Contacts of the strand formed by residues 206 - 210 (chain B) in PDB entry 1XSK
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 TYR 206 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B ARG* 4.5 1.1 - - - +
129B ILE* 3.7 30.5 - - + -
130B THR* 3.5 35.4 + - + -
154B LEU* 5.6 0.2 - - + -
155B ASP 3.6 7.4 + - - -
156B LEU* 4.3 2.4 - - - +
160B GLU* 2.6 29.3 + - - -
200B TYR* 4.7 7.2 + + - -
201B MET* 3.5 1.9 - - - +
202B THR* 3.3 42.9 + - + +
204B ARG* 3.5 25.8 - - + -
205B GLY* 1.3 79.6 - - - +
207B GLY* 1.3 64.3 + - - +
208B VAL* 4.0 23.6 - - + -
241B VAL* 4.5 5.2 - - + -
242B ILE 3.1 14.4 - - - +
243B ASP* 4.6 0.7 - - - -
250B VAL* 3.7 7.3 - - - +
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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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199B PHE* 4.3 2.7 - - - -
200B TYR 3.2 13.7 - - - -
201B MET* 3.9 3.6 - - - -
206B TYR* 1.3 75.0 - - - +
208B VAL* 1.3 67.6 + - - +
241B VAL* 3.5 1.9 - - - +
242B ILE* 2.6 44.3 + - - -
250B VAL* 3.8 14.3 - - - +
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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
----------------------------------------------------------
154B LEU* 4.1 13.7 - - + -
198B PRO 3.8 1.0 - - - +
199B PHE* 3.4 6.5 - - - -
200B TYR* 2.9 74.2 + - + +
206B TYR* 4.0 17.5 - - + -
207B GLY* 1.3 79.3 - - - +
209B LEU* 1.3 64.7 + - - +
210B VAL* 4.8 2.9 - - + -
230B PHE* 4.4 16.4 - - + -
239B TYR* 5.0 4.0 - - + -
240B PHE 3.0 13.7 - - - +
241B VAL* 4.5 6.5 - - + -
242B ILE* 4.9 0.2 - - - -
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Residues in contact with LEU 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 TYR* 4.9 2.9 - - + -
84B LEU* 4.6 10.5 - - + -
198B PRO* 3.5 27.1 - - + +
199B PHE* 4.1 19.0 - - + -
208B VAL* 1.3 74.0 - - - +
210B VAL* 1.3 72.3 + - - +
211B ASN* 3.3 5.6 + - - +
239B TYR* 3.2 5.4 - - - -
240B PHE* 3.0 44.4 + - + +
242B ILE* 4.8 4.7 - - + +
254B TYR* 4.2 7.0 - - + -
257B PHE* 4.1 24.2 - - + -
258B THR* 4.2 19.1 - - + -
470B VAL* 4.2 16.2 - - + -
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Residues in contact with VAL 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B TYR* 4.0 0.3 - - - -
198B PRO* 2.9 31.3 + - + +
208B VAL* 4.8 4.7 - - + -
209B LEU* 1.3 74.3 - - - +
211B ASN* 1.3 57.5 + - - +
212B HIS* 2.8 29.6 + - - +
216B VAL* 3.8 20.9 - - + -
218B PHE* 3.4 35.4 - - + -
230B PHE* 3.9 25.4 - - + -
232B VAL* 5.6 0.9 - - + -
237B LEU* 4.1 15.7 - - + -
238B GLU 4.0 2.7 - - - +
239B TYR* 4.2 2.9 - - + -
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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