Contacts of the helix formed by residues 33 - 42 (chain A) in PDB entry 5EN1
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 THR 33 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31A GLU 3.7 10.8 - - - +
32A THR* 1.3 79.9 - - - +
34A GLU* 1.3 59.9 + - - +
35A GLU* 3.6 20.7 + - - +
36A SER* 3.2 24.1 + - - -
37A LEU* 3.0 30.5 + - - +
52A VAL* 3.6 8.3 - - - -
54A ARG* 4.5 13.7 - - - +
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Residues in contact with GLU 34 (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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33A THR* 1.3 74.0 - - - +
35A GLU* 1.3 67.5 + - - +
38A ARG* 2.9 35.0 + - - +
50A CYS* 3.5 32.5 - - + +
51A VAL* 3.6 12.4 - - - +
52A VAL* 3.4 40.5 + - + +
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Residues in contact with GLU 35 (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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33A THR* 3.6 21.0 - - - +
34A GLU* 1.3 88.2 + - - +
36A SER* 1.3 50.4 + - - +
38A ARG* 3.7 9.5 - - - +
39A ASN* 2.7 33.1 + - - +
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Residues in contact with SER 36 (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 GLU 5.7 0.7 - - - -
32A THR* 3.6 2.6 - - - +
33A THR* 3.2 26.6 + - - -
35A GLU* 1.3 74.8 - - - +
37A LEU* 1.3 62.7 + - - +
39A ASN* 3.7 7.1 - - - +
40A TYR* 3.1 27.0 + - - +
86A ILE* 4.4 3.8 - - - +
87A ASP* 3.0 32.7 + - - -
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Residues in contact with LEU 37 (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 ILE* 4.2 5.8 - - + -
28A LEU* 4.0 24.2 - - + -
32A THR* 4.2 5.4 - - + -
33A THR 3.0 17.6 + - - +
34A GLU 3.8 3.1 - - - +
36A SER* 1.3 74.9 + - - +
38A ARG* 1.3 58.9 + - - +
40A TYR* 3.2 5.8 + - - +
41A TYR* 3.0 61.5 + - + +
47A LEU* 5.0 0.2 - - - -
50A CYS* 3.7 20.0 - - - -
51A VAL 4.3 8.3 - - - +
52A VAL* 3.8 21.5 - - + -
65A GLY* 4.6 5.6 - - - -
66A PHE 4.7 1.1 - - - +
67A VAL* 3.9 10.8 - - + -
86A ILE* 3.8 15.5 - - + -
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Residues in contact with ARG 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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34A GLU* 2.9 22.4 + - - +
35A GLU* 3.7 8.5 - - - +
37A LEU* 1.3 72.3 - - - +
39A ASN* 1.3 65.6 + - - +
42A GLU* 3.1 53.1 + - - +
47A LEU* 3.3 48.5 + - + +
48A THR 4.8 1.8 + - - -
49A ASP* 3.8 7.7 + - - +
50A CYS* 3.6 39.2 + - - +
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Residues in contact with ASN 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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35A GLU 2.7 23.0 + - - +
36A SER* 3.7 9.6 - - - +
37A LEU 3.3 0.2 - - - -
38A ARG* 1.3 76.4 - - - +
40A TYR* 1.3 65.8 + - - +
42A GLU* 3.5 18.8 + - - +
43A GLN* 4.1 5.9 + - - +
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Residues in contact with TYR 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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36A SER 3.1 17.8 + - - +
37A LEU 3.2 4.7 + - - +
39A ASN* 1.3 77.5 - - - +
41A TYR* 1.3 68.8 + + - +
43A GLN* 3.0 46.8 + - - +
44A TRP* 3.4 27.7 - + - -
83A PRO 4.2 2.1 + - - -
84A HIS* 3.1 51.5 - + + +
85A SER 3.5 20.1 + - - -
86A ILE* 3.4 33.0 - - + -
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Residues in contact with TYR 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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23A LEU* 3.8 13.0 - - + -
25A ILE* 3.5 33.8 - - + +
37A LEU* 3.0 25.4 + - + +
40A TYR* 1.3 78.6 - + - +
42A GLU* 1.3 57.7 + - - +
43A GLN 3.1 6.3 + - - -
44A TRP* 3.2 30.2 + + - -
47A LEU* 4.0 14.6 - - + -
67A VAL* 3.8 17.0 - - + -
69A PHE* 3.3 37.5 - + + -
78A ALA* 4.3 1.3 - - + -
84A HIS* 2.9 44.8 + + - +
86A ILE* 3.6 18.4 - - + -
91A VAL* 4.2 1.6 - - - +
93A PRO* 3.5 8.5 - - - +
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Residues in contact with GLU 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 ARG* 3.1 55.8 + - - +
39A ASN* 3.8 14.4 + - - +
40A TYR 3.2 0.8 + - - -
41A TYR* 1.3 73.6 - - - +
43A GLN* 1.3 62.9 + - - +
44A TRP 3.2 1.0 + - - -
45A GLY 3.3 20.6 + - - +
46A LYS* 5.2 1.3 - - - -
47A LEU* 3.8 21.8 + - + +
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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