Contacts of the strand formed by residues 206 - 213 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23B ALA* 5.1 1.3 - - + +
26B GLY* 3.3 13.4 - - - -
27B ARG* 4.5 3.8 - - - +
28B PHE* 2.9 57.1 + - + +
29B GLN* 3.0 29.1 + - - +
135B GLY* 3.2 31.1 + - - +
136B ARG 4.1 0.3 + - - +
197B GLY 3.4 5.2 - - - +
198B SER* 4.1 0.4 - - - -
204B CYS 4.0 1.1 - - - +
205B ALA* 1.3 74.2 - - - +
207B GLY* 1.3 63.8 + - - +
208B VAL* 3.4 4.6 + - - +
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Residues in contact with GLY 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135B GLY 4.9 0.9 - - - -
136B ARG 3.3 14.6 - - - +
137B PRO* 4.0 4.9 - - - -
138B GLY* 2.8 29.3 + - - -
139B GLY 3.9 1.9 + - - -
140B LEU 5.3 0.4 - - - -
196B GLU* 3.6 23.0 + - - +
197B GLY 2.9 6.2 + - - -
206B GLN* 1.3 76.7 - - - +
208B VAL* 1.3 61.2 + - - +
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Residues in contact with VAL 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140B LEU* 3.5 24.9 - - + +
142B VAL* 3.8 26.2 - - + -
196B GLU* 3.4 2.2 - - - -
197B GLY 2.8 33.3 + - - +
198B SER 3.7 0.7 - - - +
199B LEU* 3.7 24.9 - - + +
205B ALA* 3.7 23.3 - - + +
206B GLN 4.5 2.2 - - - +
207B GLY* 1.3 77.2 - - - +
209B ILE* 1.3 65.6 + - - +
210B TRP* 3.4 26.4 + - + +
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Residues in contact with ILE 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82B LEU* 3.8 21.3 - - + -
86B ARG* 3.8 24.0 - - - +
88B TYR* 3.9 10.1 - - - +
138B GLY* 3.7 28.7 - - - +
140B LEU 3.0 10.3 + - - +
141B ALA* 3.2 3.9 - - + +
142B VAL 2.9 27.9 + - - +
194B GLN* 3.8 27.6 - - + +
195B TYR 3.7 5.8 - - - +
196B GLU* 4.2 17.9 - - + +
208B VAL* 1.3 70.0 - - - +
210B TRP* 1.3 61.6 + - - +
211B THR* 4.3 2.3 + - - +
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Residues in contact with TRP 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B SER* 3.1 19.4 + - - -
107B HIS* 3.6 18.6 - + - +
119B HIS* 3.6 34.3 - + - -
142B VAL* 3.3 40.4 - - + -
144B ALA* 4.2 9.2 - - + -
193B PHE 3.9 0.2 - - - +
194B GLN* 3.2 7.3 - - - +
195B TYR* 2.8 60.0 + + + +
197B GLY 4.1 3.4 - - - -
198B SER 2.8 27.4 + - - +
200B THR* 3.8 11.2 - - + -
208B VAL* 3.5 24.4 - - + +
209B ILE* 1.3 71.7 - - - +
211B THR* 1.3 60.3 + - - +
212B VAL* 4.1 1.8 - - + -
269B Y0R 3.4 26.9 - - - -
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Residues in contact with THR 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B LEU* 4.0 21.8 - - + -
82B LEU* 3.8 10.0 - - - +
141B ALA* 6.1 0.2 - - - +
142B VAL 3.0 7.3 + - - +
143B LEU* 3.5 15.3 - - + +
144B ALA* 2.8 33.1 + - - +
192B TYR* 3.5 38.8 - - + -
193B PHE 3.3 3.4 - - - -
194B GLN* 2.9 22.9 + - - +
209B ILE* 4.3 3.3 + - - +
210B TRP* 1.3 73.3 - - - +
212B VAL* 1.3 56.6 + - - +
213B PHE* 4.0 2.8 + - + +
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Residues in contact with VAL 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B ILE* 3.9 21.1 - - + -
107B HIS* 4.1 28.3 - - + +
144B ALA* 3.4 23.6 - - + +
145B ALA* 5.4 0.2 - - - -
146B PHE* 3.8 29.4 - - + -
192B TYR* 3.4 2.6 - - - -
193B PHE* 2.8 42.8 + - + +
195B TYR* 4.8 8.5 - - + -
210B TRP* 4.9 1.6 - - + -
211B THR* 1.3 77.9 - - - +
213B PHE* 1.3 74.6 + - - +
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Residues in contact with PHE 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B LEU* 3.7 27.1 - - + -
50B LEU* 5.7 0.2 - - + -
143B LEU* 4.3 19.1 - - + -
144B ALA 3.0 29.7 + - - +
145B ALA* 4.0 5.6 - - + -
146B PHE* 4.4 8.8 - - - -
185B LEU* 4.3 20.0 - - + -
186B PRO* 3.6 30.3 - - + -
188B ASP 4.1 15.5 - - - -
189B PHE* 3.7 37.7 - + - -
191B ARG 3.9 6.7 - - - -
192B TYR* 4.2 3.8 - - + +
193B PHE* 4.8 1.8 - - - -
211B THR* 4.9 1.8 - - + -
212B VAL* 1.3 83.4 - - - +
214B ASN* 1.3 63.3 + - - +
215B GLN 3.6 18.7 - - - +
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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