Contacts of the strand formed by residues 106 - 112 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73D TYR* 3.4 29.8 - - + +
74D LEU 4.3 0.4 - - - +
75D VAL* 4.1 11.0 - - + -
101D PHE* 3.0 53.9 + - + +
102D ARG* 3.3 13.4 + - - +
104D ILE* 2.9 15.1 + - - +
105D ASN* 1.3 76.6 - - - +
107D GLU* 1.3 76.5 + - - +
195D VAL* 3.5 12.3 - - + +
199D GLN* 3.4 4.7 + - - -
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Residues in contact with GLU 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69D TYR* 3.6 41.1 - - + -
72D LYS* 3.7 31.5 + - + +
73D TYR 3.0 8.2 + - - +
74D LEU* 3.5 4.2 - - + -
75D VAL 2.8 25.1 + - - -
98D LEU* 4.8 2.5 - - - +
102D ARG* 3.1 47.9 + - - +
106D THR* 1.3 79.5 - - - +
108D VAL* 1.3 72.9 + - - +
138D PRO* 5.8 2.1 - - - +
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Residues in contact with VAL 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69D TYR* 5.6 0.2 - - - -
75D VAL* 3.3 16.8 - - + +
77D PHE* 3.7 29.2 - - + -
94D PHE* 4.1 19.5 - - + +
98D LEU* 3.9 13.3 - - + +
101D PHE* 3.8 33.9 - - + -
107D GLU* 1.3 85.6 + - - +
109D VAL* 1.3 67.1 + - - +
137D ILE* 3.6 21.6 - - + +
138D PRO* 3.4 21.5 - - - +
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Residues in contact with VAL 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51D TRP* 4.4 3.6 - - + -
64D LEU* 4.2 11.7 - - + -
69D TYR* 3.3 39.3 - - + +
74D LEU* 3.9 10.1 - - + -
75D VAL 2.9 7.2 + - - +
76D PHE* 3.5 27.0 - - + -
77D PHE* 2.9 30.2 + - - -
108D VAL* 1.3 79.9 - - - +
110D ALA* 1.3 71.7 + - - +
137D ILE* 5.1 0.4 - - - -
138D PRO* 4.0 15.3 - - + +
140D LEU* 4.2 11.7 - - + -
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Residues in contact with ALA 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77D PHE* 3.2 35.0 - - + -
79D TYR* 3.9 15.7 - - + -
91D ILE* 4.5 1.3 - - + -
109D VAL* 1.3 75.8 - - - +
111D CYS* 1.3 62.0 + - - +
137D ILE* 4.1 6.2 - - + +
138D PRO 3.2 6.5 + - - +
139D LEU* 3.6 16.8 - - + -
140D LEU* 2.8 29.1 + - - +
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Residues in contact with CYS 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76D PHE* 4.0 14.1 - - + -
77D PHE 2.8 8.5 + - - +
78D PHE* 3.1 36.9 - - + +
79D TYR* 2.9 26.9 + - - -
110D ALA* 1.3 76.8 - - - +
112D SER* 1.3 64.0 + - - +
140D LEU* 3.4 32.8 - - + -
142D ASP* 3.8 23.8 - - - -
147D ILE* 4.6 2.0 - - - -
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Residues in contact with SER 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78D PHE* 5.3 2.0 - - - -
79D TYR* 3.1 37.5 + - - -
80D PRO 4.1 2.0 - - - -
111D CYS* 1.3 73.8 - - - +
113D VAL* 1.3 60.3 + - - +
114D ASP* 2.6 36.2 + - - +
119D HIS* 3.2 13.9 + - - -
140D LEU 3.3 8.3 + - - +
142D ASP* 2.9 28.2 + - - +
148D SER* 5.3 0.7 - - - -
161D THR* 5.2 2.5 - - - -
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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