Contacts of the helix formed by residues 38 - 48 (chain D) in PDB entry 2OZB
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 GLY 38 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37D LYS* 1.3 75.1 - - - +
39D ALA* 1.3 59.6 + - - -
40D ASN 3.3 2.7 - - - -
41D GLU 3.2 1.6 + - - -
42D ALA* 2.9 29.8 + - - +
99D VAL* 4.0 2.8 - - - +
101D ALA 2.9 18.4 + - - +
30F A 4.0 9.4 - - - -
31F U 3.3 12.1 - - - -
32F G 3.3 10.1 - - - -
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Residues in contact with ALA 39 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38D GLY* 1.3 71.8 - - - -
40D ASN* 1.3 52.8 + - - +
42D ALA* 3.4 3.1 - - - +
43D THR* 2.7 39.4 + - - -
65D ILE 4.5 0.2 - - - +
66D ILE* 4.1 23.8 - - + -
68D HIS* 4.7 0.4 - - + -
69D LEU* 4.0 5.4 - - + +
100D ILE* 4.1 3.6 - - + -
101D ALA* 3.6 13.8 + - + +
304E ARG* 3.9 24.5 - - - +
31F U 2.8 18.6 + - - +
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Residues in contact with ASN 40 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38D GLY 3.3 0.6 - - - -
39D ALA* 1.3 79.2 - - - +
41D GLU* 1.3 60.0 + - - +
43D THR* 3.4 7.5 + - - -
44D LYS* 3.3 26.3 + - - +
245E PRO* 3.3 10.1 - - + +
246E ALA* 2.7 45.4 + - - +
247E CYS 5.2 0.2 - - - -
300E THR* 3.9 1.1 - - - +
301E LEU* 6.1 1.8 - - - +
304E ARG* 3.0 21.1 + - - +
31F U 4.7 3.0 + - - -
32F G 3.1 44.5 + - + +
43F G 4.6 9.6 - - + +
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Residues in contact with GLU 41 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36D ARG* 2.9 47.2 + - + +
37D LYS* 3.2 15.5 + - - +
38D GLY 3.2 3.5 + - - +
40D ASN* 1.3 73.0 - - - +
42D ALA* 1.3 68.3 + - - +
44D LYS* 3.1 14.0 + - - +
45D THR* 3.0 27.0 + - - +
30F A 4.6 0.5 - - - -
32F G 2.7 40.0 + - + +
43F G 2.7 50.3 + - + +
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Residues in contact with ALA 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36D ARG 5.0 1.2 + - - -
38D GLY 2.9 17.7 + - - +
39D ALA* 3.4 9.0 - - - +
41D GLU* 1.3 76.6 - - - +
43D THR* 1.3 62.0 + - - +
45D THR* 2.8 27.2 + - - -
46D LEU* 3.0 11.5 + - - +
54D ILE* 4.2 14.6 - - + -
69D LEU* 4.0 19.1 - - + -
101D ALA* 4.7 2.2 - - + -
102D CYS 4.5 9.0 - - - -
103D SER* 4.0 10.5 - - - -
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Residues in contact with THR 43 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39D ALA 2.7 20.2 + - - -
40D ASN* 3.4 12.0 - - - -
41D GLU 3.2 0.2 - - - -
42D ALA* 1.3 74.6 - - - +
44D LYS* 1.3 64.1 + - - +
46D LEU* 3.3 4.4 + - - +
47D ASN* 2.9 32.1 + - - +
68D HIS* 2.8 23.9 + - + +
69D LEU* 3.5 7.6 - - - +
72D LEU* 3.9 12.6 - - + -
243E LYS 3.1 33.0 - - - +
244E MET 4.4 1.1 - - - -
245E PRO* 4.3 11.9 - - + -
304E ARG* 4.3 1.6 + - - -
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Residues in contact with LYS 44 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40D ASN 3.3 18.0 + - - +
41D GLU* 3.1 13.1 + - - +
43D THR* 1.3 81.1 - - - +
45D THR* 1.3 56.8 + - + +
47D ASN* 3.4 7.8 + - + +
48D ARG* 3.0 58.4 + - - +
245E PRO* 3.6 27.1 - - + -
247E CYS* 3.5 11.4 - - - -
248E ASN* 5.5 2.5 - - - +
42F C 3.9 23.6 + - - -
43F G 2.7 48.4 + - - -
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Residues in contact with THR 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36D ARG* 4.0 33.9 - - + -
41D GLU 3.2 15.7 - - - +
42D ALA 2.8 14.3 + - - -
44D LYS* 1.3 78.3 - - + +
46D LEU* 1.3 60.0 + - - +
48D ARG* 3.7 0.4 + - - +
49D GLY 3.2 2.4 + - - -
50D ILE* 3.0 47.9 + - + +
51D SER* 3.5 9.9 + - - -
54D ILE* 4.3 0.5 - - - +
103D SER* 2.6 29.1 + - - +
105D THR* 4.4 7.4 - - - +
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Residues in contact with LEU 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42D ALA 3.0 9.9 + - - +
43D THR 3.7 6.3 - - - +
45D THR* 1.3 77.7 + - - +
47D ASN* 1.3 64.8 + - - +
49D GLY* 3.2 10.3 + - - -
51D SER* 3.9 11.4 - - - -
54D ILE* 4.0 19.5 - - + -
69D LEU* 3.8 36.1 - - + +
72D LEU* 3.8 37.2 - - + +
73D CYS* 4.0 8.1 - - - -
76D LYS* 3.3 23.7 - - + +
78D VAL* 3.9 35.7 - - + -
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Residues in contact with ASN 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43D THR* 2.9 28.2 + - - +
44D LYS* 3.7 8.0 - - + +
46D LEU* 1.3 76.7 - - - +
48D ARG* 1.3 62.0 + - + +
49D GLY 3.6 0.5 + - - -
72D LEU* 3.5 21.2 - - - +
76D LYS* 4.1 16.2 + - - +
243E LYS* 3.1 26.9 + - - +
245E PRO* 4.8 6.1 - - - +
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Residues in contact with ARG 48 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36D ARG* 6.2 0.8 - - - +
44D LYS* 3.0 46.7 + - - +
46D LEU 3.2 0.2 - - - -
47D ASN* 1.3 77.9 - - + +
49D GLY* 1.3 62.2 + - - +
50D ILE* 3.5 31.7 + - + +
248E ASN* 6.0 0.6 - - - +
41F C 3.9 24.2 + - - -
42F C 2.7 41.6 + - - -
43F G 5.9 0.4 + - - -
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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