Contacts of the strand formed by residues 199 - 206 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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199C PHE* 3.4 36.6 - + + +
142E TYR* 3.8 1.3 - - - -
144E PHE* 3.6 32.1 - + + -
145E PHE 3.5 10.1 - - - -
146E GLN* 4.1 12.6 - - + -
181E LEU* 3.8 6.6 - - - +
198E GLY* 1.3 74.8 - - - +
200E GLN* 1.3 72.7 + - - +
142F TYR* 3.1 21.8 - - - -
199F PHE* 3.4 44.6 - + + +
200F GLN* 4.6 3.1 - - + +
201F GLY 3.2 34.1 - - - -
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Residues in contact with GLN 200 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146C GLN* 3.3 41.1 + - + +
197C PHE* 4.8 15.8 - - - +
198C GLY 5.8 1.0 + - - +
199C PHE* 4.6 6.1 - - - +
144E PHE* 3.1 3.6 - - - +
145E PHE 2.8 33.6 + - - +
179E LEU* 4.4 11.1 - - + -
180E ALA* 2.9 37.7 + - - +
181E LEU* 4.0 16.5 - - + +
199E PHE* 1.3 83.9 + - - +
201E GLY* 1.3 63.1 + - - +
202E ARG* 4.8 4.1 + - - -
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Residues in contact with GLY 201 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144C PHE* 4.0 2.4 - - - -
146C GLN* 2.8 19.0 - - - +
199C PHE* 3.1 17.0 - - - -
142E TYR* 3.9 14.6 - - - -
143E VAL 3.1 14.1 - - - -
144E PHE* 3.7 8.1 - - - -
199E PHE* 3.8 5.1 - - - -
200E GLN* 1.3 78.1 - - - +
202E ARG* 1.3 58.4 + - - +
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Residues in contact with ARG 202 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94C GLN* 3.6 23.3 - - - +
96C VAL* 5.0 2.2 - - - +
117C GLY* 4.5 14.5 - - - -
144C PHE* 3.8 13.9 - - + -
146C GLN* 3.4 32.3 - - - +
231C GLY 3.6 23.8 + - - -
232C ALA* 4.6 3.8 - - - +
234C VAL* 3.9 13.2 - - + +
142E TYR* 3.9 8.9 - - - -
143E VAL* 2.9 32.0 + - + +
178E ALA 3.9 25.4 + - - +
179E LEU* 5.1 7.3 - - + +
200E GLN* 4.8 7.7 + - - -
201E GLY* 1.3 74.6 - - - +
203E LEU* 1.3 67.6 + - - +
204E LEU* 3.6 3.3 + - + +
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Residues in contact with LEU 203 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92C PHE* 4.4 10.1 - - + -
93C ALA 3.2 32.1 - - - +
94C GLN* 2.8 44.9 + - + +
117C GLY* 4.9 0.7 - - - +
119C SER* 5.1 3.8 + - - +
144C PHE* 3.9 15.7 - - + -
237C LEU 3.8 11.9 - - - +
238C PHE* 3.8 21.3 - - + -
140E VAL* 4.0 14.4 - - + -
141E TYR 3.2 11.0 - - - +
142E TYR* 4.0 13.7 - - + +
202E ARG* 1.3 74.6 + - - +
204E LEU* 1.3 59.7 + - - +
205E HIS 4.3 0.4 + - - -
240E VAL* 4.0 12.3 - - + -
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Residues in contact with LEU 204 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140E VAL* 4.3 3.1 - - - -
141E TYR 2.8 31.9 + - - +
143E VAL* 4.1 18.2 - - + -
165E LEU* 6.2 2.0 - - + -
167E LEU* 5.9 2.0 - - + -
178E ALA* 5.7 9.6 - - + -
202E ARG* 4.8 4.3 - - + +
203E LEU* 1.3 74.7 - - - +
205E HIS* 1.3 61.8 + - - +
206E LEU* 3.3 24.6 + - + +
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Residues in contact with HIS 205 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119C SER* 6.0 3.8 - - - +
139E GLY 3.5 7.4 - - - +
140E VAL* 4.0 19.4 - - + +
167E LEU* 5.2 4.3 - - - +
204E LEU* 1.3 70.2 - - - +
206E LEU* 1.3 65.7 + - - +
207E SER* 4.2 1.0 + - - -
210E GLN* 4.9 3.3 + - - -
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Residues in contact with LEU 206 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135E VAL* 3.8 26.0 - - + -
138E ALA* 3.5 2.3 - - - +
139E GLY 2.8 36.7 + - - +
141E TYR* 3.5 33.9 - - + -
143E VAL* 4.7 4.7 - - + -
165E LEU* 6.4 0.7 - - + -
167E LEU* 4.2 27.4 - - + -
204E LEU* 3.8 23.6 - - + +
205E HIS* 1.3 80.9 - - - +
207E SER* 1.3 66.8 + - - +
210E GLN* 4.4 10.3 - - + +
237E LEU* 4.4 12.1 - - + -
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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