Contacts of the strand formed by residues 106 - 112 (chain H) in PDB entry 3TKR
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 106 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73H TYR* 3.2 30.0 - - + +
74H LEU 4.6 0.2 - - - -
75H VAL* 4.0 12.3 - - + -
101H PHE* 3.0 52.6 + - + +
102H ARG* 3.2 13.3 + - - +
104H ILE* 3.1 14.0 + - - +
105H ASN* 1.3 75.5 - - - +
107H GLU* 1.3 77.2 + - - +
195H VAL* 3.4 18.0 - - + +
199H GLN* 3.5 0.2 + - - -
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Residues in contact with GLU 107 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69H TYR* 3.6 39.7 - - + -
72H LYS* 3.2 34.9 + - + +
73H TYR 3.0 8.7 + - - +
74H LEU* 3.6 5.1 - - + -
75H VAL 2.9 24.4 + - - -
98H LEU* 4.4 3.1 - - - +
102H ARG* 2.9 48.6 + - - +
106H THR* 1.3 80.0 - - - +
108H VAL* 1.3 72.6 + - - +
138H PRO* 6.0 1.0 - - - +
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Residues in contact with VAL 108 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69H TYR* 5.1 0.2 + - - -
75H VAL* 3.3 15.3 - - + +
77H PHE* 3.7 28.5 - - + -
94H PHE* 4.2 18.6 - - + +
98H LEU* 3.9 11.9 - - + +
101H PHE* 3.8 36.1 - - + -
107H GLU* 1.3 86.3 + - - +
109H VAL* 1.3 67.0 + - - +
137H ILE* 3.7 21.6 - - + +
138H PRO* 3.3 22.5 - - - +
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Residues in contact with VAL 109 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51H TRP* 4.3 11.0 - - + -
64H LEU* 4.2 9.0 - - + -
69H TYR* 3.2 41.5 - - + +
74H LEU* 4.0 8.7 - - + +
75H VAL 3.0 6.8 + - - +
76H PHE* 3.4 28.2 - - + -
77H PHE* 2.9 29.9 + - - +
108H VAL* 1.3 80.5 - - - +
110H ALA* 1.3 71.4 - - - +
138H PRO* 4.0 15.5 - - + +
140H LEU* 4.3 6.7 - - + -
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Residues in contact with ALA 110 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77H PHE* 3.2 37.7 - - + -
79H TYR* 4.0 14.8 - - + -
91H ILE* 4.4 1.8 - - + -
109H VAL* 1.3 74.3 - - - +
111H CYS* 1.3 56.7 + - - +
137H ILE* 4.1 6.1 - - + +
138H PRO 3.3 6.8 + - - +
139H LEU* 3.5 18.9 - - + -
140H LEU* 2.8 33.1 + - - +
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Residues in contact with CYS 111 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76H PHE* 4.1 13.7 - - + -
77H PHE 2.8 9.3 + - - +
78H PHE* 3.0 33.3 - - + +
79H TYR* 2.9 28.9 + - - -
110H ALA* 1.3 77.4 - - - +
112H SER* 1.3 64.4 + - - +
140H LEU* 3.4 33.7 - - + -
142H ASP* 3.8 27.1 - - - -
147H ILE* 4.7 2.0 - - - -
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Residues in contact with SER 112 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78H PHE* 5.3 2.0 - - - -
79H TYR* 3.1 37.7 + - - -
80H PRO 4.0 1.6 - - - -
111H CYS* 1.3 73.2 - - - +
113H VAL* 1.3 60.5 + - - +
114H ASP* 2.7 30.1 + - - +
119H HIS* 3.1 18.4 - - - -
140H LEU 3.3 7.3 + - - +
142H ASP* 2.9 27.7 + - - +
148H SER* 5.4 0.9 - - - -
161H THR* 5.5 2.0 - - - -
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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