Contacts of the strand formed by residues 106 - 112 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73J TYR* 3.4 30.2 - - + +
74J LEU 4.6 0.2 - - - -
75J VAL* 4.0 20.2 - - + -
98J LEU* 5.2 0.2 - - - +
101J PHE* 2.9 45.7 + - + +
102J ARG* 3.4 11.9 + - - +
104J ILE* 3.1 15.6 + - - +
105J ASN* 1.3 77.2 - - - +
107J GLU* 1.3 75.5 + - - +
195J VAL* 3.4 17.9 - - + +
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Residues in contact with GLU 107 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69J TYR* 3.5 37.3 - - + -
72J LYS* 3.1 44.4 + - + +
73J TYR 3.0 8.6 + - - +
74J LEU* 3.5 2.6 - - + -
75J VAL 2.9 24.8 + - - -
98J LEU* 5.3 1.9 - - - +
102J ARG* 3.3 44.2 + - - +
105J ASN 5.6 0.2 - - - -
106J THR* 1.3 77.3 + - - +
108J VAL* 1.3 71.4 + - - +
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Residues in contact with VAL 108 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69J TYR* 4.9 0.3 + - - -
75J VAL* 3.4 19.7 - - + +
77J PHE* 3.8 25.8 - - + -
94J PHE* 4.3 10.1 - - + -
98J LEU* 3.6 28.7 - - + +
101J PHE* 4.0 28.0 - - + -
107J GLU* 1.3 83.9 + - - +
109J VAL* 1.3 67.3 + - - +
137J ILE* 3.6 20.5 - - + +
138J PRO* 3.3 22.2 - - - +
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Residues in contact with VAL 109 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51J TRP* 4.2 11.9 - - + -
64J LEU* 4.3 9.4 - - + -
69J TYR* 3.1 40.6 - - + +
74J LEU* 3.8 13.0 - - + +
75J VAL 3.0 8.9 + - - +
76J PHE* 3.5 24.1 - - + -
77J PHE* 3.0 29.6 + - - -
108J VAL* 1.3 78.4 - - - +
110J ALA* 1.3 71.7 + - - +
137J ILE* 4.1 1.8 - - - -
138J PRO* 4.0 12.8 - - + +
140J LEU* 4.5 4.7 - - + -
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Residues in contact with ALA 110 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77J PHE* 3.2 34.3 - - + -
79J TYR* 4.0 9.0 - - + -
91J ILE* 4.7 2.5 - - + -
109J VAL* 1.3 75.7 - - - +
111J CYS* 1.3 57.1 + - - +
137J ILE* 3.8 5.5 - - + +
138J PRO 3.1 14.3 + - - +
139J LEU* 4.0 17.7 - - + -
140J LEU* 2.7 33.1 + - - +
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Residues in contact with CYS 111 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76J PHE* 4.1 12.3 - - + -
77J PHE 2.9 8.5 + - - +
78J PHE* 3.0 37.8 - - + +
79J TYR* 2.9 31.1 + - - -
110J ALA* 1.3 77.0 - - - +
112J SER* 1.3 63.2 + - - +
140J LEU* 3.4 33.0 - - + -
142J ASP* 3.8 24.7 - - - -
147J ILE* 4.6 2.9 - - - -
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Residues in contact with SER 112 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78J PHE* 5.3 1.3 - - - -
79J TYR* 3.1 36.8 + - - -
80J PRO 4.0 1.6 - - - -
111J CYS* 1.3 73.2 - - - +
113J VAL* 1.3 61.3 + - - +
114J ASP* 2.6 34.0 + - - -
119J HIS* 3.1 14.6 - - - -
140J LEU 3.2 7.4 + - - +
141J SER* 3.7 0.5 - - - -
142J ASP* 2.8 28.8 + - - +
148J SER* 5.3 0.7 - - - -
161J THR* 5.2 2.2 - - - -
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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