Contacts of the strand formed by residues 174 - 180 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42I ALA* 3.8 18.6 - - + -
43I LYS 3.7 31.0 - - - +
44I ILE* 3.4 8.8 - - + +
45I SER* 2.7 31.4 + - - -
46I LYS 2.9 17.4 + - - +
48I ALA* 3.9 11.1 - - + +
49I PRO* 5.2 3.6 - - + -
151I TYR* 5.5 0.7 - - + -
166I PHE* 3.8 22.0 - - + -
167I ILE 3.5 17.7 - - - +
168I ILE* 4.0 9.6 - - + +
172I GLY 3.9 2.2 + - - -
173I ILE* 1.3 70.2 - - - +
175I ARG* 1.3 59.5 + - - +
176I GLN 3.6 15.9 - - - +
177I ILE* 3.8 17.0 - - + -
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Residues in contact with ARG 175 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A ASP* 3.0 58.0 + - - +
183A PRO* 3.9 16.0 - - - +
44I ILE* 4.0 6.0 - - - +
73I TYR* 3.5 14.0 + - + +
167I ILE* 2.9 15.1 + - + +
169I ASP* 3.2 37.7 + - + +
173I ILE* 3.4 22.5 - - - +
174I LEU* 1.3 76.4 - - - +
176I GLN* 1.3 60.8 + - + +
198I PHE* 3.3 42.6 - - + -
201I THR* 4.9 0.8 - - - +
202I ASP* 3.0 28.1 + - - -
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Residues in contact with GLN 176 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178A THR* 3.6 11.5 - - - +
179A LEU 3.2 5.8 + - - +
180A ASN* 2.9 33.3 + - - +
44I ILE* 4.1 2.1 - - - +
165I LEU* 4.3 2.8 - - - +
166I PHE* 3.5 5.7 - - - -
167I ILE* 3.0 47.2 + - + +
174I LEU* 3.6 3.6 - - - +
175I ARG* 1.3 80.3 - - - +
177I ILE* 1.3 88.2 + - - +
178I THR* 2.7 30.4 + - - -
194I LEU* 3.7 25.1 - - + +
198I PHE* 3.9 13.0 - - + -
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Residues in contact with ILE 177 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A HIS* 6.3 1.3 - - + -
177A ILE 4.0 0.7 - - - +
178A THR* 3.6 1.6 - - - -
179A LEU* 2.8 62.3 + - + +
42I ALA* 4.2 13.7 - - + +
44I ILE* 3.9 16.4 - - + +
165I LEU 3.6 2.9 - - - -
166I PHE* 3.8 24.9 - - + -
174I LEU* 3.8 22.0 - - + -
176I GLN* 1.3 82.8 + - - +
178I THR* 1.3 63.0 + - - +
179I LEU* 3.7 33.2 - - + -
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Residues in contact with THR 178 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176A GLN* 3.5 21.5 - - - +
177A ILE 3.6 3.1 - - - -
178A THR* 4.7 4.9 - - + +
190A GLU* 6.1 1.1 - - - +
194A LEU* 6.1 1.3 - - + -
163I ARG 3.5 2.1 - - - +
164I GLY* 3.3 2.1 - - - -
165I LEU* 2.7 53.1 + - + +
176I GLN* 2.7 32.3 + - - -
177I ILE* 1.3 71.8 - - - +
179I LEU* 1.3 59.6 + - - +
180I ASN* 3.9 8.1 - - - +
186I ARG* 4.7 13.8 - - + -
194I LEU* 4.7 4.7 - - - +
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Residues in contact with LEU 179 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A ILE* 3.3 17.8 - - + +
176A GLN* 3.3 5.9 + - - -
177A ILE* 2.8 65.0 + - + +
179A LEU* 6.2 0.7 - - + -
38I HIS* 5.9 3.6 - - - +
151I TYR 5.7 0.2 - - - +
152I GLY 5.1 8.5 - - - +
153I VAL* 3.9 16.6 - - + -
162I LEU* 4.1 11.2 - - + -
163I ARG 3.5 2.0 - - - -
164I GLY* 3.6 17.5 - - - -
166I PHE* 4.3 3.6 - - + -
177I ILE* 3.7 25.6 - - + -
178I THR* 1.3 79.2 - - - +
180I ASN* 1.3 63.3 + - - +
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Residues in contact with ASN 180 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A ILE* 4.3 3.6 - - - -
175A ARG 4.2 2.5 - - - -
176A GLN* 2.9 32.4 + - - +
194A LEU* 3.7 17.2 - - - +
198A PHE* 4.7 2.0 - - + -
162I LEU* 3.8 5.2 - - - +
163I ARG* 2.9 38.9 + - + +
178I THR* 3.9 6.6 - - - +
179I LEU* 1.3 74.0 - - - +
181I ASP* 1.3 65.6 + - - +
184I VAL* 3.0 30.0 + - - +
185I GLY 3.5 19.0 + - - -
186I ARG* 3.8 12.6 - - - +
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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