Contacts of the helix formed by residues 37 - 47 (chain A) in PDB entry 4EBC
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 CYS 37 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36A ASP* 1.3 74.5 - - - +
38A PHE* 1.3 51.4 + - - +
39A TYR 3.6 1.3 - - - -
40A ALA* 3.3 9.7 + - + -
41A GLN* 2.7 44.9 + - - -
44A MET* 5.3 2.2 - - - -
65A THR* 4.0 4.7 - - - +
66A CYS 3.3 24.0 - - - +
67A ASN* 3.7 22.7 - - - -
68A TYR* 4.0 16.5 - - + -
71A ARG* 3.6 6.7 - - - +
501A 0OH 2.9 26.9 + - - -
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Residues in contact with PHE 38 (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 LEU* 3.4 38.1 - - + -
36A ASP 2.8 8.7 + - - -
37A CYS* 1.3 69.1 - - - +
39A TYR* 1.3 79.5 + + - +
41A GLN* 2.9 13.9 + - - +
42A VAL* 3.0 33.9 + - + +
102A TYR* 3.8 30.7 - - + -
105A MET* 4.2 5.6 - - + -
106A SER 4.1 11.4 - - - -
125A PHE* 3.9 23.1 - - + -
126A ASP* 4.0 16.2 - - + +
193A LEU* 4.8 10.8 - - + -
501A 0OH 2.8 36.0 + + + +
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Residues in contact with TYR 39 (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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38A PHE* 1.3 88.0 - + - +
40A ALA* 1.3 63.4 + - - +
42A VAL* 3.1 4.9 + - - +
43A GLU* 3.0 25.5 + - - +
57A VAL* 3.7 14.4 - - + -
59A GLN* 3.9 19.9 + - - -
64A VAL* 3.9 16.8 - - + -
65A THR* 3.5 9.6 - - + -
99A LEU* 3.5 22.6 - - + +
102A TYR* 3.3 54.6 - + + -
125A PHE* 4.3 7.7 - + - -
501A 0OH 3.2 54.8 + + - -
5T G 4.1 9.2 + - - -
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Residues in contact with ALA 40 (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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37A CYS* 3.3 11.4 + - + +
39A TYR* 1.3 75.8 - - - +
41A GLN* 1.3 62.7 + - - +
43A GLU* 3.2 4.9 + - - +
44A MET* 3.1 21.5 + - - +
55A LEU* 3.5 12.8 - - + +
57A VAL* 3.5 15.4 - - + +
65A THR* 3.6 3.3 - - + +
66A CYS* 3.6 11.4 - - - -
67A ASN* 3.4 37.5 - - + +
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Residues in contact with GLN 41 (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 LEU* 4.5 4.2 - - - +
36A ASP* 2.7 28.7 + - + +
37A CYS* 2.7 22.8 + - - +
38A PHE* 2.9 10.4 + - - +
40A ALA* 1.3 74.4 - - - +
42A VAL* 1.3 61.9 + - - +
44A MET* 3.2 11.5 + - + +
45A ILE* 3.1 31.4 + - + +
192A GLY 4.0 4.5 - - - +
193A LEU* 3.4 25.5 - - + +
194A THR* 2.8 51.7 + - - +
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Residues in contact with VAL 42 (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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38A PHE* 3.0 37.8 + - + +
39A TYR 3.1 1.3 + - - +
41A GLN* 1.3 76.0 - - + +
43A GLU* 1.3 63.5 + - - +
45A ILE* 3.4 11.5 + - + +
46A SER* 3.3 22.8 + - - +
101A ARG* 4.4 18.3 + - + +
102A TYR* 3.7 34.1 - - + -
105A MET* 4.4 24.5 - - + -
193A LEU* 5.1 4.0 - - + -
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Residues in contact with GLU 43 (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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39A TYR 3.0 17.2 + - - +
40A ALA 3.4 8.5 - - - +
41A GLN 3.2 0.2 - - - -
42A VAL* 1.3 77.0 - - - +
44A MET* 1.3 57.7 + - - +
46A SER* 3.1 7.8 + - - -
47A ASN* 3.0 25.3 + - - +
50A LEU* 4.2 10.2 - - + +
55A LEU* 3.8 13.2 - - + -
57A VAL* 3.8 14.8 - - + -
94A VAL* 3.2 32.5 - - + +
95A ASN 4.5 0.7 - - - +
101A ARG* 2.9 31.3 + - - +
102A TYR* 2.5 26.2 + - - +
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Residues in contact with MET 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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37A CYS* 5.3 3.1 - - - -
40A ALA 3.1 21.1 + - - +
41A GLN* 3.2 13.4 + - + +
43A GLU* 1.3 71.9 - - - +
45A ILE* 1.3 65.0 + - + +
46A SER 3.1 1.8 - - - -
47A ASN 4.0 6.1 - - - -
48A PRO* 3.3 27.0 - - - +
50A LEU* 3.8 10.8 - - + +
51A LYS* 3.4 39.7 - - + +
55A LEU* 3.6 11.7 - - + -
67A ASN* 3.0 46.9 - - + +
69A GLU* 5.5 0.4 - - - +
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Residues in contact with ILE 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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41A GLN* 3.1 20.1 + - + +
42A VAL* 3.8 10.5 - - + +
43A GLU 3.3 0.2 - - - -
44A MET* 1.3 78.5 - - + +
46A SER* 1.3 62.2 + - - +
48A PRO* 4.5 7.2 - - - +
105A MET* 5.5 10.5 - - + -
191A LEU 4.2 9.6 - - - +
192A GLY* 3.5 29.6 - - - +
193A LEU* 3.7 26.2 - - + -
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Residues in contact with SER 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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42A VAL* 3.3 13.8 + - - +
43A GLU* 3.1 10.2 + - - -
44A MET 3.1 0.2 - - - -
45A ILE* 1.3 82.3 - - - +
47A ASN* 1.3 61.1 + - - +
48A PRO* 3.3 8.4 - - - +
101A ARG* 3.9 22.2 + - - -
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Residues in contact with ASN 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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43A GLU 3.0 7.2 + - - +
44A MET* 3.5 5.6 - - - +
46A SER* 1.3 77.1 - - - +
48A PRO* 1.4 60.5 - - - +
49A GLU* 3.0 27.9 + - - +
50A LEU* 3.0 44.2 + - + +
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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