Contacts of the strand formed by residues 114 - 118 (chain B) in PDB entry 3IOT
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 SER 114 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B ALA 3.8 2.6 + - - -
113B LEU* 1.3 73.8 + - - +
115B LEU* 1.3 63.4 + - - +
116B ILE 3.8 0.7 - - - -
226B ILE* 3.5 9.2 - - - +
227B ASN 3.2 32.7 + - - +
232B TRP* 5.9 0.7 - - - -
244B VAL* 3.3 26.0 - - - -
245B THR 3.8 0.4 - - - -
247B LEU* 3.8 7.0 - - - -
320B THR* 3.7 23.5 + - - -
323B ASN* 2.9 25.2 + - - +
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Residues in contact with LEU 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B SER* 1.3 72.5 - - - +
116B ILE* 1.3 66.5 + - - +
117B TYR* 3.9 3.9 - - + -
125B PRO* 4.1 12.1 - - + -
126B PRO 4.9 7.2 - - - +
147B LEU* 4.6 3.8 - - + -
224B MET* 3.8 35.2 - - + -
225B THR 3.5 15.3 - - - +
226B ILE* 3.9 17.0 - - + -
243B GLY 3.6 1.4 - - - +
244B VAL* 3.4 2.2 - - - -
245B THR* 2.9 63.6 + - + +
246B VAL 3.7 9.4 - - - +
247B LEU* 4.0 8.4 - - + +
248B PRO* 4.2 18.8 - - + -
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Residues in contact with ILE 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B SER 4.4 0.2 - - - +
115B LEU* 1.3 73.6 - - - +
117B TYR* 1.3 62.7 + - - +
217B PHE* 3.7 24.0 - - + -
224B MET* 3.3 3.8 - - - +
225B THR* 2.7 50.1 + - + +
227B ASN* 3.7 44.6 - - + +
228B GLY 4.7 0.2 - - - +
231B ALA* 5.2 1.1 - - + -
232B TRP* 4.6 11.7 - - + +
235B ILE* 4.0 17.5 - - + -
242B TYR* 3.7 24.9 - - + -
243B GLY 3.7 4.9 - - - +
244B VAL* 4.0 14.8 - - + -
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Residues in contact with TYR 117 (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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115B LEU* 3.9 9.6 - - + -
116B ILE* 1.3 75.2 - - - +
118B ASN* 1.3 62.5 + - - +
119B LYS* 3.6 26.8 + - + +
122B LEU* 3.4 30.5 - - + -
123B PRO 4.4 4.5 + - - -
125B PRO* 3.8 43.6 - - + +
217B PHE* 3.5 7.2 - - - -
223B ALA 3.3 13.0 - - - +
224B MET* 3.6 17.3 - - + -
242B TYR* 3.4 5.4 - - - +
243B GLY* 3.0 57.0 + - - -
244B VAL 4.6 0.2 - - - -
245B THR* 3.9 14.5 - - + -
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Residues in contact with ASN 118 (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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117B TYR* 1.3 69.8 - - - +
119B LYS* 1.3 53.6 + - - +
120B ASP* 2.8 29.1 + - - +
121B LEU* 3.4 34.9 - - + +
122B LEU* 2.8 37.1 + - - +
217B PHE* 3.5 15.9 + - + -
220B GLY* 4.4 11.9 - - - -
222B THR 4.5 0.7 - - - +
223B ALA 3.0 11.7 + - - +
240B VAL* 3.4 25.2 - - + +
241B ASN 3.2 8.4 - - - +
242B TYR* 4.9 0.2 - - - -
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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
------------------------------------------------------------
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