Contacts of the strand formed by residues 183 - 187 (chain B) in PDB entry 2CUY
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 ARG 183 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55A LEU* 3.6 39.8 - - + +
57A GLU* 2.9 43.6 + - - +
116A ARG* 5.8 0.2 - - - +
119A GLN* 5.7 6.7 - - - +
132B VAL* 3.5 0.5 - - - +
133B LEU* 2.9 50.5 + - + -
134B LYS* 3.8 20.4 - - + +
181B ARG 5.8 0.7 - - - -
182B ALA* 1.3 73.9 - - - +
184B VAL* 1.3 71.3 + - - +
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Residues in contact with VAL 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A LEU* 4.4 9.2 - - - +
119A GLN* 5.8 3.8 + - - +
124A VAL* 5.8 2.4 - - + +
190A SER* 5.8 0.2 + - - -
130B ALA* 3.8 18.4 - - + -
131B ALA 3.1 12.1 - - - +
132B VAL* 3.8 19.1 - - + -
133B LEU* 5.2 0.4 - - - -
174B ALA* 4.8 7.9 - - + +
177B LEU* 4.5 15.7 - - + -
178B LYS* 4.6 16.7 - - + +
182B ALA 4.1 5.5 + - - +
183B ARG* 1.3 89.0 + - - +
185B VAL* 1.3 76.1 + - - +
186B PHE* 3.6 16.0 + - + +
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Residues in contact with VAL 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A GLU* 3.5 54.3 - - + +
54A THR* 4.4 18.4 - - + -
55A LEU* 4.1 14.8 - - + +
188A PRO 4.8 5.6 - - - +
130B ALA* 3.4 2.3 - - - -
131B ALA* 2.9 33.7 + - + +
133B LEU* 4.7 2.9 - - + -
184B VAL* 1.3 74.8 - - - +
186B PHE* 1.3 59.4 + - - +
187B LEU* 4.0 19.0 + - + +
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Residues in contact with PHE 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A VAL* 3.1 35.7 - - + -
125A GLY* 4.1 8.5 - - - -
188A PRO 4.3 0.7 - - - +
189A VAL 3.9 0.2 - - - -
190A SER* 3.4 26.1 + - - -
128B ALA* 4.4 7.6 - - + -
129B MET 3.9 1.3 - - - -
130B ALA* 3.7 15.7 - - + -
167B ARG* 5.7 0.4 - - + -
170B VAL* 3.7 24.5 - - + -
171B GLU* 3.4 38.8 - - + -
174B ALA* 3.7 11.0 - - + -
184B VAL* 3.6 10.3 + - + +
185B VAL* 1.3 74.7 - - - +
187B LEU* 1.3 66.1 + - - +
188B PRO* 3.3 44.2 - - + +
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Residues in contact with LEU 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187A LEU 5.6 0.4 - - - +
188A PRO* 3.2 47.8 - - + +
128B ALA* 3.7 4.3 - - - +
129B MET* 2.8 64.4 + - + +
130B ALA* 5.4 0.2 - - - -
185B VAL* 4.4 17.3 - - + +
186B PHE* 1.3 78.2 - - - +
188B PRO* 1.3 67.9 - - - +
189B VAL 3.3 4.0 + - - +
190B SER* 4.1 17.5 - - - +
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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