Contacts of the helix formed by residues 48 - 62 (chain D) in PDB entry 2ZJR
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 LYS 48 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46D ASP* 2.4 12.9 + - + +
47D SER* 1.3 87.1 - - - +
49D ALA* 1.3 60.3 + - - +
50D ILE 3.1 1.1 - - - -
51D ASP* 2.9 36.4 + - - +
52D LYS 3.8 0.5 + - - -
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Residues in contact with ALA 49 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40D LEU* 4.2 9.7 - - + +
44D LYS 5.5 0.2 - - - +
46D ASP* 2.8 34.9 + - + +
48D LYS* 1.3 72.4 - - - +
50D ILE* 1.3 68.4 + - - +
51D ASP 2.8 2.7 - - - -
52D LYS* 2.7 28.8 + - + +
53D ALA* 3.3 4.0 + - - +
148D LYS* 4.5 23.1 - - + +
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Residues in contact with ILE 50 (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 LEU* 4.3 20.6 - - + +
46D ASP 2.9 13.6 + - - +
47D SER* 3.4 25.8 - - - +
48D LYS 3.1 0.2 - - - -
49D ALA* 1.3 76.7 - - - +
51D ASP* 1.3 63.2 + - - +
53D ALA* 3.1 23.7 - - - +
54D ALA* 3.7 6.6 + - - +
67D ILE* 4.3 30.5 - - + -
84D PRO* 5.0 15.0 - - + +
87D ILE* 4.7 7.7 - - + +
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Residues in contact with ASP 51 (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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47D SER 3.5 16.1 - - - +
48D LYS* 2.9 21.9 - - - +
50D ILE* 1.3 76.6 - - - +
52D LYS* 1.3 65.5 + - - +
53D ALA 3.0 3.0 + - - -
54D ALA* 5.7 1.8 - - - -
55D LYS* 3.0 42.9 + - + +
147D ASP* 5.2 3.4 - - - +
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Residues in contact with LYS 52 (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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48D LYS 3.8 0.8 + - - -
49D ALA* 2.7 25.2 + - + +
51D ASP* 1.3 75.7 - - - +
53D ALA* 1.3 66.7 + - - +
55D LYS* 4.1 1.7 - - - +
56D GLU* 2.7 65.0 + - - +
135D GLN* 4.8 1.8 + - - +
141D ILE* 5.7 3.8 - - - +
146D VAL* 4.1 7.1 - - - +
147D ASP* 3.0 35.5 + - + +
148D LYS* 3.3 40.8 + - + +
149D THR* 3.0 30.1 - - - +
150D ARG* 3.5 12.0 - - + +
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Residues in contact with ALA 53 (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 GLU* 4.3 3.8 - - + -
40D LEU* 3.8 17.7 - - + +
49D ALA 3.3 1.6 + - - -
50D ILE 3.1 13.5 - - - +
51D ASP 3.0 0.4 - - - -
52D LYS* 1.3 77.3 - - - +
54D ALA* 1.3 58.1 + - - +
56D GLU* 2.6 30.1 + - - +
57D LEU* 2.7 25.2 + - + -
87D ILE* 3.4 24.5 - - + -
150D ARG* 6.5 0.4 - - - +
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Residues in contact with ALA 54 (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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50D ILE 3.7 7.0 + - - +
51D ASP* 4.7 2.0 - - - +
53D ALA* 1.3 77.1 - - - +
55D LYS* 1.3 68.8 + - + +
56D GLU 2.9 0.3 + - - -
57D LEU* 3.3 10.7 - - - +
58D ALA* 2.5 31.2 + - + +
64D LYS* 5.7 3.6 - - + -
65D PRO* 4.0 23.8 - - + +
87D ILE* 4.3 3.6 - - + +
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Residues in contact with LYS 55 (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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51D ASP* 3.0 33.7 - - + +
52D LYS* 4.1 2.5 - - - +
53D ALA 3.0 1.4 + - - -
54D ALA* 1.3 79.2 - - + +
56D GLU* 1.3 63.3 + - + +
58D ALA* 3.6 4.8 - - - +
59D LEU* 3.0 36.9 + - + +
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Residues in contact with GLU 56 (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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52D LYS* 2.7 66.3 + - - +
53D ALA* 2.6 8.4 + - - +
55D LYS* 1.3 74.0 - - + +
57D LEU* 1.3 57.8 + - + +
58D ALA 2.9 1.6 - - - -
59D LEU* 2.4 38.8 + - + +
60D ILE* 3.1 13.6 + - + +
135D GLN* 4.6 8.0 + - - +
141D ILE* 4.0 24.4 - - + +
146D VAL* 4.0 12.2 - - + +
147D ASP* 2.7 18.9 - - - +
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Residues in contact with LEU 57 (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 VAL* 3.4 32.5 - - + -
38D GLU* 3.7 32.3 - - + +
53D ALA* 2.7 44.1 + - + +
54D ALA* 3.3 10.8 - - - +
56D GLU* 1.3 71.4 - - + +
58D ALA* 1.3 57.3 + - - +
60D ILE* 2.7 38.4 - - + +
61D THR* 2.8 22.1 + - + +
63D GLN 4.5 0.2 - - - -
65D PRO* 4.3 13.9 - - + -
87D ILE* 4.0 6.5 - - + -
89D VAL* 4.7 6.5 - - + -
135D GLN* 4.3 8.1 - - - +
152D MET* 4.5 0.2 - - - -
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Residues in contact with ALA 58 (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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54D ALA* 2.5 25.7 + - + +
55D LYS* 3.6 5.8 - - - +
56D GLU 2.6 1.0 + - - -
57D LEU* 1.3 68.4 - - - +
59D LEU* 1.3 58.5 + - + +
60D ILE 3.1 5.2 - - - -
62D LEU* 2.6 32.9 + - - +
63D GLN 2.9 30.7 + - - +
64D LYS* 4.5 4.9 - - - +
65D PRO* 4.6 0.2 - - + -
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Residues in contact with LEU 59 (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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55D LYS* 3.0 24.5 - - + +
56D GLU* 2.4 27.0 + - + +
58D ALA* 1.3 73.7 - - + +
60D ILE* 1.3 58.8 + - + -
62D LEU* 4.0 13.4 - - + +
140D GLU* 3.3 28.5 - - - +
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Residues in contact with ILE 60 (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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56D GLU* 3.7 6.3 - - - +
57D LEU* 2.7 46.2 - - + +
59D LEU* 1.3 83.0 - - + +
61D THR* 1.3 55.1 + - + +
62D LEU* 4.7 3.5 - - - +
99D PHE* 2.7 36.8 - - + -
102D LYS* 4.8 3.0 + - - +
135D GLN* 4.7 2.0 - - - +
138D PHE* 3.6 35.4 - - + -
140D GLU* 3.5 33.6 - - + +
141D ILE* 3.9 25.6 - - + -
152D MET* 4.1 14.1 - - + -
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Residues in contact with THR 61 (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 VAL* 4.3 24.9 - - + -
57D LEU* 2.8 20.7 + - + +
60D ILE* 1.3 86.5 - - + +
62D LEU* 1.3 80.1 + - - +
63D GLN* 3.4 20.1 + - - +
89D VAL* 3.8 13.3 - - + +
91D LEU* 3.8 28.4 - - + +
95D ARG* 4.5 8.5 - - - +
99D PHE* 4.1 15.8 - - + +
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Residues in contact with LEU 62 (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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58D ALA 2.6 22.2 + - - +
59D LEU* 4.0 19.3 - - + +
60D ILE 4.7 1.8 - - - +
61D THR* 1.3 86.5 - - - +
63D GLN* 1.3 62.6 + - - +
95D ARG* 4.0 23.7 + - + -
98D VAL* 4.4 22.7 - - + -
99D PHE* 6.1 2.2 - - + +
102D LYS* 4.5 18.2 - - - +
140D GLU* 5.1 1.8 - - - +
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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