Contacts of the strand formed by residues 160 - 167 (chain D) in PDB entry 1FTA
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 VAL 160 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30D LEU* 3.8 31.4 - - + -
113D TYR* 4.2 8.3 - - + -
138D ILE* 3.0 17.9 + - + +
139D TYR* 4.4 0.2 - - - -
140D ARG* 3.6 48.9 - - + +
158D ASN 4.6 2.5 - - - +
159D LEU* 1.3 73.0 - - - +
161D ALA* 1.3 63.3 + - + +
177D MET* 4.0 8.9 - - + +
178D ASP* 4.2 4.7 + - - +
286D TYR* 3.5 12.9 + - - -
338D AMP 4.1 16.6 - - - +
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Residues in contact with ALA 161 (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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30D LEU* 5.5 3.6 - - + -
34D LEU* 4.8 6.1 - - + -
136D PHE* 5.1 0.4 - - + -
137D GLY* 3.6 0.2 - - - -
138D ILE* 2.8 44.7 + - + +
159D LEU* 3.7 2.5 - - - +
160D VAL* 1.3 83.9 - - + +
162D ALA* 1.3 61.3 + - - +
175D LEU* 4.4 9.0 - - + -
176D ALA 3.3 7.4 - - - +
177D MET* 3.6 24.9 - - + -
286D TYR* 4.5 3.6 - - - -
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Residues in contact with ALA 162 (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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136D PHE* 3.3 23.1 - - - +
137D GLY* 4.0 0.9 - - - -
159D LEU* 3.9 16.2 - - + -
161D ALA* 1.3 76.0 - - - +
163D GLY* 1.3 59.0 + - - +
175D LEU* 3.8 1.9 - - - +
176D ALA* 2.8 34.1 + - - +
283D PRO* 3.9 15.5 - - + +
286D TYR* 3.7 21.5 - - + -
287D VAL* 4.6 0.7 - - - -
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Residues in contact with GLY 163 (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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135D ILE* 3.6 5.7 - - - +
136D PHE* 3.0 43.2 + - - +
162D ALA* 1.3 77.9 - - - +
164D TYR* 1.3 67.1 + - - +
174D VAL 3.2 13.7 - - - -
283D PRO* 4.3 3.6 - - - +
287D VAL* 4.3 10.3 - - - -
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Residues in contact with TYR 164 (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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134D THR 3.0 15.5 - - - +
135D ILE* 4.1 4.7 - - + -
136D PHE* 3.6 9.0 - - - -
163D GLY* 1.3 77.4 - - - +
165D ALA* 1.3 65.3 + - - +
166D LEU* 4.6 3.8 - - + -
172D MET* 5.2 1.1 - - + -
173D LEU* 3.5 5.2 - - - +
174D VAL* 3.0 52.5 + - + +
249D VAL* 3.5 22.7 - - + -
252D VAL* 4.7 4.4 - - + +
253D HIS* 2.7 52.4 + + + -
256D LEU* 3.5 17.7 - - - +
284D MET* 3.7 39.0 - - + -
287D VAL* 4.5 12.1 - - + -
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Residues in contact with ALA 165 (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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41D VAL* 3.6 37.5 - - + -
133D GLY* 3.1 5.9 - - - -
134D THR* 2.8 30.9 + - - +
136D PHE* 6.0 0.4 - - + -
164D TYR* 1.3 77.2 - - - +
166D LEU* 1.3 58.4 + - - +
167D TYR* 3.8 15.4 - - + +
171D THR* 5.2 0.7 - - + -
172D MET 3.1 12.3 - - - +
173D LEU* 4.2 4.7 - - + +
249D VAL* 3.8 2.3 - - - +
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Residues in contact with LEU 166 (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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128C CYS 4.4 3.1 - - - +
129C LEU* 3.7 26.7 - - + +
131D SER* 3.8 23.6 - - - +
132D VAL 3.8 13.9 - - - +
164D TYR* 4.2 7.3 - - + -
165D ALA* 1.3 72.2 - - - +
167D TYR* 1.3 60.6 + - - +
168D GLY* 3.3 11.6 + - - +
170D ALA 3.6 0.5 - - - +
171D THR* 3.4 5.0 - - - +
172D MET* 2.9 30.7 + - + +
249D VAL* 3.8 19.7 - - + -
250D ALA* 4.0 13.0 - - - +
253D HIS* 3.5 39.0 - - + +
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Residues in contact with TYR 167 (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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169C SER* 3.9 10.7 - - - -
41D VAL* 3.7 25.8 - - + +
44D ILE* 3.6 21.1 - - + +
45D SER* 3.7 39.9 - - - -
48D VAL* 4.0 20.4 - - + -
49D ARG* 3.9 10.5 + - - +
120D LEU* 4.1 4.3 - - + -
131D SER* 3.9 0.9 - - - -
132D VAL* 3.0 34.2 + - + +
133D GLY* 3.6 24.2 - - - -
134D THR* 2.9 33.9 + - - -
165D ALA* 4.1 7.9 - - + -
166D LEU* 1.3 69.3 - - - +
168D GLY* 1.3 63.4 + - - +
171D THR* 3.8 19.7 - - + -
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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