Contacts of the strand formed by residues 106 - 112 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73B TYR* 3.4 20.5 - - + +
75B VAL* 4.0 20.6 - - + -
101B PHE* 2.9 44.0 + - + +
102B ARG* 3.4 12.3 + - - +
104B ILE* 3.0 16.0 + - - +
105B ASN* 1.3 75.3 - - - +
107B GLU* 1.3 75.9 + - - +
195B VAL* 3.3 22.8 - - + +
199B GLN* 3.3 4.9 + - - -
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Residues in contact with GLU 107 (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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69B TYR* 3.5 38.7 - - + -
72B LYS* 2.9 30.3 + - + +
73B TYR 3.0 9.1 + - - +
74B LEU* 3.4 4.2 - - + -
75B VAL 2.8 25.6 + - - -
98B LEU* 5.1 5.3 - - - +
102B ARG* 2.8 47.4 + - - +
106B THR* 1.3 81.6 + - - +
108B VAL* 1.3 67.3 + - - +
138B PRO* 6.2 0.5 - - - +
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Residues in contact with VAL 108 (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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69B TYR* 5.6 0.2 - - - -
75B VAL* 3.3 19.3 - - + +
77B PHE* 3.8 27.1 - - + -
94B PHE* 4.3 10.1 - - + -
98B LEU* 3.9 26.5 - - + +
101B PHE* 3.9 28.7 - - + -
107B GLU* 1.3 85.2 + - - +
109B VAL* 1.3 66.0 + - - +
137B ILE* 3.3 29.9 - - + +
138B PRO* 3.4 13.3 - - - +
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Residues in contact with VAL 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B TRP* 4.2 11.2 - - + -
64B LEU* 4.3 9.2 - - + -
69B TYR* 3.2 42.6 - - + +
74B LEU* 3.8 9.2 - - + -
75B VAL 2.9 9.0 + - - +
76B PHE* 3.5 26.1 - - + -
77B PHE* 2.9 27.2 + - - +
108B VAL* 1.3 81.9 - - - +
110B ALA* 1.3 73.5 + - - +
137B ILE* 3.9 4.3 - - - -
138B PRO* 4.0 11.9 - - + +
140B LEU* 4.3 5.6 - - + -
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Residues in contact with ALA 110 (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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77B PHE* 3.2 34.3 - - + -
79B TYR* 3.9 15.3 - - + -
91B ILE* 4.5 2.9 - - + -
109B VAL* 1.3 75.1 - - - +
111B CYS* 1.3 56.1 + - - +
137B ILE* 3.7 5.9 - - + +
138B PRO 3.1 8.7 + - - +
139B LEU* 3.6 17.4 - - + -
140B LEU* 2.7 34.7 + - - +
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Residues in contact with CYS 111 (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 PHE* 4.1 13.2 - - + -
77B PHE 2.9 8.9 + - - +
78B PHE* 3.1 37.1 - - + +
79B TYR* 3.0 28.8 + - - -
110B ALA* 1.3 77.6 - - - +
112B SER* 1.3 63.4 + - - +
140B LEU* 3.4 33.0 - - + -
142B ASP* 3.8 24.5 - - - -
147B ILE* 4.7 1.8 - - - -
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Residues in contact with SER 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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78B PHE* 5.3 2.7 - - - -
79B TYR* 3.1 38.3 + - - -
80B PRO 4.1 1.8 - - - -
111B CYS* 1.3 73.4 - - - +
113B VAL* 1.3 60.3 + - - +
114B ASP* 2.6 34.2 + - - +
119B HIS* 3.2 14.0 - - - -
140B LEU 3.2 8.7 + - - +
142B ASP* 2.9 29.0 + - - +
148B SER* 5.4 0.4 - - - -
161B THR* 5.3 1.6 - - - -
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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