Contacts of the strand formed by residues 70 - 76 (chain B) in PDB entry 1TKW
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 ASN 70 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1B TYR* 6.1 0.2 - - - -
59B GLN* 5.0 0.2 - - - +
68B ALA* 4.3 7.3 + - - +
69B LEU* 1.3 80.2 + - - +
71B VAL* 1.3 62.4 + - - +
117B PRO* 4.1 12.7 - - + +
118B VAL* 3.3 23.2 + - - +
119B PRO* 3.6 9.5 - - - +
120B GLY* 3.9 0.7 - - - +
154B ARG* 3.3 4.5 - - - -
155B GLY 3.2 19.8 + - - -
253B HEC 2.9 46.8 + - + +
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Residues in contact with VAL 71 (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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51B ILE* 3.4 46.2 - - + +
53B TYR* 4.9 2.9 - - + -
70B ASN* 1.3 72.9 - - - +
72B GLY* 1.3 61.1 + - - +
117B PRO* 3.5 2.9 - - - +
118B VAL* 2.6 47.5 + - + +
120B GLY* 4.1 13.4 - - - +
123B TYR 3.4 25.4 - - - +
124B SER* 4.9 0.2 - - - -
126B ILE* 3.7 11.2 - - + -
153B ASN 3.3 11.9 - - - +
154B ARG* 3.8 11.7 - - + -
253B HEC 3.3 6.1 - - - -
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Residues in contact with GLY 72 (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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2B PRO* 5.5 1.1 - - - -
51B ILE* 4.0 1.7 - - - +
71B VAL* 1.3 79.8 - - - +
73B ALA* 1.3 63.4 + - - +
115B ILE* 3.1 14.8 - - - -
116B GLY* 4.0 2.0 - - - -
118B VAL* 5.1 0.4 - - - -
152B GLY* 3.7 0.9 - - - -
153B ASN 3.0 30.0 + - - -
253B HEC 3.4 24.1 - - - +
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Residues in contact with ALA 73 (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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2B PRO* 5.2 1.1 - - - +
49B VAL* 4.6 8.7 - - + -
51B ILE* 4.3 15.0 - - + -
72B GLY* 1.3 75.7 - - - +
74B VAL* 1.3 61.6 + - - +
75B LEU 4.2 0.4 - - - -
113B LEU 3.9 0.5 - - - +
114B VAL* 3.3 4.9 - - - +
115B ILE* 3.0 44.4 + - + +
126B ILE* 4.4 2.5 - - + -
128B PHE* 4.2 13.0 - - + -
150B VAL* 4.8 2.5 - - + -
151B GLY 3.0 14.8 - - - +
152B GLY* 4.4 0.4 - - - -
253B HEC 3.9 7.0 - - - +
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Residues in contact with VAL 74 (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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12B PRO* 4.2 10.5 - - + -
19B ILE* 3.6 30.5 - - + -
21B CYS* 4.5 0.9 - - - -
73B ALA* 1.3 74.1 - - - +
75B LEU* 1.3 61.6 + - - +
76B ILE* 3.9 5.6 + - + +
105B TYR* 4.1 8.3 - - + -
112B ILE* 3.9 21.5 - - + -
113B LEU 3.3 2.9 - - - -
114B VAL* 3.7 22.4 - - + -
149B TYR 3.8 0.9 - - - +
150B VAL* 3.4 5.6 - - - -
151B GLY* 3.0 36.0 + - - +
253B HEC 4.2 14.6 - - + -
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Residues in contact with LEU 75 (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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33B ILE* 3.6 30.7 - - + -
47B ALA* 4.2 13.0 - - + -
49B VAL* 4.0 9.0 - - + -
73B ALA 4.2 0.4 - - - -
74B VAL* 1.3 72.3 - - - +
76B ILE* 1.3 64.0 + - - +
77B LEU* 3.7 36.9 - - + +
111B ASN 3.6 1.7 - - - +
112B ILE* 3.3 6.2 - - - +
113B LEU* 2.8 44.5 + - + +
128B PHE* 4.3 17.0 - - + -
130B ILE* 4.1 14.8 - - + -
148B ILE* 4.4 5.2 - - + -
149B TYR 3.6 3.4 - - - +
150B VAL* 3.8 17.9 - - + -
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Residues in contact with ILE 76 (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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11B ASN* 5.8 2.9 - - - +
12B PRO* 4.2 23.6 - - + -
13B ARG* 4.2 26.5 - - + +
19B ILE* 4.4 17.5 - - + -
74B VAL* 4.5 8.3 - - + +
75B LEU* 1.3 72.5 - - - +
77B LEU* 1.3 68.9 + - - +
111B ASN* 4.0 2.7 - - - +
112B ILE* 4.3 17.3 - - + -
147B PRO 4.3 1.4 - - - +
148B ILE* 3.6 6.4 - - - +
149B TYR* 2.8 65.2 + - + +
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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