Contacts of the helix formed by residues 206 - 214 (chain F) in PDB entry 4XLN
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 ASN 206 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109F LEU* 3.6 19.5 - - - +
114F GLU* 4.4 1.8 + - - +
202F LEU* 2.9 42.7 + - - +
203F ILE 3.8 3.1 - - - +
204F GLU 3.3 0.2 - - - -
205F ALA* 1.3 75.4 - - - +
207F LEU* 1.3 64.2 + - - +
208F ARG 3.1 2.5 - - - -
209F LEU* 3.0 23.5 + - + +
210F VAL* 3.5 8.0 + - - +
235F LEU* 4.1 8.2 - - + +
250F PHE* 3.5 27.8 - - + -
251F SER* 5.0 1.9 + - - -
30O T 2.8 37.8 + - - +
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Residues in contact with LEU 207 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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565D ILE* 4.3 13.2 - - + -
566D ILE* 4.0 17.9 - - + -
99F TYR* 3.1 32.5 - - + +
103F ILE* 3.7 19.5 - - + -
203F ILE* 3.1 11.6 + - + +
204F GLU* 3.3 25.7 + - + +
206F ASN* 1.3 71.6 - - - +
208F ARG* 1.3 58.1 + - - +
209F LEU 3.0 5.1 + - - -
210F VAL* 3.1 2.4 + - - +
211F VAL* 3.0 46.3 + - + +
232F ASN* 3.2 20.0 - - - +
235F LEU* 4.2 5.8 - - + -
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Residues in contact with ARG 208 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103F ILE* 2.7 53.8 + - + +
104F GLY* 3.3 17.4 + - - -
106F VAL 3.7 18.5 + - - +
107F PRO* 5.3 1.8 - - - +
108F LEU* 3.6 34.3 - - - +
204F GLU 4.7 3.4 - - - +
205F ALA 3.9 9.2 - - - +
207F LEU* 1.3 76.5 - - - +
209F LEU* 1.3 59.3 + - - +
211F VAL 4.2 0.9 - - - -
212F SER* 3.7 3.6 + - - -
30O T 2.9 23.7 + - - +
31O G 2.9 68.2 + - - +
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Residues in contact with LEU 209 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206F ASN* 3.0 14.5 + - + +
207F LEU 3.0 0.4 - - - -
208F ARG* 1.3 75.5 - - - +
210F VAL* 1.3 60.8 + - + +
211F VAL 3.1 1.3 - - - -
212F SER* 2.5 39.9 + - - +
213F ILE* 2.9 20.1 + - + +
251F SER* 3.7 30.1 - - - +
254F ALA* 4.7 10.3 - - + -
255F THR* 3.6 23.8 - - + -
29O C 3.7 23.6 - - + -
30O T 3.2 35.5 + - + +
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Residues in contact with VAL 210 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206F ASN 3.8 4.9 - - - +
207F LEU 3.1 2.9 + - - +
209F LEU* 1.3 76.6 - - + +
211F VAL* 1.3 62.7 + - - +
213F ILE* 3.1 19.6 + - + +
214F ALA* 3.3 14.6 + - + +
228F ILE* 3.7 7.2 - - + +
231F GLY* 3.6 7.6 - - - -
232F ASN* 3.3 43.3 - - - +
235F LEU* 3.6 34.5 - - + -
258F ILE* 3.6 28.5 - - + -
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Residues in contact with VAL 211 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99F TYR* 4.0 9.2 - - + -
100F LEU* 4.1 25.6 - - + -
103F ILE* 3.6 17.7 - - + -
207F LEU* 3.0 39.6 + - + +
208F ARG 4.3 3.4 - - - +
210F VAL* 1.3 77.2 - - - +
212F SER* 1.3 61.3 + - - +
213F ILE 3.2 0.9 + - - -
214F ALA* 3.6 10.0 + - - +
215F LYS* 3.8 10.2 + - - +
224F PHE* 5.4 0.9 - - + -
228F ILE* 3.8 35.0 - - + +
31O G 4.2 11.0 - - - +
32O G 4.8 6.3 - - - +
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Residues in contact with SER 212 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208F ARG 3.8 1.0 + - - -
209F LEU* 2.5 34.2 + - - +
211F VAL* 1.3 74.2 - - - +
213F ILE* 1.3 57.8 + - - +
214F ALA 3.5 0.2 - - - -
215F LYS* 3.1 45.3 - - - +
216F LYS* 4.7 3.3 - - - +
30O T 3.5 16.1 - - - -
31O G 3.8 29.2 - - - -
32O G 5.2 2.2 - - - -
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Residues in contact with ILE 213 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209F LEU* 2.9 31.9 + - + +
210F VAL* 3.1 12.5 + - - +
212F SER* 1.3 77.9 - - - +
214F ALA* 1.3 59.3 + - - +
215F LYS 3.1 5.8 + - - -
216F LYS* 3.7 13.2 + - - +
217F TYR* 4.0 14.8 + - + -
255F THR* 3.5 29.4 - - + +
258F ILE* 3.5 44.6 - - + -
259F ARG* 4.5 20.9 - - + +
262F ILE* 4.2 7.0 - - + -
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Residues in contact with ALA 214 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210F VAL 3.3 6.2 + - - +
211F VAL 3.6 1.7 + - - +
212F SER 3.5 0.2 - - - -
213F ILE* 1.3 77.0 - - - +
215F LYS* 1.3 62.1 + - - +
216F LYS 3.4 0.4 - - - -
217F TYR* 3.4 9.2 + - - -
218F THR* 3.5 10.0 - - - +
224F PHE* 4.4 4.8 - - + -
227F LEU* 3.5 28.9 - - + +
228F ILE* 3.6 37.0 - - + -
262F ILE* 3.8 17.9 - - + -
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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