Contacts of the strand formed by residues 73 - 78 (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 TYR 73 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69D TYR* 5.4 0.3 - - - +
72D LYS* 1.3 78.2 - - - +
74D LEU* 1.3 59.1 + - - +
105D ASN* 3.1 8.7 + - - +
106D THR* 3.4 25.7 - - + +
107D GLU* 3.0 23.0 + - - +
167D ILE* 3.9 22.4 - - + -
168D ILE 3.3 15.5 - - - -
169D ASP* 3.2 28.2 - - + +
170D ASP* 3.6 17.0 - - + -
175D ARG* 3.5 6.2 + - + -
195D VAL* 4.4 9.4 - - + -
198D PHE* 3.4 30.0 - - + +
199D GLN* 3.7 30.1 - - + +
202D ASP* 2.6 27.0 + - - -
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Residues in contact with LEU 74 (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* 4.2 8.3 - - + -
66D LEU* 3.6 30.1 - - + -
69D TYR* 4.1 34.8 - - + -
72D LYS 4.7 1.6 - - - +
73D TYR* 1.3 77.3 - - - +
75D VAL* 1.3 76.0 + - - +
76D PHE* 3.6 15.4 + - + -
106D THR* 4.6 0.2 - - - -
107D GLU 3.5 21.5 - - - +
109D VAL* 3.9 20.2 - - + -
166D PHE 3.4 3.8 - - - +
167D ILE* 3.6 2.3 - - - +
168D ILE* 2.8 47.0 + - + +
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Residues in contact with VAL 75 (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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74D LEU* 1.3 73.0 - - - +
76D PHE* 1.3 60.2 + - - +
77D PHE* 4.4 4.3 - - + -
94D PHE* 4.3 10.3 - - + -
101D PHE* 4.0 16.8 - - + -
106D THR* 4.1 7.4 - - + +
107D GLU 2.8 12.9 + - - +
108D VAL* 3.3 13.5 - - + +
109D VAL 2.9 26.3 + - - +
165D LEU* 3.9 32.8 - - + -
166D PHE 3.5 3.4 - - - -
167D ILE* 4.6 4.5 - - + -
191D THR* 3.8 23.3 - - + -
195D VAL* 4.0 15.5 - - + -
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Residues in contact with PHE 76 (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* 3.4 53.6 - + - -
74D LEU* 3.6 16.3 + - + -
75D VAL* 1.3 71.2 - - - +
77D PHE* 1.3 61.7 + - - +
78D PHE* 3.4 37.0 - + - -
109D VAL* 3.5 17.7 - - + +
111D CYS* 4.0 12.1 - - + -
140D LEU* 3.9 15.0 - - + -
147D ILE* 4.0 8.7 - - + -
151D TYR* 3.8 24.7 - + - -
166D PHE* 2.8 43.4 + + + +
168D ILE* 4.2 7.6 - - + -
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Residues in contact with PHE 77 (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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75D VAL* 4.4 5.6 - - + -
76D PHE* 1.3 76.4 - - - +
78D PHE* 1.3 65.2 + - - +
79D TYR* 4.3 6.1 - + + -
90D GLU* 4.6 8.3 - - + -
91D ILE* 4.2 25.1 - - + -
94D PHE* 3.6 33.2 - + + -
108D VAL* 3.7 23.8 - - + -
109D VAL 2.9 14.5 + - - -
110D ALA* 3.2 32.0 - - + -
111D CYS* 2.8 26.0 + - - +
137D ILE* 4.4 2.7 - - + -
164D GLY 3.4 9.4 - - - +
165D LEU* 3.8 17.3 - - + -
186D ARG* 3.7 30.1 - - - +
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Residues in contact with PHE 78 (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* 3.4 32.5 - + - -
77D PHE* 1.3 77.4 - - - +
79D TYR* 1.3 61.9 + - - +
111D CYS* 3.1 36.8 - - + -
112D SER* 5.3 0.2 - - - -
147D ILE* 3.8 11.0 - - + -
148D SER* 3.8 25.1 - - - -
151D TYR* 3.6 30.1 - - + -
153D VAL* 3.7 14.6 - - + -
161D THR* 3.6 18.4 - - + +
162D LEU 3.9 3.7 - - - +
164D GLY 2.7 23.3 + - - +
166D PHE* 3.7 15.9 - + - -
186D ARG* 2.8 26.7 + - - -
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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