Contacts of the strand formed by residues 111 - 116 (chain B) in PDB entry 1YTB
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 111 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B ARG* 3.5 6.6 - - - +
106B ILE* 3.4 18.5 + - - +
109B PRO* 3.0 17.0 + - + +
110B LYS* 1.3 84.3 - - - +
112B THR* 1.3 63.0 + - - +
123B VAL* 4.3 6.7 - - + -
124B THR 3.4 14.8 - - - +
125B GLY* 4.7 1.6 - - - -
126B ALA* 3.7 24.7 - - + +
135B ALA* 3.4 19.0 - - + +
139B TYR* 2.8 38.1 + - - -
24D A 5.9 0.4 - - - -
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Residues in contact with THR 112 (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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103B ILE* 3.8 28.0 - - + -
104B MET 3.3 7.0 - - - +
105B ARG* 3.2 20.7 + - - +
111B THR* 1.3 74.0 - - - +
113B ALA* 1.3 64.3 + - - +
114B LEU* 4.1 11.0 - - + -
123B VAL* 3.6 1.2 - - - +
124B THR* 2.9 39.9 + - + +
139B TYR* 3.8 2.2 - - - -
23D T 4.0 13.5 - - - +
24D A 3.4 25.0 - - - -
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Residues in contact with ALA 113 (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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102B VAL 3.3 2.4 - - - +
103B ILE* 3.6 3.1 - - - -
104B MET* 2.7 32.3 + - - +
112B THR* 1.3 75.2 - - - +
114B LEU* 1.3 64.5 + - - +
115B ILE* 3.8 6.3 - - + -
121B MET* 4.1 15.3 - - + -
122B VAL 3.2 9.0 - - - +
123B VAL* 4.3 2.2 - - + +
139B TYR* 3.7 39.7 + - + -
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Residues in contact with LEU 114 (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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99B PHE* 4.2 15.0 - - + -
101B ALA* 4.5 2.5 - - + -
102B VAL 3.6 3.8 - - - -
103B ILE* 4.5 12.3 - - + -
112B THR* 4.1 9.9 - - + +
113B ALA* 1.3 77.9 - - - +
115B ILE* 1.3 60.7 + - - +
116B PHE* 3.8 17.4 - - + -
121B MET* 3.3 5.7 - - - +
122B VAL* 2.8 40.5 + - + +
124B THR* 5.5 2.0 - - + -
8D A 3.8 15.7 - - + +
22D T 3.5 23.3 - - - +
23D T 3.7 43.7 - - - +
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Residues in contact with ILE 115 (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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76B LEU* 4.6 8.1 - - + -
80B LEU* 3.6 31.0 - - + -
82B LEU* 3.7 10.2 - - + +
85B VAL* 4.9 3.8 - - + -
101B ALA* 3.2 3.8 - - - +
102B VAL* 2.9 41.5 + - + +
104B MET* 3.4 47.3 - - + -
113B ALA* 4.1 7.0 - - + -
114B LEU* 1.3 76.8 - - - +
116B PHE* 1.3 60.6 + - - +
120B LYS 4.0 4.3 - - - +
121B MET* 3.8 27.6 - - + -
139B TYR* 4.6 2.2 - - + -
143B ILE* 4.3 11.4 - - + -
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Residues in contact with PHE 116 (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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80B LEU* 4.0 5.9 - - - +
82B LEU* 3.8 7.2 - - - +
99B PHE* 4.2 17.9 - + - -
100B ALA* 3.5 25.1 - - + -
101B ALA* 3.7 15.3 - - + -
114B LEU* 3.8 25.6 - - + -
115B ILE* 1.3 75.8 - - - +
117B ALA* 1.3 59.4 + - - +
118B SER* 3.2 13.7 - - - +
119B GLY* 3.0 20.6 + - - -
120B LYS* 3.0 22.6 + - + +
121B MET* 4.9 0.4 - - - -
122B VAL* 4.7 2.0 - - + -
8D A 3.4 47.3 - + + -
9D A 3.7 40.2 - - - -
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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
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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