Contacts of the strand formed by residues 167 - 172 (chain D) in PDB entry 1THF
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 GLU 167 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5D ARG* 2.9 34.8 + - - -
99D LYS* 2.7 39.1 + - - +
123D GLN* 4.9 3.4 - - - +
125D VAL 3.4 3.1 + - - +
126D VAL* 3.5 15.3 - - + +
127D VAL 3.0 24.7 + - - -
165D ALA* 3.6 4.8 - - - +
166D GLY* 1.3 81.8 - - - +
168D ILE* 1.3 66.1 + - - +
196D LEU* 4.5 3.4 - - - -
197D PRO* 3.5 23.0 - - + +
199D ILE* 3.5 21.4 - - + +
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Residues in contact with ILE 168 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126D VAL* 4.7 0.9 - - - -
127D VAL 3.4 5.8 - - - +
129D ILE* 3.8 24.7 - - + -
157D VAL* 4.0 29.6 - - + +
160D VAL* 3.9 26.5 - - + -
167D GLU* 1.3 77.9 - - - +
169D LEU* 1.3 65.1 + - - +
170D LEU* 3.6 15.1 + - + +
190D VAL* 5.2 4.0 - - + -
194D THR* 4.1 21.1 - - + +
196D LEU* 4.3 8.9 - - + +
197D PRO 3.0 10.3 + - - +
198D ILE* 3.5 9.1 - - + +
199D ILE* 2.8 32.9 + - - +
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Residues in contact with LEU 169 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48D VAL* 4.7 17.5 - - + -
78D THR* 5.6 1.8 - - + -
101D SER* 4.3 14.4 - - - +
126D VAL* 3.7 25.0 - - + +
127D VAL 2.9 8.3 + - - -
128D ALA* 3.3 13.2 - - + +
129D ILE 2.8 32.2 + - - +
168D ILE* 1.3 70.1 - - - +
170D LEU* 1.3 54.7 + - - +
171D THR* 3.4 21.7 + - - +
199D ILE* 3.5 22.9 - - + -
201D SER* 3.8 18.2 - - - +
222D LEU* 4.0 17.7 - - + -
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Residues in contact with LEU 170 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129D ILE* 3.6 16.8 - - + +
131D ALA* 5.1 0.7 - - + -
153D LEU* 4.2 15.7 - - + -
168D ILE* 3.6 10.5 + - + -
169D LEU* 1.3 69.8 - - - +
171D THR* 1.3 59.8 + - - +
172D SER 4.0 0.5 + - - -
186D MET* 3.9 34.7 - - + +
187D ILE* 4.1 17.6 - - + +
190D VAL* 3.8 38.4 - - + -
198D ILE* 4.2 19.5 - - + -
199D ILE 2.8 14.5 + - - +
200D ALA* 3.8 2.0 - - - -
201D SER* 3.0 25.3 + - - +
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Residues in contact with THR 171 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128D ALA* 5.7 0.2 - - - +
129D ILE 2.9 9.5 + - - +
130D ASP* 3.4 24.6 + - - +
131D ALA 3.1 26.0 + - - +
169D LEU* 3.4 24.1 + - - +
170D LEU* 1.3 72.4 - - - +
172D SER* 1.3 70.7 + - - +
173D ILE* 3.5 7.0 + - + +
176D ASP* 3.9 21.8 - - - +
186D MET* 4.2 4.9 - - - +
201D SER* 3.3 18.5 + - - +
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Residues in contact with SER 172 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131D ALA 3.8 5.7 + - - -
132D LYS* 5.9 0.3 - - - -
170D LEU 4.0 1.0 + - - -
171D THR* 1.3 73.6 - - - +
173D ILE* 1.3 63.9 + - - +
174D ASP* 4.0 6.2 + - - +
175D ARG* 3.1 18.4 + - - +
176D ASP* 3.0 21.1 + - - +
183D ASP* 2.8 45.7 + - - +
186D MET* 3.7 11.7 - - - +
201D SER 3.2 10.6 + - - -
202D GLY* 4.4 1.8 - - - -
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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