Contacts of the strand formed by residues 146 - 150 (chain B) in PDB entry 2CUK
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 THR 146 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144B GLY 3.7 2.3 + - - -
145B LEU* 1.3 71.3 - - - +
147B LEU* 1.3 63.8 + - - +
168B MET* 4.4 2.0 - - - -
169B ARG* 2.9 49.7 + - - +
171B VAL* 3.6 29.2 - - + -
193B GLU* 3.9 12.7 + - - +
194B ALA* 3.6 8.9 - - - -
195B ASP* 2.7 44.1 + - - +
196B VAL 3.0 7.2 + - - -
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Residues in contact with LEU 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B LEU* 6.1 0.2 - - + -
110B LEU* 5.4 4.5 - - + -
145B LEU 3.8 1.0 + - - -
146B THR* 1.3 72.5 - - - +
148B GLY* 1.3 59.7 + - - +
149B LEU* 3.9 31.2 - - + -
159B VAL* 4.0 15.5 - - + +
160B ALA* 4.7 1.6 - - - -
163B ALA* 3.5 26.7 - - + -
168B MET* 3.8 18.4 - - + -
169B ARG 2.7 13.6 + - - +
170B VAL* 3.5 11.5 - - + +
171B VAL* 3.0 26.2 + - - +
196B VAL* 3.3 35.9 - - + +
198B SER* 4.1 10.8 - - - -
226B LEU* 5.0 2.9 - - + -
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Residues in contact with GLY 148 (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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147B LEU* 1.3 72.4 - - - +
149B LEU* 1.3 62.7 + - - -
150B VAL 3.8 0.5 + - - -
171B VAL* 3.4 19.3 - - - -
190B LEU* 3.8 14.7 - - - +
194B ALA* 3.8 7.4 - - - +
196B VAL 2.7 13.4 + - - -
197B VAL* 3.4 9.2 - - - +
198B SER 3.1 22.9 + - - +
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Residues in contact with LEU 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B LEU* 3.9 23.6 - - + -
148B GLY* 1.3 71.7 - - - -
150B VAL* 1.3 61.6 + - - +
151B GLY 3.4 13.5 + - - +
152B MET* 3.3 19.1 - - + -
156B GLY* 3.0 30.7 - - - +
159B VAL* 4.3 4.0 - - + -
160B ALA* 3.9 16.4 - - + +
170B VAL* 4.7 3.1 - - + -
171B VAL 3.0 14.8 + - - +
172B TYR* 3.2 6.2 - - + +
173B HIS 3.0 26.3 + - - -
190B LEU* 3.4 1.9 - - - +
198B SER* 3.5 28.3 - - - +
200B HIS* 3.7 11.4 - - + +
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Residues in contact with VAL 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B LEU* 1.3 70.3 - - - +
151B GLY* 1.3 58.8 - - - +
173B HIS* 4.0 12.1 - - + +
187B LEU* 4.1 26.7 - - + -
190B LEU* 4.3 10.5 - - + -
191B LEU* 5.3 1.3 - - + -
197B VAL* 4.0 17.0 - - + -
198B SER 3.0 6.7 + - - -
199B LEU* 3.8 26.9 - - + -
200B HIS 3.0 25.6 + - - -
201B THR* 3.5 10.7 + - + -
210B LEU* 4.1 26.5 - - + -
211B LEU* 5.5 0.9 - - + -
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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
------------------------------------------------------------
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