Contacts of the helix formed by residues 39 - 51 (chain C) in PDB entry 3DBL
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 39 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37C ASN* 3.3 6.7 + - + -
38C ALA* 1.3 77.6 - - - +
40C ALA* 1.3 68.3 + - - +
41C THR 3.9 2.1 + - - -
42C GLY 2.8 2.3 + - - -
43C THR* 2.7 19.8 + - - -
69C ASP* 5.0 5.6 - - - +
73C ASN* 4.2 4.3 - - - +
85C ARG* 3.0 34.3 - - - +
129C THR* 3.3 9.9 + - - -
130C GLN* 3.1 32.7 - - + +
489C GLU* 3.2 18.8 + - - +
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Residues in contact with ALA 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C THR* 1.3 73.5 - - - +
41C THR* 1.3 59.2 + - - +
43C THR* 3.2 1.5 + - - -
44C GLU* 2.8 36.9 + - - +
72C ASN* 3.5 31.6 + - - +
73C ASN* 4.1 17.0 - - - +
489C GLU* 3.3 24.0 + - + +
491C HIS* 4.4 5.8 - - - +
494C ALA* 4.0 9.0 - - + -
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Residues in contact with THR 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C THR* 3.2 1.1 - - - -
40C ALA* 1.3 77.5 - - - +
42C GLY* 1.3 63.5 + - - +
44C GLU* 3.4 1.6 + - - +
45C ILE* 3.1 44.1 + - + +
129C THR* 4.0 17.7 - - + -
130C GLN* 4.1 2.4 + - - -
153C CYS* 4.3 7.2 - - + +
155C THR* 2.6 30.1 + - - +
489C GLU* 3.1 14.5 + - - -
494C ALA* 3.2 16.4 - - - +
497C LEU* 4.2 23.1 - - + -
498C GLY* 4.7 0.2 - - - -
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Residues in contact with GLY 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C LEU* 3.5 32.2 - - - +
37C ASN 3.7 10.3 - - - -
39C THR 2.8 10.4 + - - -
41C THR* 1.3 76.3 - - - +
43C THR* 1.3 63.2 + - - +
45C ILE* 3.3 4.0 + - - +
46C LEU* 3.0 24.6 + - - +
129C THR* 3.8 9.4 + - - -
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Residues in contact with THR 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C LEU* 4.3 3.0 - - - +
38C ALA* 3.9 5.9 + - - +
39C THR 2.7 17.5 + - - -
40C ALA 3.6 2.7 - - - +
42C GLY* 1.3 72.3 - - - +
44C GLU* 1.3 72.0 + - - +
46C LEU* 3.5 6.9 + - - +
47C LYS* 3.0 26.5 + - - +
73C ASN* 2.7 38.8 + - - +
75C PHE* 3.1 33.8 - - + +
89C ALA* 4.1 9.5 - - - +
93C LEU* 3.8 10.1 - - - +
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Residues in contact with GLU 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40C ALA 2.8 25.2 + - - +
41C THR 3.8 4.0 - - - +
43C THR* 1.3 91.0 - - - +
45C ILE* 1.3 67.1 + - - +
47C LYS* 2.9 41.7 + - - +
48C ASN* 2.9 22.6 + - - +
74C PHE* 4.2 2.6 - - - +
75C PHE* 4.0 7.1 - - - -
491C HIS* 3.0 33.1 - - + +
494C ALA 4.1 3.6 - - - +
495C ALA* 4.0 19.4 - - - +
498C GLY* 4.0 13.7 - - - -
62D GLU* 4.0 1.6 - - - +
65D LYS* 3.1 12.9 + - - -
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Residues in contact with ILE 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C LEU* 5.1 1.8 - - + -
41C THR* 3.1 31.4 + - + +
42C GLY* 3.3 5.4 + - - +
44C GLU* 1.3 73.8 - - - +
46C LEU* 1.3 65.3 + - + +
48C ASN* 3.0 14.9 + - - +
49C LEU* 3.1 29.0 + - + +
127C VAL* 3.7 35.0 - - + -
129C THR* 4.1 7.6 - - + -
153C CYS* 4.2 5.2 - - - -
497C LEU 3.9 4.3 - - - +
498C GLY* 3.7 23.8 - - - +
501C ALA* 3.8 15.7 - - + -
502C ALA* 3.9 15.8 - - - +
505C VAL* 5.0 0.7 - - + -
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Residues in contact with LEU 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C VAL* 4.8 4.0 - - + -
35C LEU* 3.4 39.7 - - + +
42C GLY 3.0 11.0 + - - +
43C THR 3.6 4.7 - - - +
45C ILE* 1.3 80.0 - - - +
47C LYS* 1.3 51.6 + - - +
49C LEU* 2.7 22.7 + - + -
50C VAL* 2.6 54.3 + - + +
54C ILE* 5.5 0.4 - - + -
57C PHE* 4.0 28.5 - - + -
59C ILE* 3.9 11.9 - - + -
93C LEU* 3.7 26.0 - - + -
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Residues in contact with LYS 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C THR 3.0 14.0 + - - +
44C GLU* 2.9 35.9 + - - +
46C LEU* 1.3 74.2 - - - +
48C ASN* 1.3 83.2 + - - +
50C VAL* 4.1 0.7 - - - +
51C LEU* 3.0 52.9 + - + +
75C PHE* 3.5 26.0 - - + -
93C LEU* 3.9 8.9 - - - +
96C LEU* 3.9 11.6 - - + +
62D GLU* 3.2 28.5 + - - +
65D LYS* 3.3 13.3 - - - +
92D PHE* 4.2 12.6 - - + -
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Residues in contact with ASN 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44C GLU* 2.9 21.4 + - - +
45C ILE 3.0 2.5 + - - +
47C LYS* 1.3 97.6 - - - +
49C LEU* 1.3 62.4 + - - +
52C PRO* 3.0 22.8 - - - +
495C ALA 5.0 0.4 + - - -
498C GLY* 3.3 23.8 - - - -
499C GLY* 3.5 3.6 - - - +
502C ALA* 3.4 20.4 - - + +
506C ILE* 4.2 6.9 - - - +
62D GLU* 4.8 0.3 - - - +
293D ALA* 3.7 29.1 - - - +
294D SER* 4.2 16.7 + - - +
297D ALA* 3.7 7.2 - - - +
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Residues in contact with LEU 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C LEU* 5.2 1.6 - - + +
33C VAL* 4.0 25.6 - - + -
45C ILE* 3.1 27.6 + - + +
46C LEU* 2.7 21.2 + - + +
48C ASN* 1.3 79.8 - - - +
50C VAL* 1.3 64.4 + - - +
52C PRO* 3.4 8.4 - - - +
54C ILE* 3.1 42.4 + - + +
127C VAL* 5.0 0.9 - - + -
502C ALA* 3.7 26.9 - - + +
505C VAL* 3.9 25.6 - - + -
506C ILE* 3.8 17.7 - - + -
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Residues in contact with VAL 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46C LEU* 2.6 36.2 + - + +
47C LYS* 4.1 2.9 - - - +
49C LEU* 1.3 75.1 - - - +
51C LEU* 1.3 69.0 + - - +
52C PRO 3.3 0.2 - - - -
53C GLY 3.0 10.9 + - - -
54C ILE* 4.0 6.3 - - + -
57C PHE* 3.9 28.3 - - + -
93C LEU* 3.8 25.1 - - + +
94C GLN* 5.8 0.4 - - - -
96C LEU* 4.2 8.7 - - + -
97C ASN* 3.1 22.5 + - + +
100C VAL* 3.6 24.8 - - + +
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Residues in contact with LEU 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C LYS* 5.1 0.2 + - - -
13C TYR* 3.7 7.8 - - - -
47C LYS* 3.0 38.3 + - + +
50C VAL* 1.3 75.8 - - - +
52C PRO* 1.4 66.1 - - + +
96C LEU* 4.4 23.3 - - + +
97C ASN* 3.0 19.7 + - - +
88D LEU 3.9 21.5 - - - +
89D ASN* 3.9 16.6 - - - +
90D ARG* 4.0 11.9 - - - -
92D PHE* 3.9 36.3 - - + +
293D ALA* 3.9 20.0 - - + -
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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