Contacts of the strand formed by residues 41 - 48 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34D MET 3.8 0.2 - - - +
35D LEU* 3.4 3.8 - - - -
36D ILE* 2.8 41.3 + - - +
39D PRO* 4.4 6.4 + - + +
40D PRO* 1.3 76.5 - - - +
42D LYS* 1.3 62.6 + - - +
43D LEU* 3.5 7.7 + - + +
67D TYR 3.7 5.8 - - - +
68D PHE* 3.1 38.1 - - + -
69D ASP* 3.0 38.9 + - - +
72D ARG* 4.0 34.1 + - + +
73D SER* 4.4 7.1 - - - -
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Residues in contact with LYS 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D GLU* 2.9 38.6 + - + +
35D LEU* 3.8 18.8 - - + +
40D PRO 4.1 1.2 + - - -
41D GLN* 1.3 70.4 - - - +
43D LEU* 1.3 71.6 + - - +
44D GLN* 4.0 18.4 + - - +
66D THR* 4.5 11.4 + - - +
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Residues in contact with LEU 43 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D GLU* 3.5 5.2 - - - +
34D MET 2.9 36.2 + - - +
36D ILE* 3.2 32.3 - - + -
41D GLN* 4.1 10.1 - - + +
42D LYS* 1.3 84.5 - - - +
44D GLN* 1.3 70.0 + - - +
45D ILE* 3.9 9.6 - - + -
56D VAL* 3.6 28.0 - - + -
66D THR* 4.4 6.5 - - - +
67D TYR* 4.2 22.7 - - - +
68D PHE* 3.8 14.4 - - + +
132D ASN* 3.7 17.3 - - - +
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Residues in contact with GLN 44 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D GLN* 4.9 3.1 - - - +
31D TYR* 3.7 26.0 - - + -
32D LEU 3.6 1.3 - - - -
33D GLU* 3.6 28.0 + - - +
42D LYS* 4.0 22.2 + - - +
43D LEU* 1.3 86.1 + - - +
45D ILE* 1.3 61.3 + - - +
66D THR* 6.0 1.1 - - + -
130D LYS 3.5 25.8 - - - +
131D TRP* 3.0 9.1 - - - +
132D ASN* 2.9 37.0 + - - +
133D GLY 3.5 0.9 + - - -
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Residues in contact with ILE 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31D TYR* 2.9 4.3 - - - -
32D LEU* 2.6 47.0 + - + +
34D MET* 3.3 37.9 - - + -
43D LEU* 4.1 18.2 - - + -
44D GLN* 1.3 78.0 - - - +
46D LEU* 1.3 64.0 + - - +
47D VAL* 3.5 0.7 + - + +
54D PHE* 3.9 14.1 - - + -
56D VAL* 4.1 7.0 - - + -
132D ASN* 4.6 0.2 - - - +
133D GLY* 3.4 20.0 - - - +
134D ILE 3.5 5.6 - - - -
135D LEU* 3.2 42.4 - - + +
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Residues in contact with LEU 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28D ARG 4.6 2.5 - - - +
29D GLY* 4.0 9.2 - - - -
30D TYR 3.2 34.3 - - - +
31D TYR* 4.0 3.3 - - - +
44D GLN 3.9 0.8 + - - -
45D ILE* 1.3 71.4 - - - +
47D VAL* 1.3 70.6 + - - +
48D ASP* 3.3 3.5 + - + +
131D TRP* 3.5 39.5 - - + +
133D GLY 2.7 18.4 + - - +
134D ILE* 3.4 9.2 - - + +
135D LEU 2.7 30.5 + - - -
242D SER 5.6 3.6 - - - +
243D GLY* 5.7 2.5 - - - -
1004D DBO 3.5 32.8 - - + -
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Residues in contact with VAL 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D LEU* 4.1 21.1 - - + -
30D TYR* 2.9 18.8 + - + +
32D LEU* 4.1 11.4 - - + -
45D ILE 3.5 0.4 + - - +
46D LEU* 1.3 79.8 - - - +
48D ASP* 1.3 61.0 + - - +
49D THR* 4.8 0.2 - - + -
135D LEU* 4.1 11.2 - - + -
137D LEU* 4.2 16.8 - - + -
168D MET* 3.5 36.5 - - + +
187D LEU* 3.7 26.0 - - + -
242D SER* 2.9 19.4 + - - +
243D GLY* 4.4 0.2 - - - -
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Residues in contact with ASP 48 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46D LEU* 3.3 2.8 + - + +
47D VAL* 1.3 73.3 - - - +
49D THR* 1.3 59.2 + - - +
50D GLY 2.8 21.3 + - - -
51D SER* 2.6 27.1 + - - +
134D ILE* 3.5 24.3 - - + +
135D LEU 2.9 15.9 + - - +
136D GLY* 3.3 2.9 - - - -
137D LEU* 2.9 22.8 + - - -
241D ASP* 3.2 0.3 - - - +
242D SER* 3.5 1.3 - - - -
243D GLY* 2.9 25.4 - - - +
1004D DBO 2.7 25.3 + - + -
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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