Contacts of the strand formed by residues 181 - 187 (chain C) 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 181 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174C VAL* 3.6 28.9 - - + -
175C LEU 3.8 4.7 - - - +
176C ALA* 3.9 10.5 - - + -
180C GLY* 1.3 73.4 - - - -
182C ASN* 1.3 65.6 + - - +
183C CYS* 4.8 0.4 - - - -
199C ASP* 3.1 8.2 + - - +
200C VAL* 2.9 51.5 + - + +
256C LEU* 4.5 6.3 - - + -
287C VAL* 3.6 30.3 - - + +
290C LYS* 3.9 8.0 + - + -
291C ALA* 3.9 16.8 - - + +
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Residues in contact with ASN 182 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C PHE* 3.8 30.7 - - + -
174C VAL* 3.6 1.9 - - - +
175C LEU 3.0 33.1 + - - +
177C MET* 6.0 0.2 - - - +
179C CYS* 4.4 7.6 - - - -
180C GLY* 3.7 12.1 - - - +
181C VAL* 1.3 79.2 - - - +
183C CYS* 1.3 61.8 + - - +
184C PHE* 3.8 21.7 - - + -
195C LEU* 4.1 4.9 - - + +
197C ASP 3.5 9.2 - - - +
198C LYS* 3.5 30.1 - - - +
199C ASP* 3.6 11.0 + - - +
200C VAL* 4.7 0.4 - - - -
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Residues in contact with CYS 183 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172C MET* 4.1 17.7 - - + -
173C LEU 3.6 5.8 - - - +
174C VAL* 3.9 25.1 - - + +
181C VAL* 4.8 0.2 - - - -
182C ASN* 1.3 74.2 - - - +
184C PHE* 1.4 59.9 + - - +
195C LEU* 3.6 2.8 - - - +
196C VAL* 3.1 22.6 + - + +
197C ASP* 2.9 26.4 + - + +
200C VAL* 3.9 22.7 - - - -
253C HIS* 4.8 7.2 - - - -
256C LEU* 4.4 11.0 - - - -
257C VAL* 5.6 4.0 - - - -
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Residues in contact with PHE 184 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C THR 4.2 0.2 - - - -
13C LEU* 3.7 46.7 - - + -
16C PHE* 3.6 34.1 - + + -
172C MET* 3.4 9.3 - - - +
173C LEU* 2.8 48.4 + - + +
175C LEU* 4.4 9.9 - - + -
182C ASN* 3.8 24.0 - - + -
183C CYS* 1.4 73.4 - - - +
185C MET* 1.3 59.2 + - - +
193C PHE* 3.8 19.1 - - + -
194C ILE 3.1 7.0 - - - +
195C LEU* 3.6 40.6 - - + -
196C VAL 4.3 0.2 - - - +
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Residues in contact with MET 185 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170C ALA* 3.7 25.4 - - - -
171C THR 3.8 9.0 - - - +
172C MET* 3.9 19.2 - - + +
184C PHE* 1.3 71.7 - - - +
186C LEU* 1.3 67.2 + - - +
187C ASP 3.5 0.7 + - - -
193C PHE* 3.2 2.4 - - - -
194C ILE* 2.8 31.3 + - - +
196C VAL* 3.8 20.1 - - + +
50D LYS* 3.9 26.0 - - + -
53D ILE* 3.5 26.1 - - + +
129D LEU* 4.2 19.5 - - + -
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Residues in contact with LEU 186 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42C LYS* 4.0 29.8 - - + +
45C SER* 3.8 25.8 - - - +
49C ARG* 5.6 1.8 - - - +
171C THR* 2.9 34.6 + - + +
185C MET* 1.3 80.1 - - - +
187C ASP* 1.3 64.3 + - - +
188C PRO* 3.1 24.0 - - + +
191C GLY* 4.2 2.9 - - - -
192C GLU 3.4 30.7 - - - +
193C PHE* 3.8 17.1 - - + -
49D ARG 3.9 7.8 - - - +
50D LYS* 4.1 1.4 - - - +
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Residues in contact with ASP 187 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185C MET 3.5 1.6 + - - -
186C LEU* 1.3 71.9 - - - +
188C PRO* 1.3 63.9 - - - +
189C ALA* 2.9 25.9 + - - +
190C ILE* 3.2 17.6 + - + +
191C GLY* 3.0 19.8 + - - -
192C GLU 2.8 16.7 + - - +
194C ILE* 4.4 5.4 - - + -
50D LYS 3.9 3.6 - - - -
52D GLY* 2.8 31.9 + - - -
53D ILE* 3.9 13.7 - - + -
54D ALA* 3.1 31.9 + - - +
55D HIS* 5.5 0.7 - - - -
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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