Contacts of the strand formed by residues 171 - 176 (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 THR 171 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49C ARG 5.3 1.0 + - - -
41D VAL* 4.8 2.9 - - + -
45D SER* 2.7 32.3 + - - +
49D ARG* 3.2 15.5 + - - +
165D ALA* 5.2 0.4 - - + -
166D LEU 3.4 6.1 - - - +
167D TYR* 3.8 23.7 - - + -
170D ALA* 1.3 73.4 - - - +
172D MET* 1.3 64.4 + - - +
185D MET* 3.8 2.8 - - - +
186D LEU* 2.9 52.0 + - + +
193D PHE* 4.2 13.6 - - + -
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Residues in contact with MET 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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129C LEU* 3.5 21.5 - - + -
164D TYR* 4.1 1.6 - - + +
165D ALA* 3.1 6.1 - - - +
166D LEU* 2.9 36.2 + - + +
170D ALA 3.7 0.4 + - - -
171D THR* 1.3 76.1 - - - +
173D LEU* 1.3 70.1 + - - +
174D VAL* 4.3 5.3 + - + -
183D CYS* 3.9 20.0 - - + -
184D PHE 3.1 11.2 - - - +
185D MET* 3.3 35.4 - - + -
193D PHE* 4.5 2.7 - - - -
196D VAL* 3.8 20.2 - - + -
253D HIS* 4.0 23.1 - - + -
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Residues in contact with LEU 173 (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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13D LEU* 4.0 28.7 - - + -
37D LEU* 5.9 1.3 - - + -
38D CYS* 4.8 5.2 - - - -
41D VAL* 4.2 21.8 - - + -
136D PHE* 4.9 14.1 - - + -
164D TYR 3.5 10.1 - - - +
165D ALA* 4.2 4.0 - - + +
172D MET* 1.3 74.5 - - - +
174D VAL* 1.3 67.9 + - - +
175D LEU* 4.1 23.8 - - + -
182D ASN 3.7 1.6 - - - +
183D CYS* 3.6 1.6 - - - -
184D PHE* 2.9 35.9 + - + +
193D PHE* 3.8 35.1 - - + -
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Residues in contact with VAL 174 (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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163D GLY* 3.2 23.4 - - - -
164D TYR* 3.0 55.0 + - + +
172D MET* 4.2 4.2 - - + -
173D LEU* 1.3 77.2 - - - +
175D LEU* 1.3 59.3 + - - +
181D VAL* 3.5 32.1 - - + -
182D ASN 3.6 4.5 - - - +
183D CYS* 3.8 24.0 - - + -
253D HIS* 3.9 10.3 - - + -
256D LEU* 4.3 2.9 - - + -
287D VAL* 4.3 9.0 - - + -
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Residues in contact with LEU 175 (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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13D LEU* 4.3 20.2 - - + -
16D PHE* 4.5 8.7 - - + -
17D VAL* 4.3 13.0 - - + -
34D LEU* 4.1 24.7 - - + -
136D PHE* 4.5 11.9 - - + -
161D ALA* 4.4 4.5 - - + -
162D ALA 4.0 8.5 - - - +
173D LEU* 4.0 13.4 - - + -
174D VAL* 1.3 73.3 - - - +
176D ALA* 1.3 65.8 + - - +
177D MET* 4.1 37.2 - - + -
180D GLY 3.7 1.6 - - - +
181D VAL* 3.3 3.0 - - - -
182D ASN* 2.9 37.1 + - + +
184D PHE* 4.5 4.3 - - + -
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Residues in contact with ALA 176 (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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161D ALA* 3.3 4.9 - - - +
162D ALA 2.8 41.5 + - - +
175D LEU* 1.3 76.2 - - - +
177D MET* 1.3 62.6 + - - +
180D GLY 3.4 4.9 - - - +
181D VAL* 3.9 17.5 - - + -
286D TYR* 3.5 14.0 - - + -
287D VAL* 3.6 28.7 - - + -
290D LYS* 4.6 2.5 - - + -
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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