Contacts of the helix formed by residues 206 - 214 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109L LEU* 3.6 19.8 - - - +
114L GLU* 4.4 2.0 + - - +
202L LEU* 2.9 43.9 + - - +
203L ILE 3.8 3.1 - - - +
204L GLU 3.3 0.2 - - - -
205L ALA* 1.3 75.8 - - - +
207L LEU* 1.3 63.7 + - - +
208L ARG 3.1 2.2 - - - -
209L LEU* 3.0 23.8 + - + +
210L VAL* 3.5 7.8 + - - +
235L LEU* 4.1 7.6 - - + -
250L PHE* 3.5 28.4 - - + +
251L SER* 5.0 1.6 + - - -
30R T 2.8 40.5 + - + +
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Residues in contact with LEU 207 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
565J ILE* 4.3 11.7 - - + -
566J ILE* 4.0 18.4 - - + -
99L TYR* 3.1 32.1 - - + +
103L ILE* 3.7 20.2 - - + -
203L ILE 3.1 9.9 + - - +
204L GLU* 3.3 26.3 + - + +
206L ASN* 1.3 72.6 - - - +
208L ARG* 1.3 57.8 + - - +
209L LEU 3.0 5.9 + - - -
210L VAL* 3.1 2.4 + - - +
211L VAL* 3.0 46.1 + - + +
232L ASN* 3.2 19.5 - - - +
235L LEU* 4.2 6.1 - - + -
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Residues in contact with ARG 208 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103L ILE* 2.7 53.3 + - + +
104L GLY* 3.3 17.2 + - - -
106L VAL 3.7 18.7 + - - -
107L PRO* 5.3 2.0 - - - +
108L LEU* 3.6 35.6 - - - +
204L GLU 4.7 3.6 - - - +
205L ALA 3.9 9.4 - - - +
206L ASN 3.1 0.2 - - - -
207L LEU* 1.3 75.7 - - - +
209L LEU* 1.3 60.1 + - - +
211L VAL 4.2 1.1 - - - -
212L SER* 3.7 3.5 + - - -
30R T 2.9 22.3 + - - +
31R G 2.8 69.4 + - - +
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Residues in contact with LEU 209 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206L ASN* 3.0 15.3 + - + +
207L LEU 3.0 0.4 - - - -
208L ARG* 1.3 74.9 - - - +
210L VAL* 1.3 60.0 + - + +
211L VAL 3.1 1.6 - - - -
212L SER* 2.5 40.0 + - - +
213L ILE* 2.9 19.2 + - + +
235L LEU* 6.3 0.2 - - + -
251L SER* 3.7 30.5 - - - +
254L ALA* 4.7 11.0 - - + -
255L THR* 3.6 24.7 - - + -
29R C 3.7 23.1 - - + -
30R T 3.2 34.6 + - + +
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Residues in contact with VAL 210 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206L ASN 3.8 5.2 - - - +
207L LEU 3.1 2.4 + - - +
209L LEU* 1.3 76.1 - - + +
211L VAL* 1.3 62.6 + - - +
213L ILE* 3.1 19.6 + - + +
214L ALA* 3.3 14.1 + - + +
228L ILE* 3.7 6.6 - - - +
231L GLY* 3.6 7.2 - - - -
232L ASN* 3.3 44.2 - - - +
235L LEU* 3.6 34.5 - - + -
258L ILE* 3.6 28.7 - - + +
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Residues in contact with VAL 211 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99L TYR* 4.0 9.0 - - + -
100L LEU* 4.1 26.0 - - + -
103L ILE* 3.6 17.5 - - + -
207L LEU* 3.0 38.7 + - + +
208L ARG 4.3 3.1 - - - +
210L VAL* 1.3 76.5 - - - +
212L SER* 1.3 61.8 + - - +
213L ILE 3.3 0.9 + - - -
214L ALA* 3.6 9.5 + - - +
215L LYS* 3.8 11.1 + - - +
224L PHE* 5.4 0.7 - - + -
228L ILE* 3.8 35.0 - - + +
31R G 4.2 10.3 - - - +
32R G 4.8 6.3 - - - +
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Residues in contact with SER 212 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208L ARG 3.8 9.3 + - - -
209L LEU* 2.5 33.9 + - - +
211L VAL* 1.3 75.1 - - - +
213L ILE* 1.3 57.7 + - - +
215L LYS* 3.1 44.3 - - - +
216L LYS* 4.7 3.3 - - - +
30R T 3.5 15.8 - - - -
31R G 3.9 21.5 + - - -
32R G 5.2 2.0 - - - -
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Residues in contact with ILE 213 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209L LEU* 2.9 30.6 + - + +
210L VAL* 3.1 12.5 + - - +
212L SER* 1.3 77.5 - - - +
214L ALA* 1.3 60.1 + - - +
215L LYS 3.1 5.3 + - - -
216L LYS* 3.7 12.0 + - - +
217L TYR* 4.0 14.5 + - + -
255L THR* 3.5 30.5 - - + +
258L ILE* 3.5 44.0 - - + -
259L ARG* 4.5 20.6 - - + +
262L ILE* 4.2 6.5 - - + -
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Residues in contact with ALA 214 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210L VAL 3.3 6.0 + - - +
211L VAL 3.6 1.7 + - - +
212L SER 3.5 0.4 - - - -
213L ILE* 1.3 77.2 - - - +
215L LYS* 1.3 62.7 + - - +
216L LYS 3.4 0.9 - - - -
217L TYR* 3.4 8.8 + - - -
218L THR* 3.5 10.2 - - - +
224L PHE* 4.4 4.2 - - - -
227L LEU* 3.5 28.4 - - + +
228L ILE* 3.6 37.2 - - + -
262L ILE* 3.8 18.2 - - + -
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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