Contacts of the strand formed by residues 199 - 206 (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 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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142C TYR* 3.4 21.1 - - - -
199C PHE* 3.5 26.2 - + + +
200C GLN* 4.6 3.1 - - - +
201C GLY 3.4 30.5 - - - -
197E PHE* 6.0 1.6 - - - +
199E PHE* 3.4 54.3 + + + +
142F TYR* 3.8 1.1 - - - -
144F PHE* 3.6 31.9 - + + -
145F PHE 3.5 9.6 - - - -
146F GLN* 4.1 16.6 - - + -
181F LEU* 3.8 6.7 - - - +
198F GLY* 1.3 75.0 - - - +
200F GLN* 1.3 73.6 + - - +
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Residues in contact with GLN 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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146E GLN* 3.2 37.7 + - + +
147E LEU 6.3 0.2 - - - -
148E GLU* 5.8 1.8 - - - +
197E PHE* 3.6 24.2 - - - +
198E GLY 5.5 1.0 - - - +
199E PHE* 4.6 5.1 - - - +
144F PHE* 3.1 3.5 - - - +
145F PHE* 2.8 41.2 + - + +
179F LEU* 3.7 16.4 - - + +
180F ALA 2.9 35.2 + - - +
181F LEU* 4.0 13.6 - - + +
199F PHE* 1.3 84.8 + - - +
201F GLY* 1.3 62.4 + - - +
202F ARG* 4.6 4.2 + - - -
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Residues in contact with GLY 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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144E PHE* 4.1 2.1 - - - -
146E GLN* 2.6 22.1 - - - +
199E PHE* 3.2 16.6 - - - -
142F TYR* 3.9 13.7 - - - -
143F VAL 3.1 13.9 - - - -
144F PHE* 3.7 8.1 - - - -
179F LEU* 4.1 2.0 - - - -
199F PHE* 3.9 5.5 - - - -
200F GLN* 1.3 78.2 - - - +
202F ARG* 1.3 59.5 + - - +
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Residues in contact with ARG 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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94E GLN* 3.8 19.8 - - - +
96E VAL* 5.2 1.8 - - - +
117E GLY* 5.2 9.7 - - - -
144E PHE* 3.9 13.7 - - + -
146E GLN* 3.2 29.9 - - - +
231E GLY 3.0 27.7 + - - -
232E ALA* 4.3 5.9 - - - +
234E VAL* 3.7 13.2 - - + +
142F TYR* 3.9 9.5 - - - -
143F VAL* 2.9 30.4 + - - +
178F ALA 3.9 16.9 + - - -
179F LEU* 3.4 23.5 - - + +
180F ALA 5.9 0.2 - - - +
200F GLN* 4.6 5.1 + - - -
201F GLY* 1.3 74.1 - - - +
203F LEU* 1.3 68.0 + - - +
204F LEU* 3.6 10.8 + - + +
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Residues in contact with LEU 203 (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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92E PHE* 4.4 13.7 - - + -
93E ALA 3.4 27.8 - - - +
94E GLN* 2.8 49.3 + - + +
117E GLY* 5.0 1.4 - - - +
119E SER* 5.2 3.1 - - - +
144E PHE* 3.9 12.6 - - + -
237E LEU 4.2 9.0 - - - +
238E PHE* 4.2 9.0 - - + -
140F VAL* 4.0 14.4 - - + -
141F TYR 3.2 11.7 - - - +
142F TYR* 4.0 18.8 - - + +
202F ARG* 1.3 71.5 - - - +
204F LEU* 1.3 68.5 + - - +
240F VAL* 4.0 20.0 - - + -
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Residues in contact with LEU 204 (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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140F VAL* 4.3 3.1 - - - -
141F TYR 2.8 32.6 + - - -
143F VAL* 3.7 28.5 - - + -
165F LEU* 3.8 26.7 - - + -
167F LEU* 5.0 3.1 - - + -
178F ALA* 3.9 33.2 - - + +
179F LEU* 5.1 2.2 - - + -
202F ARG* 4.0 16.6 - - + +
203F LEU* 1.3 81.9 - - - +
205F HIS* 1.3 62.7 + - - +
206F LEU* 3.3 25.2 + - + +
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Residues in contact with HIS 205 (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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138F ALA* 5.3 3.1 - - + -
139F GLY* 3.4 19.4 + - - -
140F VAL* 4.0 17.9 - - + +
167F LEU* 5.3 5.0 - - - +
203F LEU 4.3 0.8 + - - -
204F LEU* 1.3 70.4 - - - +
206F LEU* 1.3 80.2 + - - +
207F SER* 4.2 8.6 + - - -
210F GLN* 5.0 2.6 + - - -
39H ASN* 4.4 12.6 + - - -
60H ARG* 4.4 23.9 - - + +
61H THR* 6.3 1.1 - - + -
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Residues in contact with LEU 206 (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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135F VAL* 3.9 26.7 - - + -
138F ALA* 3.5 2.3 - - - +
139F GLY 2.8 36.7 + - - +
141F TYR* 3.5 33.2 - - + -
143F VAL* 4.7 3.8 - - + -
167F LEU* 4.2 26.9 - - + -
204F LEU* 3.8 26.2 - - + +
205F HIS* 1.3 87.1 + - - +
207F SER* 1.3 68.0 + - - +
210F GLN* 4.4 10.8 - - + +
237F LEU* 4.5 11.9 - - + -
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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