Contacts of the strand formed by residues 236 - 243 (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 TYR 236 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68F ARG* 3.4 40.4 + - + +
69F ILE 3.3 7.0 - - - +
70F GLU* 3.2 31.0 - - + +
72F PHE 6.1 0.4 - - - -
77F ASN* 3.5 36.7 - - + +
81F HIS* 5.2 8.3 + - - -
150F MET* 3.6 6.7 - - - +
211F ASN* 5.0 3.2 + - - -
212F HIS* 3.5 31.4 + + - -
232F VAL* 4.2 0.9 - - - +
234F SER* 2.9 36.4 + - - -
235F GLU* 1.3 81.0 - - + +
237F LEU* 1.3 62.8 + - - +
238F GLU* 4.2 11.4 - - + -
435F LYS* 4.6 13.3 + - - -
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Residues in contact with LEU 237 (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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67F VAL 3.4 2.3 - - - +
68F ARG* 3.4 0.7 - - - -
69F ILE* 2.8 49.1 + - + +
150F MET* 3.7 16.8 - - + +
151F PHE* 3.5 39.7 - - - +
152F GLU* 3.6 16.8 - - + +
210F VAL* 4.2 3.6 - - + -
212F HIS* 3.5 24.0 - - + +
230F PHE* 3.9 22.9 - - + +
232F VAL* 4.0 11.7 - - + +
236F TYR* 1.3 75.4 - - - +
238F GLU* 1.3 60.8 + - - +
239F TYR* 4.3 10.4 - - + -
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Residues in contact with GLU 238 (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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58F PHE* 3.5 26.9 - - + -
67F VAL 3.1 12.8 - - - +
68F ARG* 3.1 37.8 + - + +
210F VAL* 3.7 0.9 - - - +
211F ASN* 2.7 65.4 + - + +
212F HIS* 3.1 13.2 + - - +
236F TYR* 4.2 16.3 - - + -
237F LEU* 1.3 75.6 - - - +
239F TYR* 1.3 58.5 + - - +
240F PHE* 4.1 6.7 - - + -
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Residues in contact with TYR 239 (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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65F VAL 3.9 0.5 - - - +
66F GLY* 3.5 1.2 - - - -
67F VAL* 2.8 59.3 + - + +
69F ILE* 4.3 6.5 - - + -
120F LEU* 3.7 7.1 - - - +
122F PHE* 3.5 23.2 - + - -
152F GLU* 2.9 40.8 + - + -
154F LEU* 3.7 16.4 - - + +
208F VAL* 4.9 3.4 - - + -
209F LEU 3.1 12.3 - - - +
210F VAL* 4.0 9.2 - - + -
211F ASN 4.2 0.7 - - - +
230F PHE* 3.8 26.2 - + + -
237F LEU* 4.3 7.9 - - + -
238F GLU* 1.3 77.3 - - - +
240F PHE* 1.3 65.7 + - - +
241F VAL* 3.8 26.2 - - + -
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Residues in contact with PHE 240 (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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58F PHE* 3.7 26.5 - + - -
60F PRO* 3.6 20.0 - - + -
64F ILE* 3.6 24.2 - - + -
65F VAL 3.6 1.6 - - - -
66F GLY* 3.3 30.1 - - - -
84F LEU* 4.0 7.9 - - + -
86F ILE* 5.1 4.0 - - + -
208F VAL* 3.0 7.3 - - - -
209F LEU* 2.7 56.3 + - + +
211F ASN* 3.9 27.1 - - + -
238F GLU* 4.1 6.5 - - - -
239F TYR* 1.3 75.8 - - - +
241F VAL* 1.3 61.7 + - - +
242F ILE* 3.7 3.8 + - + +
257F PHE* 3.8 27.8 - + + -
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Residues in contact with VAL 241 (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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64F ILE* 3.4 2.6 - - - -
65F VAL* 3.0 34.4 + - + +
108F LEU* 3.3 23.7 - - + +
122F PHE* 3.6 53.4 - - + -
129F ILE* 4.8 3.8 - - + -
130F THR* 5.0 2.5 - - + -
154F LEU* 4.9 6.7 - - + -
206F TYR* 4.7 14.4 - - + -
207F GLY 3.6 7.4 - - - +
208F VAL* 4.5 3.4 - - + -
239F TYR* 3.8 18.2 - - + -
240F PHE* 1.3 70.8 - - - +
242F ILE* 1.3 63.3 + - - +
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Residues in contact with ILE 242 (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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63F GLY 3.8 2.2 - - - -
64F ILE* 3.8 27.6 - - + -
108F LEU* 4.5 0.7 - - - -
199F PHE* 4.2 11.2 - - + -
206F TYR* 3.2 6.8 - - - +
207F GLY 2.6 42.9 + - - +
209F LEU* 4.5 10.1 - - + -
240F PHE* 3.9 11.9 - - + +
241F VAL* 1.3 75.9 - - - +
243F ASP* 1.3 63.2 + - - +
250F VAL* 4.0 15.6 - - + +
253F ARG* 3.5 32.3 - - + -
254F TYR* 4.0 30.7 - - + +
257F PHE* 4.6 6.1 - - + -
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Residues in contact with ASP 243 (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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63F GLY* 3.0 22.9 + - - +
107F ASN* 4.1 17.3 + - - +
108F LEU* 3.8 25.0 + - + +
124F ARG* 2.6 55.3 + - - +
129F ILE* 4.7 0.7 - - - +
205F GLY 4.4 0.9 - - - -
206F TYR* 4.6 3.4 - - - -
242F ILE* 1.3 74.9 - - - +
244F GLY* 1.3 61.8 + - - +
245F PRO* 4.7 2.1 - - - +
250F VAL* 4.0 7.9 - - - -
253F ARG* 2.7 34.6 + - - +
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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