Contacts of the strand formed by residues 150 - 157 (chain A) 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 VAL 150 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144A LEU* 4.0 27.7 - - + +
147A LEU* 3.5 47.8 - - + +
149A GLY* 1.3 81.8 + - - +
151A GLU* 1.3 67.9 + - - +
163A ILE* 4.2 18.8 - - + -
164A SER 3.9 2.5 - - - +
169A ALA* 3.9 11.2 - - + +
170A VAL* 4.2 14.4 - - + -
173A ALA* 4.1 9.9 - - + -
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Residues in contact with GLU 151 (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 LEU* 5.2 3.8 - - - -
149A GLY 5.5 3.0 - - - +
150A VAL* 1.3 78.5 - - - +
152A ILE* 1.3 71.3 + - - +
153A ALA* 4.4 0.7 - - - +
163A ILE* 3.3 6.6 - - - -
164A SER 2.9 39.3 + - - +
194A HIS 4.8 0.6 - - - +
195A SER* 3.9 12.4 - - - -
196A SER* 3.0 44.4 + - - -
197A LEU* 4.8 2.4 - - - +
245A THR 4.7 5.9 - - - +
247A PRO* 5.9 2.3 - - - +
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Residues in contact with ILE 152 (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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137A LEU* 4.4 11.2 - - + -
140A ILE* 3.9 8.7 - - + -
141A GLN* 4.8 13.5 - - + +
144A LEU* 3.9 15.9 - - + -
151A GLU* 1.3 78.0 - - - +
153A ALA* 1.3 61.1 + - - +
154A ASN 3.9 5.6 - - - +
155A LEU* 3.3 42.8 - - + -
161A THR* 3.8 19.3 - - + -
162A VAL 3.8 3.6 - - - +
163A ILE* 3.9 13.9 - - + -
194A HIS 4.0 6.2 - - - +
247A PRO* 3.3 20.3 - - + +
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Residues in contact with ALA 153 (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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129A MET* 3.7 18.8 - - + -
151A GLU 3.4 1.2 + - - -
152A ILE* 1.3 74.5 - - - +
154A ASN* 1.4 70.2 + - - +
162A VAL* 2.8 15.0 + - + +
163A ILE 4.3 0.2 - - - -
164A SER* 3.7 11.7 - - - +
193A PHE 3.6 23.8 - - - +
194A HIS* 3.6 16.9 - - + +
247A PRO* 3.4 3.6 - - - +
248A VAL 2.8 21.6 + - - -
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Residues in contact with ASN 154 (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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88A HIS* 3.3 21.8 - - - -
129A MET* 4.8 5.1 - - - +
153A ALA* 1.4 102.2 + - - +
155A LEU* 1.3 64.1 + - - +
156A ASN* 3.3 26.6 + - - +
161A THR* 3.6 12.5 - - - +
162A VAL* 3.1 47.3 + - + +
187A LEU* 5.9 0.5 - - - +
194A HIS* 4.1 10.7 - - - -
248A VAL* 3.6 19.0 - - - +
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Residues in contact with LEU 155 (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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137A LEU* 3.8 32.8 - - + -
152A ILE* 3.3 31.6 - - + -
154A ASN* 1.3 78.0 - - - +
156A ASN* 1.3 57.7 + - - +
157A ALA 3.6 2.5 - - - -
160A GLN 4.6 1.3 - - - -
161A THR* 4.1 8.1 - - - +
247A PRO* 3.9 17.9 - - + -
248A VAL 2.7 22.7 + - - +
249A ARG* 4.1 15.7 - - + -
250A TRP* 3.1 5.4 - - - +
251A VAL* 2.8 34.3 + - + +
252A GLU* 5.3 5.6 - - + +
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Residues in contact with ASN 156 (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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88A HIS* 2.7 29.7 + - - -
154A ASN* 3.3 32.0 + - - +
155A LEU* 1.3 74.9 + - - +
157A ALA* 1.3 64.1 + - - +
160A GLN* 3.2 22.1 + - - +
162A VAL* 3.5 15.2 - - - +
248A VAL 4.8 0.2 - - - +
250A TRP* 3.5 23.6 - - - +
251A VAL* 3.6 2.4 - - - +
277A LEU* 3.6 28.2 - - + +
281A THR* 3.8 3.8 + - - -
51B GLU* 5.7 2.4 + - - -
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Residues in contact with ALA 157 (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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155A LEU 5.1 0.2 - - - -
156A ASN* 1.3 81.1 - - - +
158A PRO* 1.3 75.7 - - + +
159A GLU 3.0 0.5 + - - -
160A GLN* 2.8 42.9 + - + +
161A THR* 4.7 1.4 + - - -
251A VAL* 3.3 13.5 - - - +
277A LEU* 4.1 7.0 - - + +
280A ARG* 4.2 15.3 - - + -
281A THR* 3.4 11.2 - - - +
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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