Contacts of the strand formed by residues 234 - 239 (chain F) in PDB entry 6CU0
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 VAL 234 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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202C ARG* 3.5 30.3 - - + +
94F GLN* 3.6 30.5 - - + +
95F LEU 3.4 15.0 - - - +
96F VAL* 4.5 7.0 - - + -
109F TRP* 4.1 4.3 - - - -
144F PHE* 4.5 8.3 - - + -
145F PHE* 3.2 7.0 - - - +
146F GLN* 2.9 42.8 + - + +
163F LEU* 6.2 0.2 - - - -
231F GLY 4.0 3.8 - - - +
232F ALA 3.4 13.4 + - - +
233F THR* 1.3 79.9 - - - +
235F LEU* 1.3 64.7 + - - +
236F GLY 4.4 1.1 - - - +
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Residues in contact with LEU 235 (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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94F GLN* 3.3 1.4 - - - -
95F LEU* 2.7 49.1 + - + +
109F TRP* 3.6 26.4 - - + +
133F LEU* 4.9 12.8 - - + -
143F VAL* 4.0 22.2 - - + -
144F PHE 3.6 10.3 - - - +
145F PHE* 4.0 15.0 - - + -
165F LEU* 4.2 17.5 - - + -
212F LEU* 5.3 5.6 - - + +
214F VAL* 3.8 20.0 - - + -
234F VAL* 1.3 76.8 - - - +
236F GLY* 1.3 64.4 + - - +
237F LEU* 5.6 6.3 - - + -
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Residues in contact with GLY 236 (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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93F ALA 3.4 11.4 - - - -
94F GLN* 4.0 2.7 - - - -
143F VAL* 3.5 3.5 - - - +
144F PHE* 2.8 59.3 + - - +
235F LEU* 1.3 78.2 - - - +
237F LEU* 1.3 65.7 + - - +
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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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203C LEU* 3.8 1.4 - - - +
92F PHE* 3.3 4.4 - - - +
93F ALA* 2.9 53.8 + - + +
124F LEU* 3.9 30.3 - - + -
133F LEU* 5.9 5.8 - - + -
135F VAL* 4.9 3.8 - - + -
141F TYR* 4.1 13.7 - - + -
142F TYR 3.2 12.8 - - - +
143F VAL* 3.9 27.8 - - + -
144F PHE* 3.8 3.0 - - - -
206F LEU* 4.5 15.3 - - + -
212F LEU* 5.8 7.4 - - + -
235F LEU* 5.6 7.0 - - + -
236F GLY* 1.3 75.7 - - - +
238F PHE* 1.3 65.8 + - - +
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Residues in contact with PHE 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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142C TYR* 3.7 23.3 - + + -
203C LEU* 3.8 17.9 - - + -
238C PHE* 4.0 20.6 - + - -
240C VAL* 3.9 21.1 - - + -
238E PHE* 3.9 22.9 - + - -
91F MET 3.6 6.5 - - - -
92F PHE* 3.6 15.5 - - + -
141F TYR* 3.3 6.9 - - - -
142F TYR* 3.0 68.0 + + + -
144F PHE* 4.4 4.5 - + - -
237F LEU* 1.3 78.6 - - - +
239F ARG* 1.3 71.9 + - - +
240F VAL* 4.4 4.0 - - + -
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Residues in contact with ARG 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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240C VAL* 5.5 2.6 - - - +
91F MET* 3.0 30.2 + - + +
140F VAL 3.8 2.7 - - - +
141F TYR* 3.4 29.9 - - + -
238F PHE* 1.3 79.8 - - - +
240F VAL* 1.3 60.9 + - - +
241F THR 4.3 12.8 - - - +
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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