Contacts of the strand formed by residues 160 - 166 (chain C) in PDB entry 1KTD
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 PHE 160 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123C ARG* 3.9 0.9 - - - +
124C ASN* 3.1 65.4 + - + +
125C GLY* 3.9 8.7 - - - -
158C ASP 5.2 1.8 - - - -
159C ASP* 1.3 80.6 - - - +
161C TYR* 1.3 68.4 + - - +
162C ASP* 3.8 21.8 - - - -
177C THR* 5.2 2.7 - - - +
178C TRP 3.4 6.3 - - - +
179C GLU* 3.6 27.6 - - + +
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Residues in contact with TYR 161 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91C VAL* 5.8 0.4 - - - -
105C LEU* 3.4 27.4 - - + -
121C TRP* 4.9 3.4 - - + -
122C LEU 3.3 6.1 - - - +
123C ARG* 2.9 55.3 + - + -
151C LEU* 3.4 28.3 - - + -
153C PHE* 3.5 37.7 - + + +
154C LEU 4.3 7.5 + - - -
159C ASP* 4.1 25.9 + - + +
160C PHE* 1.3 76.6 - - - +
162C ASP* 1.3 75.1 + - - +
177C THR 3.5 0.2 - - - -
178C TRP* 2.6 48.9 + + + +
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Residues in contact with ASP 162 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91C VAL* 5.5 0.7 - - - -
121C TRP* 3.7 5.0 - - - -
122C LEU* 2.9 51.4 + - + +
125C GLY* 5.2 2.9 + - - -
160C PHE* 3.8 21.8 - - - -
161C TYR* 1.3 88.4 - - - +
163C CYS* 1.3 59.9 + - - +
164C GLU 3.9 0.2 - - - -
175C ARG* 3.8 28.2 + - + -
176C LYS 3.1 8.1 - - - +
177C THR* 2.7 32.5 + - - -
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Residues in contact with CYS 163 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89C VAL* 4.7 1.4 - - + +
91C VAL* 3.5 18.6 - - + +
107C CYS* 2.0 51.1 - - + -
119C VAL* 3.7 24.5 - - - -
120C THR 3.7 3.4 - - - -
121C TRP* 4.1 12.5 - - + -
162C ASP* 1.3 70.5 - - - +
164C GLU* 1.3 60.7 + - - +
165C VAL* 3.8 7.6 + - - +
174C LEU 3.3 4.3 - - - +
175C ARG* 4.4 0.7 - - - -
176C LYS* 3.0 29.8 + - - +
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Residues in contact with GLU 164 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118C ASN 3.8 0.9 - - - +
119C VAL* 3.5 4.5 - - - +
120C THR* 3.0 48.8 + - - +
122C LEU* 4.0 12.3 - - + +
162C ASP 3.8 1.6 + - - -
163C CYS* 1.3 72.5 - - - +
165C VAL* 1.3 61.2 + - - +
173C PRO* 3.7 31.5 - - + +
174C LEU 3.3 2.7 - - - +
175C ARG* 2.9 48.2 + - + +
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Residues in contact with VAL 165 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C PRO* 4.2 20.6 - - + -
89C VAL* 3.8 35.9 - - + -
109C ILE* 4.0 20.4 - - + -
117C VAL* 3.4 25.4 - - + -
118C ASN 3.6 3.1 - - - +
119C VAL* 4.1 2.7 - - + -
163C CYS* 3.9 13.2 - - - -
164C GLU* 1.3 79.0 - - - +
166C ASP* 1.3 63.3 + - - +
170C LEU* 3.6 4.5 - - + +
173C PRO* 3.4 3.1 - - - +
174C LEU* 2.6 41.6 + - + +
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Residues in contact with ASP 166 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117C VAL* 3.0 20.9 - - - +
118C ASN* 2.9 38.2 + - + +
165C VAL* 1.3 76.0 - - - +
167C HIS* 1.3 71.2 + - - +
170C LEU* 4.0 3.4 - - - +
172C GLU 4.5 1.4 - - - -
173C PRO* 3.5 34.9 - - + +
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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