Contacts of the strand formed by residues 196 - 202 (chain D) 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 ASN 196 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168D ARG* 2.9 37.4 + - - +
180D GLU 3.3 8.8 - - - +
181D THR* 3.8 18.6 - - - -
182D TRP 3.2 13.1 + - - +
183D ASN* 2.7 38.3 + - - +
193D ALA* 3.0 26.8 + - - +
195D LYS* 1.3 71.2 - - - +
197D ILE* 1.3 75.9 + - - +
198D PRO* 4.4 3.8 - - - +
438D ASN* 4.9 5.5 - - - +
468D ALA 3.8 7.9 + - - +
469D SER* 4.1 5.9 + - - -
470D VAL 4.6 0.2 + - - -
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Residues in contact with ILE 197 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165D LEU* 3.0 26.9 + - - +
166D GLY* 3.8 20.6 - - - +
181D THR* 3.9 3.8 - - - +
195D LYS* 4.5 3.4 - - + +
196D ASN* 1.3 89.6 - - - +
198D PRO* 1.3 63.8 - - - +
199D PHE* 2.8 23.6 + - + +
254D TYR* 3.6 23.1 - - - +
468D ALA 4.9 1.3 - - - -
469D SER* 3.6 8.5 - - - +
470D VAL* 3.6 30.7 - - + +
473D GLN* 5.3 0.2 - - - +
503D SER* 4.3 11.0 - - - +
505D PHE* 3.7 29.2 - - + -
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Residues in contact with PRO 198 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82D TYR* 3.4 29.6 - - + +
165D LEU* 4.3 0.2 - - + -
181D THR* 3.8 27.1 - - + +
196D ASN 4.4 2.7 - - - +
197D ILE* 1.3 79.1 - - - +
199D PHE* 1.3 57.4 + - - +
208D VAL 3.7 1.4 - - - +
209D LEU* 3.5 5.5 - - + +
210D VAL* 2.9 48.5 + - + +
212D HIS 4.3 3.4 - - - +
216D VAL* 4.3 7.6 - - + -
218D PHE* 3.9 20.6 - - + -
470D VAL* 3.7 10.8 - - + -
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Residues in contact with PHE 199 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164D GLY* 4.1 0.2 - - - -
165D LEU* 2.8 28.2 + - - +
197D ILE* 2.8 22.9 + - + +
198D PRO* 1.3 75.4 - - - +
200D TYR* 1.3 77.1 + - - +
201D MET* 4.1 7.0 - - + -
207D GLY* 4.0 2.2 - - - -
208D VAL 3.4 26.5 - - - -
209D LEU* 4.1 5.4 - - + -
242D ILE* 3.9 10.1 - - + -
250D VAL* 3.9 21.5 - - + -
251D LEU* 4.2 13.9 - - + -
254D TYR* 3.5 44.4 - + + -
502D LEU 3.7 23.3 - - - -
503D SER* 4.2 10.4 + - - -
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Residues in contact with TYR 200 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154D LEU* 3.7 22.2 - - - +
156D LEU* 5.5 0.4 - - + -
162D VAL* 3.6 21.1 - - + -
163D TYR 3.3 14.8 - - - +
165D LEU* 4.0 12.1 - - + -
199D PHE* 1.3 81.3 - - - +
201D MET* 1.3 67.7 + - - +
202D THR* 4.1 15.7 - - + -
206D TYR* 4.7 6.4 + + - -
207D GLY* 3.2 2.3 - - - -
208D VAL* 2.9 72.3 + - + +
218D PHE* 3.9 24.0 - + - -
220D VAL* 6.2 0.2 - - + -
228D VAL* 3.6 41.4 - - + +
230D PHE* 4.4 4.3 - + - -
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Residues in contact with MET 201 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162D VAL* 3.6 2.3 - - - +
163D TYR* 2.9 38.0 + - + +
199D PHE* 4.1 8.3 - - + -
200D TYR* 1.3 77.8 - - - +
202D THR* 1.3 68.8 + - - +
206D TYR 3.4 14.4 - - - +
207D GLY* 3.9 5.8 - - - -
247D PRO* 3.3 45.1 - - + +
250D VAL* 4.5 6.5 - - + -
251D LEU* 4.1 23.8 - - + -
502D LEU* 4.0 41.1 - - + +
592D MET* 4.5 6.1 - - + -
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Residues in contact with THR 202 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156D LEU* 4.2 1.6 - - + -
160D GLU* 2.9 31.7 + - - +
161D THR 3.1 14.8 - - - +
162D VAL* 4.1 16.6 - - + -
163D TYR* 4.4 5.2 - - - -
200D TYR* 4.1 11.9 - - + -
201D MET* 1.3 84.1 - - - +
203D ASN* 1.3 59.9 + - - +
204D ARG 3.0 14.0 + - - -
205D GLY* 3.5 9.0 + - - -
206D TYR* 3.1 33.8 + - + +
247D PRO* 4.7 5.9 - - - +
592D MET* 4.5 4.6 - - - +
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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