Contacts of the helix formed by residues 45 - 60 (chain A) in PDB entry 1ZEB
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 45 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43A GLY 3.0 12.3 + - - -
44A MET* 1.3 76.2 - - - +
46A VAL* 1.3 66.3 + - - -
47A SER 3.2 2.9 - - - -
48A THR* 3.0 7.6 + - - -
49A VAL* 2.9 22.1 + - - +
359A SER* 3.4 28.2 + - - +
437A VAL* 4.2 9.6 - - - -
438A ALA* 5.9 0.9 - - - -
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Residues in contact with VAL 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A GLY* 1.3 71.8 - - - -
47A SER* 1.3 62.6 + - - +
49A VAL* 3.3 8.6 + - + +
50A THR* 3.0 30.5 + - - +
79A LEU* 5.0 8.7 - - + -
359A SER* 4.5 1.6 + - - -
435A GLU* 4.6 6.8 + - + +
436A ASP 4.2 17.9 + - - +
437A VAL 4.8 0.7 - - - -
438A ALA* 4.4 22.7 - - + +
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Residues in contact with SER 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A VAL* 1.3 78.7 - - - +
48A THR* 1.3 64.1 + - - +
50A THR* 4.1 4.9 - - - +
51A ALA* 3.1 25.8 + - - +
359A SER* 4.7 4.9 + - - -
360A HIS 4.7 4.0 + - - -
362A PHE* 2.8 43.7 + - - +
363A SER* 4.7 5.2 - - - -
364A PHE* 5.0 9.2 - - - +
435A GLU* 5.1 3.6 + - - -
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Residues in contact with THR 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A GLY 3.7 5.7 + - - -
44A MET* 3.9 12.1 - - + -
45A GLY* 3.0 17.1 + - - -
47A SER* 1.3 77.9 + - - +
49A VAL* 1.3 58.9 + - - +
51A ALA* 3.4 1.6 + - - +
52A ALA* 2.9 32.4 + - - +
315A ILE* 4.0 7.0 - - + -
319A HIS* 2.7 36.0 + - + +
327A ALA 4.8 0.2 - - - +
328A LEU* 3.8 8.4 - - + +
331A THR* 3.4 24.9 - - - +
359A SER* 5.3 0.9 + - - -
360A HIS* 5.4 0.7 - - - +
362A PHE* 3.7 11.2 - - - +
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Residues in contact with VAL 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A MET* 3.6 40.2 - - + +
45A GLY 2.9 18.5 + - - +
46A VAL* 3.3 10.1 + - + +
48A THR* 1.3 75.2 - - - +
50A THR* 1.3 58.5 + - - +
52A ALA* 3.3 5.9 + - - +
53A ARG* 2.9 43.6 + - - +
69A LEU* 3.5 20.7 - - + +
71A MET* 4.1 9.4 - - - -
72A ASP* 4.3 2.9 - - - +
331A THR* 5.1 0.7 - - - -
438A ALA* 5.9 3.4 - - + -
440A PHE* 4.5 13.0 - - + -
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Residues in contact with THR 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A VAL* 3.0 22.4 + - - +
47A SER* 4.1 5.6 - - - -
49A VAL* 1.3 76.4 - - - +
51A ALA* 1.3 64.7 + - - +
53A ARG* 3.1 30.3 + - - +
54A ILE* 3.1 37.3 + - + +
65A PRO* 6.1 2.0 - - + -
364A PHE* 4.6 12.3 - - + -
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Residues in contact with ALA 51 (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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47A SER 3.1 18.6 + - - +
48A THR 3.8 1.8 - - - +
50A THR* 1.3 76.4 - - - +
52A ALA* 1.3 62.2 + - - +
54A ILE* 3.3 5.4 + - - +
55A LEU* 3.0 22.9 + - - +
328A LEU* 3.7 20.8 - - + +
362A PHE* 3.8 18.8 - - + -
364A PHE* 5.1 4.9 - - + -
374A ILE* 4.0 24.9 - - + +
391A LEU* 4.6 2.0 - - + -
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Residues in contact with ALA 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A THR 2.9 17.7 + - - +
49A VAL* 3.5 5.4 - - - +
51A ALA* 1.3 73.3 - - - +
53A ARG* 1.3 60.1 + - - +
55A LEU* 3.3 6.5 + - - +
56A LYS* 2.9 32.1 + - - +
69A LEU* 4.3 8.5 - - + -
328A LEU* 3.9 13.1 - - + +
331A THR* 3.6 33.2 - - + -
332A ILE* 4.0 7.5 - - + +
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Residues in contact with ARG 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A VAL* 2.9 26.9 + - - +
50A THR* 3.1 42.1 + - - +
52A ALA* 1.3 75.1 - - - +
54A ILE* 1.3 54.5 + - - +
56A LYS* 3.4 1.6 + - - +
57A GLY* 2.8 32.9 + - - -
64A GLY 3.6 3.5 - - - +
65A PRO* 3.5 24.5 + - - +
67A ILE 3.0 29.0 - - - +
68A PRO* 4.8 0.4 - - - -
69A LEU* 3.6 18.7 - - + +
72A ASP* 2.6 39.9 + - - +
440A PHE* 6.0 0.6 - - - -
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Residues in contact with ILE 54 (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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50A THR* 3.1 20.0 + - + +
51A ALA 3.6 6.7 - - - +
53A ARG* 1.3 75.5 - - + +
55A LEU* 1.3 64.2 + - - +
57A GLY 3.2 1.4 + - - -
58A GLN* 3.0 47.1 + - - +
64A GLY* 3.4 11.2 - - - -
65A PRO* 3.8 33.2 - - + -
364A PHE* 3.4 38.1 - - + -
372A SER 4.6 3.4 - - - +
374A ILE* 4.1 19.7 - - + -
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Residues in contact with LEU 55 (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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51A ALA 3.0 13.4 + - - +
52A ALA* 3.7 7.6 - - - +
53A ARG 3.3 0.2 - - - -
54A ILE* 1.3 78.6 - - - +
56A LYS* 1.3 57.1 + - - +
58A GLN* 3.2 11.4 + - + +
59A LYS* 2.8 30.2 + - + +
325A TYR* 5.9 1.1 - - + -
328A LEU* 3.7 27.1 - - + -
329A THR* 4.4 10.8 - - + -
332A ILE* 3.6 22.4 - - + -
373A SER* 5.9 0.7 - - - +
374A ILE* 4.2 11.9 - - + +
375A PHE* 3.7 32.5 - - + -
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Residues in contact with LYS 56 (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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52A ALA 2.9 17.4 + - - +
53A ARG 3.8 2.9 - - - +
55A LEU* 1.3 73.2 - - - +
57A GLY* 1.3 66.1 + - - +
59A LYS* 3.2 11.5 + - + +
60A LYS* 3.1 53.4 + - - +
67A ILE* 6.1 0.4 - - + -
68A PRO 5.7 0.2 - - - +
69A LEU* 3.7 22.4 - - + -
70A ALA 4.7 2.1 - - - +
332A ILE* 3.7 29.3 + - + +
335A ASP* 2.7 31.2 + - - +
336A ASP* 2.8 30.9 + - - +
339A GLU* 4.7 11.2 + - - -
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Residues in contact with GLY 57 (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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53A ARG 2.8 20.3 + - - -
54A ILE 3.7 2.2 - - - -
56A LYS* 1.3 75.0 - - - +
58A GLN* 1.3 58.7 + - - +
60A LYS* 3.4 7.9 + - - +
62A LYS* 3.1 30.3 + - - +
64A GLY* 3.9 13.7 - - - -
67A ILE* 3.9 20.8 - - - +
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Residues in contact with GLN 58 (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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54A ILE* 3.0 25.9 + - - +
55A LEU* 3.7 12.9 - - + +
57A GLY* 1.3 72.6 - - - +
59A LYS* 1.3 57.1 + - - +
60A LYS 2.4 21.3 - - - +
61A ASP* 4.6 0.2 - - - -
62A LYS 3.3 13.7 + - - +
63A LEU 2.8 30.6 + - - +
371A GLY 3.4 14.4 + - - +
372A SER 2.9 23.0 + - - -
373A SER* 3.7 19.8 - - - -
374A ILE 4.3 1.7 + - - -
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Residues in contact with LYS 59 (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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55A LEU* 2.8 16.9 + - + +
56A LYS* 3.3 14.1 - - + +
58A GLN* 1.3 70.1 - - - +
60A LYS* 1.3 68.7 + - + +
332A ILE* 3.9 36.0 - - + +
336A ASP* 4.3 9.1 + - - -
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Residues in contact with LYS 60 (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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56A LYS* 3.1 53.2 + - - +
57A GLY 3.5 9.4 - - - +
58A GLN 2.4 24.6 - - - +
59A LYS* 1.3 79.6 - - + +
61A ASP* 1.3 60.5 + - - +
62A LYS* 3.3 14.4 - - + -
67A ILE* 4.0 24.9 - - + +
68A PRO 4.4 7.9 + - - -
339A GLU* 5.5 4.2 + - - -
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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