Contacts of the strand formed by residues 174 - 180 (chain J) 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 LEU 174 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42J ALA* 3.9 12.6 - - + -
43J LYS 3.7 31.2 - - - +
44J ILE* 3.5 8.8 - - + -
45J SER* 2.8 31.2 + - - -
46J LYS 2.9 18.1 + - - +
48J ALA* 4.0 11.0 - - + +
49J PRO* 5.1 4.7 - - + -
151J TYR* 5.5 0.2 - - + -
166J PHE* 3.8 22.7 - - + -
167J ILE 3.5 17.3 - - - +
168J ILE* 4.0 9.6 - - + +
172J GLY 3.8 2.4 + - - -
173J ILE* 1.3 71.1 - - - +
175J ARG* 1.3 60.5 + - - +
176J GLN 3.6 15.9 - - - +
177J ILE* 3.8 21.8 - - + -
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Residues in contact with ARG 175 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180E ASN 4.0 0.2 - - - -
181E ASP* 3.0 58.0 + - - +
183E PRO* 3.8 16.2 - - - +
44J ILE* 4.2 4.7 - - - -
73J TYR* 3.4 14.0 + - + +
167J ILE* 2.8 14.8 + - + +
169J ASP* 3.2 37.1 + - + +
173J ILE* 3.4 23.4 - - - +
174J LEU* 1.3 78.1 - - - +
176J GLN* 1.3 60.9 + - + +
198J PHE* 3.2 43.1 - - + -
201J THR* 4.8 1.2 + - - -
202J ASP* 2.9 28.3 + - - -
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Residues in contact with GLN 176 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178E THR* 3.6 10.9 - - - +
179E LEU 3.3 12.1 + - - +
180E ASN* 3.0 28.4 + - - +
44J ILE* 4.1 2.7 - - - +
165J LEU* 4.3 2.8 - - - +
166J PHE* 3.5 4.7 - - - -
167J ILE* 3.0 50.4 + - + +
174J LEU* 3.6 3.4 - - - +
175J ARG* 1.3 81.4 - - - +
177J ILE* 1.3 78.5 + - - +
178J THR* 2.8 30.1 + - - -
194J LEU* 3.8 20.9 - - + +
198J PHE* 3.9 18.2 - - + -
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Residues in contact with ILE 177 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38E HIS* 6.4 0.9 - - + -
177E ILE 3.9 0.7 - - - +
178E THR* 3.6 1.2 - - - -
179E LEU* 2.8 57.3 + - + -
42J ALA* 4.3 14.6 - - + +
44J ILE* 3.9 16.6 - - + +
165J LEU 3.5 3.4 - - - -
166J PHE* 3.8 24.5 - - + -
174J LEU* 3.8 24.0 - - + -
176J GLN* 1.3 82.5 + - - +
178J THR* 1.3 65.1 + - - +
179J LEU* 3.6 34.5 - - + -
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Residues in contact with THR 178 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176E GLN* 3.6 18.8 - - - +
177E ILE 3.6 2.5 - - - -
178E THR* 4.7 4.9 - - + +
190E GLU* 6.1 0.4 - - - +
194E LEU* 6.1 1.3 - - + -
163J ARG 3.5 2.1 - - - +
164J GLY* 3.4 2.1 - - - -
165J LEU* 2.7 53.0 + - + +
176J GLN* 2.8 31.0 + - - -
177J ILE* 1.3 72.3 - - - +
179J LEU* 1.3 62.5 + - - +
180J ASN* 3.8 8.5 - - - +
186J ARG* 4.6 13.2 - - + -
194J LEU* 4.8 4.3 - - - +
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Residues in contact with LEU 179 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44E ILE* 3.2 16.9 - - + +
176E GLN* 3.4 5.5 + - - -
177E ILE* 2.8 66.3 + - + +
179E LEU* 6.1 0.7 - - + -
38J HIS* 6.1 1.6 - - - +
151J TYR 6.1 0.2 - - - +
152J GLY 5.1 9.2 - - - +
153J VAL* 3.9 16.8 - - + -
162J LEU* 4.2 11.9 - - + -
163J ARG 3.6 2.2 - - - -
164J GLY* 3.6 17.0 - - - -
166J PHE* 4.2 3.6 - - + -
177J ILE* 3.6 27.4 - - + -
178J THR* 1.3 81.5 - - - +
180J ASN* 1.3 62.4 + - - +
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Residues in contact with ASN 180 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44E ILE* 4.3 3.4 - - - -
175E ARG 4.1 2.5 - - - -
176E GLN* 3.0 29.8 + - - +
194E LEU* 3.7 17.1 - - - +
198E PHE* 4.7 2.0 - - + -
162J LEU* 3.7 6.1 - - - +
163J ARG* 2.9 37.9 + - + +
178J THR* 3.8 8.0 - - - +
179J LEU* 1.3 73.5 - - - +
181J ASP* 1.3 66.0 + - - +
184J VAL* 3.0 31.6 + - - +
185J GLY 3.4 18.2 + - - -
186J ARG* 3.9 12.9 - - - +
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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