Contacts of the strand formed by residues 163 - 168 (chain H) 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 ARG 163 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78H PHE 3.9 0.2 - - - -
80H PRO* 3.4 18.3 - - + +
84H THR* 5.3 0.8 + - - -
86H VAL* 3.4 25.0 - - - +
87H CYS* 3.2 36.8 - - - +
90H GLU* 2.9 31.8 + - - -
162H LEU* 1.3 79.0 - - - +
164H GLY* 1.3 55.3 + - - +
178H THR 3.4 4.5 - - - +
180H ASN* 2.9 38.3 + - + +
181H ASP 4.1 2.5 - - - +
182H LEU* 2.8 31.3 + - - +
184H VAL 3.4 22.0 + - - -
186H ARG* 3.2 29.5 + - - +
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Residues in contact with GLY 164 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77H PHE* 3.4 1.0 - - - -
78H PHE* 2.8 38.1 + - - +
153H VAL* 4.1 7.0 - - - -
162H LEU* 3.2 12.5 + - - +
163H ARG* 1.3 72.0 - - - +
165H LEU* 1.3 57.7 + - - -
166H PHE* 3.8 6.1 - - - -
178H THR 3.3 5.8 - - - -
179H LEU* 3.6 17.9 - - - -
186H ARG* 3.1 6.7 + - - +
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Residues in contact with LEU 165 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75H VAL* 3.8 16.8 - - + -
76H PHE 3.7 2.5 - - - -
77H PHE* 3.8 15.7 - - + -
94H PHE* 3.7 21.3 - - + -
164H GLY* 1.3 72.6 - - - +
166H PHE* 1.3 70.4 + - - +
167H ILE* 3.8 26.7 - - + -
176H GLN* 4.2 8.7 - - - +
177H ILE* 3.5 4.3 - - - -
178H THR* 2.7 46.5 + - - +
186H ARG* 3.7 19.9 - - + +
191H THR* 3.7 25.6 - - + +
194H LEU* 6.2 0.4 - - + -
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Residues in contact with PHE 166 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42H ALA* 4.0 7.6 - - + -
74H LEU 3.5 2.4 - - - +
75H VAL* 3.5 2.8 - - - -
76H PHE* 2.8 51.3 + + + +
78H PHE* 3.6 26.7 - + - -
151H TYR* 3.4 52.5 - + + -
153H VAL* 3.6 17.3 - - + -
164H GLY 3.8 8.3 - - - -
165H LEU* 1.3 78.7 - - - +
167H ILE* 1.3 63.7 + - - +
168H ILE* 3.9 3.8 + - + -
174H LEU* 3.8 17.3 - - + -
176H GLN 3.5 2.0 - - - -
177H ILE* 3.8 33.0 - - + -
179H LEU* 4.3 8.3 - - + -
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Residues in contact with ILE 167 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73H TYR* 4.0 28.3 - - + -
74H LEU 3.6 4.7 - - - +
75H VAL* 4.7 3.1 - - + -
165H LEU* 3.8 14.4 - - + -
166H PHE* 1.3 75.0 - - - +
168H ILE* 1.3 61.9 + - - +
174H LEU* 3.5 2.1 - - - +
175H ARG* 2.8 32.1 + - + +
176H GLN* 3.0 37.0 + - + +
191H THR* 4.2 19.5 - - + +
194H LEU* 3.6 34.1 - - + -
195H VAL* 4.1 14.6 - - + +
198H PHE* 4.8 5.8 - - + -
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Residues in contact with ILE 168 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48H ALA* 3.7 25.4 - - + -
66H LEU* 4.1 21.8 - - + -
73H TYR* 3.4 6.4 - - - -
74H LEU* 2.7 46.9 + - + +
76H PHE* 4.0 27.4 - - + -
151H TYR* 4.1 10.3 - - + +
166H PHE* 4.5 6.1 - - + +
167H ILE* 1.3 78.4 - - - +
169H ASP* 1.3 72.9 + - - +
172H GLY* 3.7 25.6 - - - +
173H ILE 3.5 4.3 - - - +
174H LEU* 4.0 10.5 - - + -
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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