Contacts of the strand formed by residues 208 - 213 (chain A) 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 VAL 208 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140A LEU* 3.5 26.0 - - + +
142A VAL* 3.9 24.2 - - + -
196A GLU* 3.4 3.6 - - - -
197A GLY 2.8 35.2 + - - +
198A SER 4.5 0.4 - - - +
199A LEU* 3.7 24.2 - - + +
205A ALA* 3.6 23.6 - - + +
206A GLN 4.2 2.2 - - - +
207A GLY* 1.3 78.8 - - - +
209A ILE* 1.3 66.4 + - - +
210A TRP* 3.5 25.8 + - + +
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Residues in contact with ILE 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A LEU* 3.9 21.3 - - + +
86A ARG* 4.1 8.3 - - - +
88A TYR* 4.3 8.3 - - - +
138A GLY* 3.8 27.4 - - - +
140A LEU 3.1 9.8 + - - +
141A ALA* 3.3 4.1 - - + +
142A VAL 2.9 27.4 + - - +
194A GLN* 3.8 33.2 - - + +
195A TYR 3.7 3.6 - - - +
196A GLU* 4.1 26.9 - - + +
208A VAL* 1.3 73.2 - - - +
210A TRP* 1.3 61.5 + - - +
211A THR* 4.0 1.4 + - - +
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Residues in contact with TRP 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A SER* 3.0 17.7 + - - -
107A HIS* 3.6 19.1 - + - +
119A HIS* 3.6 31.4 - + - -
142A VAL* 3.3 42.2 - - + -
144A ALA* 4.2 8.5 - - + -
193A PHE 3.9 0.2 - - - +
194A GLN* 3.2 8.4 - - - +
195A TYR* 2.8 59.0 + + + +
197A GLY 4.1 3.8 - - - -
198A SER 2.8 27.0 + - - +
200A THR* 3.7 12.1 - - + -
208A VAL* 3.6 25.5 - - + +
209A ILE* 1.3 72.3 - - - +
211A THR* 1.3 59.7 + - - +
212A VAL* 4.2 2.2 - - + -
268A Y0R 3.4 27.1 - - - -
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Residues in contact with THR 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A LEU* 3.9 19.1 - - + -
82A LEU* 3.8 10.6 - - - +
142A VAL 3.0 7.1 + - - -
143A LEU* 3.5 14.8 - - + +
144A ALA* 2.8 33.3 + - - +
192A TYR* 3.5 37.0 - - + -
193A PHE 3.3 3.4 - - - -
194A GLN* 2.9 24.1 + - - +
209A ILE* 4.6 2.3 + - - +
210A TRP* 1.3 73.0 - - - +
212A VAL* 1.3 59.9 + - - +
213A PHE* 4.1 6.1 + - + -
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Residues in contact with VAL 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A ILE* 3.8 31.2 - - + -
107A HIS* 4.1 24.2 - - + +
117A GLU* 6.1 0.2 - - - -
144A ALA* 3.3 20.0 - - + +
145A ALA 6.1 0.2 - - - -
146A PHE* 3.9 28.9 - - + -
192A TYR* 3.3 2.2 - - - -
193A PHE* 2.8 47.3 + - + +
195A TYR* 4.6 10.5 - - + -
210A TRP* 4.9 0.9 - - + -
211A THR* 1.3 77.8 - - - +
213A PHE* 1.3 67.5 + - - +
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Residues in contact with PHE 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A LEU* 3.9 27.1 - - + -
143A LEU* 4.1 25.8 - - + -
144A ALA 3.0 27.7 + - - +
145A ALA* 4.0 5.5 - - + -
146A PHE* 4.5 11.4 + - - -
185A LEU* 4.3 13.9 - - + -
186A PRO* 3.8 23.1 - - + -
188A ASP 3.7 15.0 - - - +
189A PHE* 3.6 40.4 - + - -
191A ARG 3.9 3.6 - - - +
192A TYR* 4.0 11.2 - + + -
193A PHE* 5.1 2.1 - - - -
211A THR* 4.6 5.6 - - + -
212A VAL* 1.3 83.1 - - - +
214A ASN* 1.3 63.7 + - - +
215A GLN 3.6 18.6 - - - +
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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