Contacts of the strand formed by residues 43 - 51 (chain A) in PDB entry 5ES4
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 43 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A ILE* 3.6 5.9 - - - +
39A THR* 3.2 35.6 + - - +
40A ALA* 3.1 34.2 + - - +
41A ALA 3.7 8.1 - - - +
42A ASN* 1.3 82.6 - - - +
44A THR* 1.3 63.5 + - - +
64A VAL* 4.1 33.4 + - + +
65A PRO 4.2 11.3 + - - -
66A PRO* 4.5 10.1 - - - +
68A ALA 4.7 9.4 + - - +
69A VAL* 5.6 0.4 - - - -
70A ASN* 4.5 4.3 - - - +
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Residues in contact with THR 44 (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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35A PRO 3.6 9.6 - - - -
36A GLN* 4.3 13.0 - - - +
37A LYS 3.0 9.0 - - - +
38A ILE* 4.3 11.9 - - + -
39A THR* 5.1 1.6 - - - -
43A GLN* 1.3 80.5 - - - +
45A GLY* 1.3 61.5 + - - +
70A ASN* 3.3 27.5 - - + +
71A MET* 3.9 7.6 - - - +
72A SER* 2.9 40.9 + - - +
73A LEU* 3.3 4.0 + - - +
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Residues in contact with GLY 45 (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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34A ALA 3.4 5.4 - - - -
35A PRO 3.2 5.0 + - - -
37A LYS 2.8 10.8 + - - -
39A THR* 3.2 21.0 + - - +
44A THR* 1.3 76.8 - - - +
46A GLY* 1.3 58.2 + - - -
73A LEU* 3.0 40.8 - - - +
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Residues in contact with GLY 46 (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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32A VAL 3.8 0.5 - - - +
33A GLY 3.5 0.7 - - - -
34A ALA* 2.7 45.2 + - - +
37A LYS* 3.7 24.8 - - - +
39A THR* 4.6 1.8 - - - -
45A GLY* 1.3 74.4 - - - -
47A LEU* 1.3 66.8 + - - +
48A TYR* 4.4 3.3 - - - -
73A LEU* 3.4 2.2 + - - +
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Residues in contact with LEU 47 (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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31A VAL* 4.9 2.0 - - + -
32A VAL 3.5 3.4 - - - +
33A GLY* 3.8 9.4 - - - +
46A GLY* 1.3 81.0 - - - +
48A TYR* 1.3 59.9 + - - +
59A PRO* 3.3 6.6 - - - +
60A ILE* 2.8 60.6 + - + +
62A LEU* 4.7 15.5 - - + -
73A LEU* 3.6 16.5 - - + +
74A GLY* 3.8 25.6 - - - +
77A LEU* 4.6 7.9 - - + -
86A LEU* 4.8 8.5 - - + -
88A ALA* 3.4 31.0 - - + -
110A LEU* 5.4 2.7 - - + -
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Residues in contact with TYR 48 (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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13A VAL* 4.1 12.1 - - + +
15A SER* 2.5 37.6 + - - -
18A PHE* 3.7 33.7 - + + -
30A VAL 3.8 1.0 - - - +
31A VAL* 3.3 10.2 - - - +
32A VAL* 2.9 36.2 + - + +
34A ALA* 4.6 1.6 - - + -
37A LYS* 3.0 29.0 + - + -
46A GLY 4.4 6.1 - - - -
47A LEU* 1.3 81.2 - - - +
49A GLN* 1.3 60.3 + - - +
50A CYS* 4.0 0.9 - - - -
57A CYS* 4.4 18.2 - - + -
58A GLU 3.3 6.5 - - - -
59A PRO* 3.5 40.1 - - + +
60A ILE* 4.1 2.9 - - - -
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Residues in contact with GLN 49 (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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25A TYR* 5.1 6.7 - - + -
29A TRP* 3.2 62.3 - - + +
30A VAL 4.1 2.0 - - - -
31A VAL* 4.9 5.8 - - + +
48A TYR* 1.3 72.2 - - - +
50A CYS* 1.3 60.5 + - - +
56A ALA 4.4 1.0 - - - +
57A CYS* 3.8 0.3 - - - -
58A GLU* 2.7 38.3 + - + +
59A PRO 5.6 0.4 - - - +
60A ILE* 3.9 24.7 - - + +
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Residues in contact with CYS 50 (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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11A PHE* 3.6 18.2 - - + -
18A PHE* 4.5 1.3 - - - -
29A TRP* 3.0 15.8 - - - -
30A VAL* 3.1 49.2 + - + +
32A VAL* 4.1 17.5 - - - -
48A TYR* 4.7 0.7 - - - -
49A GLN* 1.3 73.2 - - - +
51A GLY* 1.3 58.2 + - - +
56A ALA 3.8 5.2 - - - +
57A CYS* 2.0 48.5 - - - -
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Residues in contact with GLY 51 (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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11A PHE* 3.7 11.6 - - - -
28A SER 4.0 7.6 - - - -
29A TRP* 3.4 20.5 - - - -
30A VAL* 5.8 0.2 - - - -
50A CYS* 1.3 75.5 - - - +
52A TYR* 1.3 60.7 + - - -
53A SER 3.5 1.8 - - - -
54A THR* 3.6 5.8 + - - -
55A GLY* 3.0 24.1 + - - -
56A ALA 3.7 5.9 + - - -
593A LEU* 6.0 0.2 - - - -
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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