Contacts of the strand formed by residues 45 - 53 (chain D) in PDB entry 5E94
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 45 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100C SER* 5.5 6.3 - - - +
40D HIS* 3.6 1.0 - - - -
41D PHE* 2.8 59.9 + - + -
42D PRO 4.4 9.9 - - - +
43D GLY* 3.2 13.4 - - - +
44D ASN* 1.3 76.0 - - - +
46D LEU* 1.3 68.1 + - - +
47D GLU* 5.8 0.4 - - + -
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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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38C GLN* 5.6 0.4 - - - +
87C PHE* 3.4 42.0 - - + -
97C THR* 5.9 0.3 - - - -
98C PHE* 3.7 59.6 + - + +
99C GLY 4.9 3.2 + - - +
38D ILE* 4.9 7.6 - - + -
39D ARG 3.4 7.9 - - - +
40D HIS* 3.1 37.2 - - + -
44D ASN 3.7 1.2 + - - +
45D ILE* 1.3 80.4 - - - +
47D GLU* 1.3 62.4 + - - +
48D TRP 4.3 0.4 - - - -
113D TRP* 5.5 4.7 - - + -
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Residues in contact with GLU 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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98C PHE* 4.9 0.4 - - - -
38D ILE* 3.5 3.7 - - - -
39D ARG* 2.7 83.1 + - + -
41D PHE* 3.9 18.9 - - + -
45D ILE* 5.8 0.7 - - + -
46D LEU* 1.3 76.8 - - - +
48D TRP* 1.3 77.0 + - - +
49D MET* 3.4 2.8 + - - +
61D ASN* 3.9 8.8 + - - +
63D SER* 3.4 19.1 + - - -
64D LEU* 3.8 13.5 - - + +
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Residues in contact with TRP 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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94C LEU* 4.2 17.5 - - + -
95C PRO* 3.5 33.7 - - + -
96C PHE* 3.3 48.2 + + + +
98C PHE* 4.3 10.8 - - + -
36D HIS* 2.7 28.9 + - - -
37D TRP 4.1 3.4 - - - -
38D ILE* 4.1 19.1 - - + -
47D GLU* 1.3 75.0 - - - +
49D MET* 1.3 59.3 + - - +
50D GLY* 3.5 24.0 + - - -
51D TYR* 3.8 17.0 - + - -
59D ASN 3.8 15.7 - - - -
60D TYR 3.7 8.7 - - - -
61D ASN* 3.0 48.4 + - + +
62D PRO* 5.3 0.2 - - + -
110D PHE* 4.2 5.6 - + - -
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Residues in contact with MET 49 (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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37D TRP* 2.9 24.8 + - + +
38D ILE 4.6 0.4 - - - -
39D ARG* 3.7 19.1 - - + +
47D GLU* 3.7 13.5 - - - +
48D TRP* 1.3 75.1 - - - +
50D GLY* 1.3 60.8 + - - +
60D TYR* 3.6 2.8 - - - +
61D ASN* 3.0 23.9 + - - +
64D LEU* 3.9 27.1 - - + +
68D ILE* 3.7 21.0 - - + +
81D LEU* 3.8 30.5 - - + -
83D LEU* 4.0 17.3 - - + -
94D TYR* 3.7 34.8 - - + -
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Residues in contact with GLY 50 (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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36D HIS* 3.3 3.1 - - - -
37D TRP 3.0 25.0 + - - +
48D TRP* 3.5 17.9 + - - -
49D MET* 1.3 81.7 - - - +
51D TYR* 1.3 60.7 + - - +
59D ASN 3.1 14.4 - - - -
60D TYR* 4.0 1.1 - - - -
70D ILE* 3.3 14.6 - - - +
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Residues in contact with TYR 51 (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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94C LEU* 4.6 3.4 - - + -
96C PHE* 5.2 0.2 - + - -
34D ASP* 4.2 6.7 - - + -
35D TRP 3.2 13.2 - - - +
36D HIS* 3.4 37.0 - + + +
48D TRP* 3.8 11.7 - + - -
50D GLY* 1.3 74.8 - - - +
52D ILE* 1.3 71.4 + - - +
53D SER* 3.9 3.8 - - - -
57D SER* 4.4 5.2 - - - -
58D THR* 3.3 10.4 - - - +
59D ASN* 2.8 61.4 + - + +
70D ILE* 3.5 8.3 - - - +
108D TYR* 4.4 0.7 - - - -
31H SER* 3.0 36.6 + - - -
33H TRP* 3.5 35.6 - + + -
34H GLU* 5.0 2.8 - - - +
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Residues in contact with ILE 52 (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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35D TRP* 2.8 41.5 + - + +
51D TYR* 1.3 76.8 - - - +
53D SER* 1.3 73.0 + - - +
56D GLY* 3.8 16.6 - - - +
57D SER 3.3 11.4 - - - +
58D THR* 4.0 3.1 - - + -
70D ILE* 3.5 27.5 - - + +
71D THR* 3.8 20.6 - - - -
72D HIS* 3.7 30.5 - - + +
79D PHE* 4.1 20.9 - - + -
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Residues in contact with SER 53 (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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29D ILE 4.6 0.7 - - - +
33D TYR 3.8 1.1 - - - -
34D ASP* 3.2 24.2 - - - -
35D TRP* 4.4 2.8 - - - -
51D TYR* 3.9 1.9 - - - -
52D ILE* 1.3 82.1 - - - +
54D TYR* 1.3 64.2 + - - +
55D SER* 3.2 12.1 + - - -
56D GLY* 3.0 11.8 + - - -
57D SER 2.9 19.6 + - - -
72D HIS* 4.3 5.5 + - - -
30H VAL 2.7 19.0 + - - -
31H SER* 3.4 23.3 - - - -
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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