Contacts of the strand formed by residues 41 - 48 (chain B) in PDB entry 2EWY
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 GLN 41 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35B LEU* 3.4 2.7 - - - -
36B ILE* 2.8 41.5 + - + +
39B PRO* 4.4 5.8 + - + +
40B PRO* 1.3 77.0 - - - +
42B LYS* 1.3 64.5 + - - +
43B LEU* 3.5 7.4 + - + +
67B TYR 3.7 5.7 - - - +
68B PHE* 3.1 38.2 - - + -
69B ASP* 3.0 39.8 + - - +
72B ARG* 4.0 33.0 + - + +
73B SER* 4.4 7.1 - - - -
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Residues in contact with LYS 42 (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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33B GLU* 2.9 40.6 + - - +
35B LEU* 3.8 19.6 - - + +
40B PRO 4.1 1.8 + - - -
41B GLN* 1.3 69.8 - - - +
43B LEU* 1.3 71.6 + - - +
44B GLN* 4.0 17.8 + - - +
66B THR* 4.5 11.6 + - - +
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Residues in contact with LEU 43 (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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33B GLU* 3.5 5.0 - - - +
34B MET 2.9 36.2 + - - +
36B ILE* 3.2 31.4 - - + -
41B GLN* 4.1 10.3 - - + +
42B LYS* 1.3 85.5 - - - +
44B GLN* 1.3 68.3 + - - +
45B ILE* 3.9 10.3 - - + -
56B VAL* 3.6 28.7 - - + -
66B THR* 4.4 7.4 - - - +
67B TYR* 4.2 22.2 - - - +
68B PHE* 3.8 15.5 - - + +
132B ASN* 3.7 18.2 - - - +
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Residues in contact with GLN 44 (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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23B GLN* 4.9 2.4 - - - +
31B TYR* 3.7 26.4 - - + -
32B LEU 3.7 1.6 - - - -
33B GLU* 3.6 28.3 + - - +
42B LYS* 4.0 21.4 + - - +
43B LEU* 1.3 86.2 + - - +
45B ILE* 1.3 61.6 + - - +
66B THR* 6.0 1.1 - - + -
130B LYS 3.5 25.8 - - - +
131B TRP* 3.0 8.9 - - - +
132B ASN* 2.9 38.4 + - - +
133B GLY 3.5 0.9 + - - -
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Residues in contact with ILE 45 (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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31B TYR* 2.9 4.8 - - - -
32B LEU* 2.6 45.6 + - + +
34B MET* 3.3 37.9 - - + -
43B LEU* 4.1 17.5 - - + -
44B GLN* 1.3 78.4 - - - +
46B LEU* 1.3 63.7 + - - +
47B VAL 3.5 0.3 + - - -
54B PHE* 3.9 14.4 - - + -
56B VAL* 4.1 7.4 - - + -
132B ASN* 4.6 0.2 - - - +
133B GLY* 3.4 19.5 - - - +
134B ILE 3.5 5.8 - - - +
135B LEU* 3.2 42.8 - - + +
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Residues in contact with LEU 46 (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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28B ARG 4.6 2.0 - - - +
29B GLY* 4.0 10.1 - - - -
30B TYR 3.2 34.1 - - - +
31B TYR* 4.0 2.9 - - - +
44B GLN 3.9 0.8 + - - -
45B ILE* 1.3 71.6 - - - +
47B VAL* 1.3 70.0 + - - +
48B ASP* 3.4 2.7 + - + -
131B TRP* 3.5 38.6 - - + +
133B GLY 2.7 19.4 + - - +
134B ILE* 3.4 9.6 - - + +
135B LEU 2.7 30.0 + - - -
242B SER 5.6 3.4 - - - +
243B GLY* 5.7 3.6 - - - +
1002B DBO 3.5 32.8 - - + -
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Residues in contact with VAL 47 (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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22B LEU* 4.1 20.4 - - + -
30B TYR* 2.9 19.1 + - + +
32B LEU* 4.1 11.9 - - + -
45B ILE 4.4 0.2 - - - +
46B LEU* 1.3 79.9 - - - +
48B ASP* 1.3 59.8 + - - +
49B THR* 4.8 0.4 - - + -
135B LEU* 4.1 9.9 - - + -
137B LEU* 4.2 15.9 - - + -
168B MET* 3.5 36.6 - - + -
187B LEU* 3.7 26.9 - - + -
242B SER* 2.9 18.8 + - - +
243B GLY 4.2 0.2 + - - -
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Residues in contact with ASP 48 (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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46B LEU* 3.4 2.6 + - + -
47B VAL* 1.3 75.5 - - - +
49B THR* 1.3 59.2 + - - +
50B GLY 2.8 21.2 + - - -
51B SER* 2.6 27.8 + - - +
134B ILE* 3.5 23.6 - - + +
135B LEU 2.9 14.7 + - - +
136B GLY* 3.3 2.6 - - - -
137B LEU* 2.9 23.7 + - - -
241B ASP* 3.2 0.3 - - - +
242B SER* 3.5 1.1 - - - -
243B GLY* 2.9 26.2 - - - +
1002B DBO 2.7 24.7 + - + -
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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