Contacts of the strand formed by residues 199 - 202 (chain F) 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 PHE 199 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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165F LEU* 2.8 27.4 + - - +
166F GLY 4.5 0.5 + - - -
197F ILE* 2.8 25.2 + - + +
198F PRO* 1.3 75.4 - - - +
200F TYR* 1.3 78.4 + - - +
201F MET* 4.1 6.5 - - + -
207F GLY* 4.2 3.8 - - - -
208F VAL 3.4 24.7 - - - -
209F LEU* 4.2 5.2 - - + -
242F ILE* 4.2 8.5 - - + -
250F VAL* 4.0 19.7 - - + -
251F LEU* 4.1 11.2 - - + -
254F TYR* 3.6 46.4 - + + +
502F LEU 3.5 24.9 - - - -
503F SER* 4.2 11.6 + - - -
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Residues in contact with TYR 200 (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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154F LEU* 3.6 24.9 + - - +
156F LEU* 5.5 0.2 - - + -
162F VAL* 3.6 21.5 - - + -
163F TYR 3.4 13.2 - - - +
165F LEU* 3.8 13.0 - - + -
199F PHE* 1.3 80.2 - - - +
201F MET* 1.3 67.5 + - - +
202F THR* 4.0 18.8 - - + -
206F TYR* 4.7 6.1 + + - -
207F GLY* 3.2 2.1 - - - -
208F VAL* 2.8 74.8 + - + +
218F PHE* 4.0 22.0 - + - -
228F VAL* 3.8 35.0 - - + +
230F PHE* 4.5 4.1 - + - -
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Residues in contact with MET 201 (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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162F VAL* 3.6 3.3 - - - +
163F TYR* 2.9 36.0 + - + +
199F PHE* 4.1 5.2 - - + -
200F TYR* 1.3 77.4 - - - +
202F THR* 1.3 67.4 + - - +
206F TYR 3.4 14.4 - - - +
207F GLY* 3.8 5.6 - - - -
247F PRO* 3.4 41.3 - - + +
250F VAL* 4.4 7.2 - - + -
251F LEU* 3.8 32.5 - - + -
502F LEU* 3.4 43.1 - - + +
592F MET* 4.2 7.4 - - + -
593F MET* 5.2 0.4 - - + -
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Residues in contact with THR 202 (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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156F LEU* 4.3 3.1 - - + -
160F GLU* 3.1 29.1 + - - +
161F THR 3.1 14.6 - - - +
162F VAL* 4.1 11.0 - - + -
163F TYR* 4.4 1.3 - - - -
200F TYR* 4.0 19.1 - - + -
201F MET* 1.3 83.4 - - - +
203F ASN* 1.3 59.1 + - - +
204F ARG* 2.9 14.0 + - - +
205F GLY* 3.3 11.3 + - - -
206F TYR* 3.1 32.8 + - + +
247F PRO* 4.6 5.4 - - - +
592F MET* 4.4 9.4 - - - +
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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