Contacts of the helix formed by residues 32 - 42 (chain A) in PDB entry 4ED5
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 32 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30A ASN 3.9 9.9 - - - +
31A MET* 1.3 79.5 - - - +
33A GLN* 1.3 59.3 + - - +
34A ASP* 3.5 10.6 + - - +
35A GLU* 3.1 37.9 + - - +
36A LEU* 3.0 27.5 + - - +
51A LEU* 4.2 6.2 - - - +
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Residues in contact with GLN 33 (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 THR* 1.3 74.0 - - - +
34A ASP* 1.3 61.7 + - - +
36A LEU* 3.3 5.4 + - + +
37A ARG* 2.9 32.0 + - + +
49A ALA* 3.5 26.7 + - + +
50A LYS* 3.4 9.7 - - - +
51A LEU* 3.1 38.0 + - + +
53A ARG* 3.8 27.5 + - - +
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Residues in contact with ASP 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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32A THR* 3.2 9.5 + - - +
33A GLN* 1.3 82.1 + - - +
35A GLU* 1.3 57.1 + - + +
37A ARG* 3.5 10.9 + - - +
38A SER* 3.0 33.1 + - - -
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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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30A ASN* 3.9 4.1 + - - +
31A MET* 3.3 25.1 - - + +
32A THR* 3.1 41.1 + - - +
34A ASP* 1.3 74.1 - - + +
36A LEU* 1.3 58.7 + - - +
38A SER* 3.9 5.2 - - - +
39A LEU* 2.9 32.4 + - - +
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Residues in contact with LEU 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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24A VAL* 4.5 4.0 - - + -
27A LEU* 4.1 31.0 - - + -
31A MET* 3.8 14.2 - - + +
32A THR 3.0 12.3 + - - +
33A GLN* 3.5 8.3 - - - +
35A GLU* 1.3 77.1 - - - +
37A ARG* 1.3 63.6 + - - +
39A LEU 3.5 0.2 + - - -
40A PHE* 3.1 56.1 + - + +
49A ALA* 4.3 4.9 - - + -
50A LYS 3.7 29.2 - - - +
51A LEU* 4.4 4.7 - - + +
64A GLY* 4.2 12.8 - - - -
65A PHE 4.3 2.2 - - - +
66A VAL* 4.0 19.7 - - + -
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Residues in contact with ARG 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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33A GLN* 2.9 20.4 + - + +
34A ASP* 3.7 10.4 + - - +
36A LEU* 1.3 77.1 - - - +
38A SER* 1.3 57.9 + - - +
40A PHE* 3.4 3.5 + - - +
41A SER* 2.9 33.2 + - - -
46A VAL* 4.4 16.9 - - + +
48A SER* 5.6 2.4 - - - +
49A ALA* 4.0 30.0 + - + +
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Residues in contact with SER 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 ASP* 3.0 19.4 + - - +
35A GLU* 3.9 6.3 - - - -
37A ARG* 1.3 73.6 - - - +
39A LEU* 1.3 67.2 + - - +
41A SER* 2.6 24.5 + - - -
42A SER* 3.7 4.7 + - - -
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Residues in contact with LEU 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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27A LEU* 6.1 0.4 - - + -
31A MET* 3.9 11.9 - - + -
35A GLU 2.9 18.1 + - - +
36A LEU* 3.7 2.9 - - + +
38A SER* 1.3 77.9 - - - +
40A PHE* 1.3 81.0 + - + +
42A SER* 3.1 25.3 + - - +
81A LEU* 4.4 13.2 - - + +
84A LEU* 3.8 25.1 - - + -
86A LEU* 3.9 32.3 - - + -
91A ILE* 4.6 2.7 - - + -
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Residues in contact with PHE 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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22A LEU* 4.5 5.6 - - + -
24A VAL* 3.5 35.4 - - + -
27A LEU* 5.7 0.2 - - + -
36A LEU* 3.1 41.8 + - + +
37A ARG* 4.1 2.0 - - - +
39A LEU* 1.3 96.1 - - + +
41A SER* 1.3 62.9 + - - +
42A SER 3.1 2.9 - - - -
43A ILE* 3.2 9.6 + - - +
46A VAL* 3.9 3.6 - - + -
66A VAL* 3.8 28.0 - - + -
68A TYR* 2.7 43.1 + + - +
77A ALA* 4.4 1.6 - - + -
81A LEU* 3.7 19.5 - - + -
91A ILE* 4.4 2.7 - - + -
93A VAL* 3.8 25.6 - - + -
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Residues in contact with SER 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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37A ARG* 2.9 18.6 + - - -
38A SER* 2.6 26.7 + - - -
40A PHE* 1.3 73.8 - - - +
42A SER* 1.3 63.7 + - - +
43A ILE 3.2 0.2 - - - -
44A GLY* 3.3 22.6 + - - +
46A VAL* 3.9 9.2 - - - +
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Residues in contact with SER 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 SER 3.7 2.6 + - - -
39A LEU* 3.1 19.5 + - - +
40A PHE 3.1 0.2 - - - -
41A SER* 1.3 80.9 + - - +
43A ILE* 1.3 74.5 + - - +
76A ARG* 5.0 2.4 + - - -
81A LEU* 5.1 4.0 - - - +
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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