Contacts of the strand formed by residues 142 - 147 (chain B) in PDB entry 2E4Y
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 ILE 142 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40B VAL* 3.6 18.2 - - + -
42B GLY* 4.0 14.4 - - - +
94B HIS* 4.3 10.3 - - + +
112B PHE* 3.7 36.3 - - + +
115B ALA* 3.9 13.7 + - + -
116B SER* 5.1 6.0 + - - +
140B LEU* 2.8 21.0 + - + +
141B LEU* 1.3 81.6 - - - +
143B ALA* 1.3 63.5 + - - +
144B GLY* 3.5 27.8 - - - +
145B VAL* 4.2 11.7 - - + -
166B ILE* 4.4 15.3 - - + +
425B LEU* 4.9 2.3 - - - +
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Residues in contact with ALA 143 (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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39B LEU* 4.4 8.7 - - + -
40B VAL 2.7 20.2 + - - +
41B LEU* 4.4 2.0 - - + -
141B LEU 3.7 0.9 + - - +
142B ILE* 1.3 76.4 - - - +
144B GLY* 1.3 57.0 + - - +
166B ILE* 4.6 1.9 - - - +
167B PRO* 3.3 24.5 - - - +
400B MET* 5.2 0.4 - - - -
404B LEU* 4.2 24.9 - - + -
425B LEU* 3.5 27.8 - - + +
430B LEU* 3.7 8.4 - - - +
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Residues in contact with GLY 144 (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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40B VAL 3.9 0.8 + - - -
41B LEU* 3.3 13.2 - - - +
42B GLY 2.8 22.0 + - - -
142B ILE* 3.5 2.3 - - - +
143B ALA* 1.3 80.6 - - - +
145B VAL* 1.3 65.3 + - - -
166B ILE* 4.1 4.5 - - - -
167B PRO* 3.2 13.9 - - - -
400B MET* 3.9 15.5 - - - -
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Residues in contact with VAL 145 (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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42B GLY* 3.8 10.3 - - - +
44B LEU* 4.3 25.4 - - + -
112B PHE* 4.0 31.0 - - + -
142B ILE* 4.2 5.4 - - + -
144B GLY* 1.3 74.9 - - - +
146B ILE* 1.3 74.4 + - - +
147B GLY* 3.7 2.9 + - - +
161B LEU* 4.4 16.6 - - + -
166B ILE* 4.1 15.5 - - + +
167B PRO 2.8 12.3 + - - +
168B GLN* 3.2 10.7 - - + -
169B ILE* 2.9 27.1 + - - +
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Residues in contact with ILE 146 (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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41B LEU* 4.8 11.7 - - + -
42B GLY 3.0 14.6 + - - +
43B GLY* 3.4 3.3 - - - -
44B LEU 3.1 20.6 + - - +
45B PHE* 4.5 2.4 - - + -
72B MET* 3.9 15.0 - - + -
145B VAL* 1.3 70.8 - - - +
147B GLY* 1.3 59.6 + - - +
169B ILE* 3.5 28.0 - - + +
171B TYR* 4.2 20.3 - - + -
393B VAL* 5.0 1.1 - - + +
396B ALA* 3.5 35.2 - - + +
397B VAL* 3.7 28.5 - - + +
400B MET* 4.1 9.0 - - + -
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Residues in contact with GLY 147 (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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44B LEU* 3.7 19.1 - - - -
145B VAL* 3.7 5.6 + - - +
146B ILE* 1.3 76.9 - - - +
148B GLY* 1.3 62.0 + - - -
154B SER* 3.5 2.4 + - - -
168B GLN* 3.3 22.1 + - - +
169B ILE 2.8 15.5 + - - +
170B SER* 3.5 13.5 - - - -
171B TYR* 3.8 8.5 - - - -
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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