Contacts of the strand formed by residues 163 - 168 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A PHE 3.8 2.5 - - - -
80A PRO* 3.4 19.2 - - + +
84A THR* 5.4 0.6 + - - -
86A VAL* 3.3 27.9 - - - +
87A CYS* 3.2 32.7 - - - +
90A GLU* 2.8 38.7 + - - -
162A LEU* 1.3 77.5 - - - +
164A GLY* 1.3 56.4 + - - +
178A THR 3.5 4.2 - - - +
180A ASN* 2.9 38.5 + - + +
181A ASP 4.2 2.7 - - - +
182A LEU* 2.9 32.6 + - - +
184A VAL 3.4 22.2 + - - -
186A ARG* 3.2 27.9 + - - +
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Residues in contact with GLY 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A PHE* 3.4 1.0 - - - -
78A PHE* 2.8 36.5 + - - +
153A VAL* 4.1 7.2 - - - -
162A LEU* 3.3 12.3 + - - +
163A ARG* 1.3 72.7 - - - +
165A LEU* 1.3 59.9 + - - -
166A PHE* 3.8 5.3 - - - -
178A THR 3.3 5.8 - - - -
179A LEU* 3.6 18.4 - - - -
186A ARG* 3.2 6.2 + - - +
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Residues in contact with LEU 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A VAL* 3.8 17.0 - - + -
76A PHE 3.8 2.5 - - - -
77A PHE* 3.8 16.8 - - + -
94A PHE* 3.7 21.8 - - + -
164A GLY* 1.3 74.3 - - - -
166A PHE* 1.3 69.3 + - - +
167A ILE* 3.9 25.8 - - + -
176A GLN* 4.2 9.0 - - - +
177A ILE* 3.5 4.2 - - - +
178A THR* 2.7 45.8 + - + +
186A ARG* 3.7 21.1 - - + +
191A THR* 3.7 25.6 - - + +
194A LEU* 6.1 0.9 - - + -
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Residues in contact with PHE 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A ALA* 4.0 7.4 - - + -
74A LEU 3.5 2.1 - - - +
75A VAL* 3.6 2.9 - - - -
76A PHE* 2.9 49.3 + + + +
78A PHE* 3.6 27.6 - + - -
151A TYR* 3.4 55.6 - + + -
153A VAL* 3.6 14.1 - - + -
164A GLY 3.8 9.9 - - - -
165A LEU* 1.3 78.4 - - - +
167A ILE* 1.3 63.4 + - - +
168A ILE* 4.0 3.1 - - + -
174A LEU* 3.8 16.4 - - + -
176A GLN 3.4 2.7 - - - -
177A ILE* 3.8 33.7 - - + -
179A LEU* 4.2 8.5 - - + -
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Residues in contact with ILE 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A TYR* 3.9 28.9 - - + -
74A LEU 3.6 4.5 - - - +
75A VAL* 4.6 5.8 - - + -
165A LEU* 3.9 16.6 - - + -
166A PHE* 1.3 74.4 - - - +
168A ILE* 1.3 63.1 + - - +
174A LEU* 3.4 3.6 - - - +
175A ARG* 2.8 33.0 + - + +
176A GLN* 3.0 32.4 + - + +
191A THR* 4.2 12.8 - - + +
194A LEU* 3.6 34.1 - - + -
195A VAL* 4.1 15.7 - - + +
198A PHE* 4.8 4.9 - - + -
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Residues in contact with ILE 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A ALA* 3.8 24.5 - - + -
66A LEU* 4.1 20.9 - - + -
73A TYR* 3.3 6.2 - - - -
74A LEU* 2.7 47.2 + - + +
76A PHE* 4.0 27.8 - - + -
151A TYR* 4.0 14.1 - - + +
166A PHE* 4.6 2.5 - - + +
167A ILE* 1.3 79.6 - - - +
169A ASP* 1.3 72.7 + - - +
172A GLY* 3.7 26.7 - - - +
173A ILE 3.5 3.8 - - - +
174A LEU* 4.1 9.9 - - + -
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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