Contacts of the strand formed by residues 199 - 206 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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142A TYR* 3.8 2.2 - - - -
144A PHE* 3.6 31.9 - + + -
145A PHE 3.5 9.9 - - - -
146A GLN* 4.1 14.8 - - + -
181A LEU* 3.8 7.2 - - - +
198A GLY* 1.3 74.8 - - - +
200A GLN* 1.3 74.0 + - - +
142B TYR* 3.2 20.4 - - - -
199B PHE* 3.5 26.0 + + - +
200B GLN* 4.7 3.6 - - - +
201B GLY 3.1 32.5 - - - -
197D PHE* 6.2 0.5 - - - +
199D PHE* 3.5 53.3 + + + +
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Residues in contact with GLN 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A PHE* 3.1 3.5 - - - +
145A PHE* 2.8 39.4 + - + +
179A LEU* 3.7 15.9 - - + +
180A ALA 2.9 34.7 + - - +
181A LEU* 4.0 13.6 - - + +
199A PHE* 1.3 85.0 + - - +
201A GLY* 1.3 62.5 + - - +
202A ARG* 4.1 5.4 + - - -
146D GLN* 3.1 42.9 + - + +
148D GLU* 5.9 1.6 - - - +
197D PHE* 3.8 19.6 - - - +
198D GLY 5.7 1.4 + - - +
199D PHE* 4.6 5.1 - - - +
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Residues in contact with GLY 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A TYR* 3.9 13.9 - - - -
143A VAL 3.1 12.8 - - - -
144A PHE* 3.7 8.5 - - - -
179A LEU* 4.1 1.6 - - - -
199A PHE* 3.8 5.5 - - - -
200A GLN* 1.3 78.3 - - - +
202A ARG* 1.3 60.4 + - - +
144D PHE* 3.9 2.9 - - - -
146D GLN* 2.7 19.4 + - - +
199D PHE* 3.3 15.5 - - - -
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Residues in contact with ARG 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A TYR* 3.9 8.1 - - - -
143A VAL* 2.9 31.5 + - - +
177A ALA 5.8 0.2 + - - -
178A ALA 3.9 17.8 + - - -
179A LEU* 3.4 24.8 - - + +
180A ALA 5.5 0.4 - - - +
200A GLN* 4.1 7.3 + - - -
201A GLY* 1.3 74.1 - - - +
203A LEU* 1.3 69.0 + - - +
204A LEU* 3.6 9.9 + - + +
94D GLN* 3.5 22.3 - - - +
96D VAL* 5.1 4.6 - - - +
117D GLY* 5.3 6.5 - - - -
144D PHE* 3.9 12.1 - - + -
146D GLN* 3.1 29.4 - - - +
231D GLY 2.7 29.3 + - - -
232D ALA* 4.3 6.3 - - - +
234D VAL* 3.5 14.3 - - + +
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Residues in contact with LEU 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A VAL* 4.0 14.6 - - + -
141A TYR 3.2 10.8 - - - +
142A TYR* 4.0 19.3 - - + +
202A ARG* 1.3 71.0 - - - +
204A LEU* 1.3 65.3 + - - +
205A HIS 4.3 0.2 - - - -
240A VAL* 4.0 19.7 - - + -
92D PHE* 4.1 14.6 - - + -
93D ALA 3.3 29.2 - - - +
94D GLN* 2.7 45.7 + - + +
117D GLY* 4.7 3.3 - - - +
119D SER* 4.9 4.7 + - - +
144D PHE* 4.2 11.7 - - + -
237D LEU 4.0 10.3 - - - +
238D PHE* 4.1 10.1 - - + -
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Residues in contact with LEU 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A VAL* 4.3 2.9 - - - -
141A TYR 2.8 30.9 + - - -
143A VAL* 3.7 28.9 - - + -
165A LEU* 3.8 26.7 - - + -
167A LEU* 5.0 3.4 - - + -
178A ALA* 3.9 33.2 - - + +
179A LEU* 5.1 2.0 - - + -
202A ARG* 4.1 16.4 - - + +
203A LEU* 1.3 83.3 - - - +
205A HIS* 1.3 61.5 + - - +
206A LEU* 3.3 24.7 + - + +
212A LEU* 5.3 0.4 - - + -
117D GLY* 6.5 1.1 - - - -
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Residues in contact with HIS 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A ALA* 5.3 3.8 - - + -
139A GLY* 3.4 20.8 + - - -
140A VAL* 4.0 17.0 - - + +
167A LEU* 5.3 4.3 - - - +
203A LEU 4.3 0.4 + - - -
204A LEU* 1.3 70.2 - - - +
206A LEU* 1.3 79.2 + - - +
207A SER* 4.2 8.2 + - - -
210A GLN* 4.9 2.9 + - - -
119D SER* 6.3 2.5 - - - -
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Residues in contact with LEU 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A VAL* 3.9 26.7 - - + -
138A ALA* 3.5 2.4 - - - +
139A GLY 2.8 36.9 + - - +
141A TYR* 3.5 33.7 - - + -
143A VAL* 4.6 2.2 - - + -
167A LEU* 4.2 27.6 - - + -
204A LEU* 3.8 26.7 - - + +
205A HIS* 1.3 86.8 + - - +
207A SER* 1.3 66.6 - - - +
210A GLN* 4.4 7.6 - - + +
212A LEU* 4.2 10.5 - - + -
237A LEU* 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