* 3.5 37.0 - - + +
101T THR* 1.4 81.7 - - - -
103T TYR* 1.3 60.2 + - - +
106T THR* 2.9 33.4 + - - +
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Residues in contact with TYR 103 (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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19T PHE* 3.7 7.6 - + - -
67T VAL* 2.8 33.3 + - + +
68T LYS* 3.6 50.7 + - + -
101T THR* 3.3 0.8 - - + -
102T PRO* 1.3 72.4 - - - +
104T LEU* 1.3 75.1 + - + +
146T VAL* 3.7 19.4 + - + -
147T PHE* 3.3 50.3 + + - -
150T ASP* 2.4 34.4 + - - -
193T ILE* 6.0 2.0 - - + -
196T ARG* 3.1 18.4 + - - -
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Residues in contact with LEU 104 (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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101T THR* 3.0 33.2 + - + +
103T TYR* 1.3 96.4 - - + +
105T GLU* 1.4 62.5 + - + +
196T ARG* 3.3 30.1 + - + +
198T VAL 4.9 3.1 - - - +
199T ASN* 5.7 0.2 - - - +
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Residues in contact with GLU 105 (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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16T SER 4.9 0.5 - - - +
99T GLU 4.0 7.3 - - - +
100T PHE* 3.5 32.0 - - + -
101T THR* 2.8 36.8 + - - +
102T PRO 3.1 0.2 + - - -
104T LEU* 1.4 87.9 - - + +
106T THR* 1.3 70.4 + - - +
107T ASN* 3.3 1.6 + - - +
196T ARG* 4.0 0.9 - - - +
199T ASN* 3.1 18.3 + - - +
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Residues in contact with THR 106 (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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16T SER* 2.6 33.6 + - - -
18T ASN* 3.3 7.3 + - - +
19T PHE* 3.0 52.0 + - + +
100T PHE* 4.2 2.1 - - - -
102T PRO 2.9 20.8 + - - +
105T GLU* 1.3 75.3 - - - +
107T ASN* 1.3 65.9 + - - +
108T LEU* 4.4 1.9 - - + +
143T LEU* 5.8 0.2 - - + -
147T PHE* 4.6 4.7 - - + -
196T ARG* 2.9 33.3 + - - +
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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