Contacts of the strand formed by residues 206 - 213 (chain C) in PDB entry 5FL6
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 GLN 206 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23C ALA* 5.1 1.8 - - + +
26C GLY* 3.3 12.6 - - - -
27C ARG 4.5 3.0 - - - +
28C PHE* 3.0 57.4 + - + +
29C GLN* 3.0 29.2 + - - +
135C GLY* 3.3 28.9 + - - +
136C ARG 4.5 0.2 - - - +
197C GLY 3.4 6.7 - - - +
198C SER* 4.1 0.4 - - - -
204C CYS 3.4 1.5 + - - +
205C ALA* 1.3 74.6 - - - +
207C GLY* 1.3 64.0 + - - +
208C VAL* 3.3 4.6 + - - +
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Residues in contact with GLY 207 (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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135C GLY 4.8 1.6 - - - -
136C ARG 3.5 15.5 - - - +
137C PRO* 4.0 4.0 - - - -
138C GLY* 2.8 27.7 + - - -
139C GLY 4.0 0.5 + - - -
140C LEU 4.0 1.6 - - - +
196C GLU* 3.4 25.4 + - - +
197C GLY 3.1 4.6 + - - -
206C GLN* 1.3 77.0 - - - +
208C VAL* 1.3 62.9 + - - +
209C ILE 3.5 1.0 + - - -
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Residues in contact with VAL 208 (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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140C LEU* 3.5 25.1 - - + +
142C VAL* 3.8 25.8 - - + -
196C GLU* 3.3 1.9 - - - -
197C GLY 2.8 35.5 + - - +
198C SER 3.7 0.4 - - - +
199C LEU* 3.7 26.2 - - + +
205C ALA* 3.6 22.7 - - + +
206C GLN 4.3 2.7 - - - +
207C GLY* 1.3 78.2 - - - +
209C ILE* 1.3 65.6 + - - +
210C TRP* 3.5 25.9 + - + +
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Residues in contact with ILE 209 (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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82C LEU* 3.9 19.5 - - + -
86C ARG* 3.8 21.3 - - - +
88C TYR* 3.7 12.8 - - - +
138C GLY* 3.6 31.0 - - - +
140C LEU 3.0 11.6 + - - +
141C ALA* 3.2 3.8 - - + +
142C VAL 2.9 27.0 + - - +
194C GLN* 3.9 28.3 - - + +
195C TYR 3.8 5.8 - - - +
196C GLU* 4.5 14.6 - - + +
207C GLY 3.5 0.9 + - - +
208C VAL* 1.3 71.8 - - - +
210C TRP* 1.3 61.6 + - - +
211C THR* 4.0 2.7 + - - +
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Residues in contact with TRP 210 (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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30C SER* 3.1 19.9 + - - -
107C HIS* 3.5 19.5 - + - +
119C HIS* 3.5 37.2 - + - -
142C VAL* 3.4 38.8 - - + -
144C ALA* 4.1 10.1 - - + -
193C PHE 3.8 0.2 - - - +
194C GLN* 3.2 7.4 - - - +
195C TYR* 2.8 57.3 + + + +
197C GLY 4.0 3.4 - - - -
198C SER 2.8 26.2 + - - +
200C THR* 3.7 11.4 - - + -
208C VAL* 3.5 25.2 + - + +
209C ILE* 1.3 70.9 - - - +
211C THR* 1.3 61.5 + - - +
212C VAL* 4.1 1.8 - - + -
267C Y0R 3.4 23.3 - - - -
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Residues in contact with THR 211 (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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48C LEU* 3.9 24.0 - - + -
82C LEU* 3.9 9.0 - - - +
141C ALA* 6.1 0.3 - - - +
142C VAL 3.0 7.3 + - - +
143C LEU* 3.5 16.0 - - + -
144C ALA* 2.8 27.5 + - - +
192C TYR* 3.6 36.6 - - + -
193C PHE 3.2 3.4 - - - -
194C GLN* 2.9 23.7 + - - +
209C ILE* 4.3 3.1 + - - +
210C TRP* 1.3 71.9 - - - +
212C VAL* 1.3 62.4 + - - +
213C PHE* 4.1 2.6 + - + +
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Residues in contact with VAL 212 (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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34C ILE* 3.9 19.1 - - + -
107C HIS* 4.2 28.0 - - + +
144C ALA* 3.3 22.9 - - + +
145C ALA* 5.5 0.2 - - - -
146C PHE* 3.9 28.3 - - + -
192C TYR* 3.3 2.4 - - - -
193C PHE* 2.7 47.7 + - + +
195C TYR* 4.8 8.5 - - + -
210C TRP* 4.9 1.8 - - + +
211C THR* 1.3 78.2 - - - +
213C PHE* 1.3 75.2 + - - +
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Residues in contact with PHE 213 (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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48C LEU* 3.9 27.4 - - + -
50C LEU* 5.7 0.4 - - + -
143C LEU* 4.3 19.7 - - + -
144C ALA 2.9 30.2 + - - +
145C ALA* 4.0 6.3 - - + -
146C PHE* 4.4 9.7 - - - -
185C LEU* 4.2 20.6 - - + -
186C PRO* 3.6 29.6 - - + -
188C ASP 4.0 14.6 - - - -
189C PHE* 3.7 38.8 - + - -
191C ARG 3.8 6.5 - - - -
192C TYR* 4.1 3.8 - - + -
193C PHE* 4.7 1.6 - - - -
211C THR* 4.1 2.0 - - + -
212C VAL* 1.3 83.6 - - - +
214C ASN* 1.3 64.5 + - - +
215C GLN 3.5 19.2 - - - +
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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