Contacts of the helix formed by residues 40 - 58 (chain B) in PDB entry 2ZI0
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 SER 40 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B ARG* 3.6 2.8 - - - +
39B LYS* 1.3 74.2 - - - +
41B PRO* 1.3 73.0 - - - +
42B SER* 3.5 3.1 + - - -
43B GLU* 2.7 51.1 + - - +
44B GLN* 3.0 12.7 + - - +
14D C 3.4 29.6 - - - -
15D U 3.2 21.1 + - - -
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Residues in contact with PRO 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B LYS 4.3 1.1 - - - +
40B SER* 1.3 85.4 - - - +
42B SER* 1.3 62.1 + - - +
44B GLN* 3.3 16.5 + - - +
45B ARG* 3.2 33.6 + - - +
14D C 3.2 25.8 - - - +
15D U 3.3 19.1 - - - +
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Residues in contact with SER 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B SER* 3.5 4.2 + - - -
41B PRO* 1.3 69.7 - - - +
43B GLU* 1.3 62.7 + - - +
45B ARG* 3.2 14.9 + - - +
46B ARG* 3.0 44.1 + - - +
15D U 2.8 40.9 + - - -
16D G 3.2 30.0 + - - -
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Residues in contact with GLU 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B ARG* 2.9 32.7 + - - -
38B HIS 4.3 2.6 - - - +
39B LYS* 3.8 20.4 - - + +
40B SER* 2.7 31.3 + - - +
42B SER* 1.3 80.1 + - - +
44B GLN* 1.3 62.7 + - - +
46B ARG* 3.4 32.1 + - - +
47B SER* 3.2 24.8 + - - -
14D C 4.8 2.1 + - - -
15D U 4.2 10.1 - - - +
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Residues in contact with GLN 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B LYS* 3.9 28.2 - - + +
40B SER 3.0 9.0 + - - +
41B PRO* 3.4 28.2 - - - +
43B GLU* 1.3 72.9 - - - +
45B ARG* 1.3 66.5 + - - +
47B SER* 3.2 6.6 + - - -
48B GLU* 3.0 38.0 + - - +
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Residues in contact with ARG 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B PRO* 3.2 24.2 + - - +
42B SER* 3.5 13.9 - - - +
44B GLN* 1.3 76.4 - - - +
46B ARG* 1.3 63.8 + - - +
48B GLU* 3.1 11.9 + - - +
49B LEU* 2.9 38.2 + - + +
15D U 3.8 20.2 + - - -
16D G 5.4 5.3 + - - -
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Residues in contact with ARG 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B SER* 3.0 29.1 + - - +
43B GLU* 3.4 35.1 - - - +
45B ARG* 1.3 74.8 - - - +
47B SER* 1.3 58.9 + - - +
49B LEU* 3.5 8.9 + - + +
50B TRP* 3.1 27.5 + - - +
1C A 4.2 7.6 + - - +
2C G 3.2 13.6 + - - -
3C A 3.0 26.8 - - - +
4C C 4.8 2.0 - - - +
15D U 4.7 4.4 + - - -
16D G 3.7 19.8 + - - -
17D U 3.3 23.1 + - - -
18D C 3.7 15.9 - - - +
19D U 5.0 4.1 - - - +
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Residues in contact with SER 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B LYS* 4.2 15.8 - - - -
43B GLU 3.2 14.8 + - - -
44B GLN* 3.2 8.9 + - - -
46B ARG* 1.3 76.4 - - - +
48B GLU* 1.3 64.9 + - - +
50B TRP* 3.5 0.9 + - - +
51B HIS* 3.0 40.6 + - - -
1C A 4.0 36.2 + - - -
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Residues in contact with GLU 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B GLN* 3.0 27.9 + - - +
45B ARG* 3.5 11.4 + - - +
47B SER* 1.3 80.2 + - - +
49B LEU* 1.3 59.9 + - + +
51B HIS* 3.3 6.6 + - - +
52B ALA* 2.8 31.5 + - - +
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Residues in contact with LEU 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B ARG* 2.9 29.1 + - + +
46B ARG* 3.8 7.9 - - + +
48B GLU* 1.3 78.5 - - + +
50B TRP* 1.3 58.5 + - - +
52B ALA* 3.7 8.1 - - + +
53B ARG* 3.2 48.2 + - - +
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Residues in contact with TRP 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B ARG 3.1 18.5 + - - +
47B SER 3.7 3.8 - - - +
48B GLU 3.2 0.2 - - - -
49B LEU* 1.3 74.1 - - - +
51B HIS* 1.3 92.0 + + - +
53B ARG* 3.1 19.3 + - + +
54B GLN* 2.9 69.5 + - + +
1C A 3.3 82.5 - + + +
19D U 4.2 15.4 + + - +
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Residues in contact with HIS 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B SER* 3.0 35.0 + - - +
48B GLU* 3.8 5.4 - - - +
50B TRP* 1.3 102.6 - + - +
52B ALA* 1.3 56.1 + - - +
54B GLN* 3.8 4.0 - - - +
55B VAL* 3.0 39.3 + - + +
1C A 2.4 43.7 + - - -
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Residues in contact with ALA 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B GLU 2.8 18.1 + - - +
49B LEU* 3.7 12.6 - - + +
51B HIS* 1.3 74.5 - - - +
53B ARG* 1.3 64.5 + - + +
55B VAL* 3.6 4.2 + - - +
56B GLU* 3.1 26.2 + - - +
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Residues in contact with ARG 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B LEU* 3.2 32.1 + - - +
50B TRP* 3.1 19.3 + - + +
52B ALA* 1.3 77.6 - - + +
54B GLN* 1.3 62.7 + - + +
56B GLU* 3.6 14.9 + - - +
57B LEU* 3.4 26.2 + - - +
19D U 4.6 23.0 + - - -
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Residues in contact with GLN 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B TRP* 2.9 69.2 + - + +
51B HIS* 3.8 8.5 - - - +
52B ALA 3.3 0.2 - - - -
53B ARG* 1.3 76.6 - - + +
55B VAL* 1.3 64.9 + - + +
57B LEU* 3.4 34.7 + - - +
58B SER* 3.7 6.8 + - - -
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Residues in contact with VAL 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B HIS* 3.0 25.8 + - + +
52B ALA* 4.2 4.7 - - - +
54B GLN* 1.3 73.2 - - + +
56B GLU* 1.3 65.0 + - - +
57B LEU 3.2 0.7 - - - -
58B SER* 3.3 25.9 + - - +
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Residues in contact with GLU 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B ALA 3.1 19.2 + - - +
53B ARG* 3.7 15.9 - - - +
54B GLN 3.3 0.2 - - - -
55B VAL* 1.3 75.3 - - - +
57B LEU* 1.3 63.6 + - - +
58B SER 4.5 2.4 - - - -
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Residues in contact with LEU 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B ARG 3.5 15.7 - - - +
54B GLN* 3.4 32.5 + - - +
55B VAL 3.2 0.6 - - - -
56B GLU* 1.3 81.6 - - - +
58B SER* 1.3 61.4 + - - +
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Residues in contact with SER 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B GLN 3.7 4.6 + - - -
55B VAL* 3.3 29.0 + - - +
56B GLU 4.5 2.5 - - - -
57B LEU* 1.3 82.9 - - - +
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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