Contacts of the helix formed by residues 41 - 53 (chain E) in PDB entry 3ZPL
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 PRO 41 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31E ASP* 4.1 16.2 - - - +
34E LEU* 4.6 1.8 - - - -
35E GLN* 3.6 17.9 - - - +
40E MET* 1.3 94.4 - - + +
42E HIS* 1.3 67.4 + - - +
43E VAL* 3.3 4.9 + - + +
44E TYR* 3.4 39.3 + - + +
45E TYR* 3.2 17.3 + - - +
12H T 3.9 26.2 - - - +
13H C 5.5 1.6 - - - +
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Residues in contact with HIS 42 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27E GLU* 5.4 5.1 - - - +
30E LEU* 4.2 20.2 - - + +
31E ASP* 2.9 30.9 + - - +
34E LEU* 3.6 28.5 - - + +
41E PRO* 1.3 71.2 - - - +
43E VAL* 1.3 66.2 + - + +
45E TYR* 3.5 5.8 + + - +
46E GLY* 3.1 20.8 + - - -
119E HIS* 3.7 21.5 + + - -
16F TRP* 4.4 4.1 + + - -
20F ILE* 3.8 34.5 - - + +
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Residues in contact with VAL 43 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31E ASP* 5.5 2.2 - - - +
41E PRO* 3.3 4.4 - - + -
42E HIS* 1.3 78.4 - - + +
44E TYR* 1.3 69.2 + - + +
46E GLY* 3.2 4.9 + - - -
47E LEU* 3.2 24.4 + - + +
68E ALA* 5.4 3.8 - - + +
70E ILE* 4.2 31.9 - - + -
74E ARG* 3.5 29.2 - - - +
24F THR* 6.3 2.2 - - + -
13H C 4.2 7.4 - - - +
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Residues in contact with TYR 44 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40E MET* 4.0 11.9 - - - -
41E PRO* 3.4 32.6 + - + +
42E HIS 3.3 0.2 - - - -
43E VAL* 1.3 77.9 - - + +
45E TYR* 1.3 57.4 + - - +
47E LEU* 2.7 35.6 + - + +
48E LEU* 3.2 12.0 + - - +
74E ARG* 5.8 0.4 - - + -
77E HIS* 4.7 2.4 + - - +
78E ALA* 3.4 35.9 + - + -
81E ARG* 3.7 38.4 - - + +
82E LEU* 3.9 21.7 - - + +
12H T 3.5 24.3 + - - +
13H C 3.2 30.2 + - - -
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Residues in contact with TYR 45 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34E LEU* 3.6 29.4 - - + -
40E MET* 3.5 33.2 - - + -
41E PRO 3.2 9.9 + - - +
42E HIS* 3.6 11.2 - + - +
44E TYR* 1.3 76.9 - - - +
46E GLY* 1.3 64.5 + - - +
48E LEU* 3.1 6.0 + - - +
49E VAL* 3.0 46.9 + - + +
112E LEU* 4.4 13.2 + - + +
115E THR* 3.3 21.8 - - - -
116E ALA* 3.0 36.0 + - - +
119E HIS* 3.7 33.4 - + + +
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Residues in contact with GLY 46 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42E HIS* 3.1 15.1 + - - -
43E VAL* 3.2 5.6 + - - -
44E TYR 3.1 1.4 - - - -
45E TYR* 1.3 75.5 - - - +
47E LEU* 1.3 66.5 + - - +
49E VAL* 3.3 9.7 + - - +
50E LYS* 3.0 23.9 + - - +
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Residues in contact with LEU 47 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43E VAL* 3.2 15.3 + - + +
44E TYR* 2.7 24.5 + - + +
46E GLY* 1.3 71.9 - - - -
48E LEU* 1.3 63.3 + - + +
50E LYS* 3.2 4.0 + - - +
51E LEU* 3.1 28.2 + - + +
64E LEU* 4.1 28.5 - - + +
68E ALA* 3.7 30.5 - - + -
70E ILE* 4.2 12.6 - - + -
75E LEU* 3.8 19.1 - - + -
78E ALA* 4.0 22.0 - - + -
79E VAL* 5.0 2.0 - - + -
82E LEU* 4.2 14.6 - - + -
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Residues in contact with LEU 48 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40E MET* 3.6 31.4 - - + -
44E TYR 3.9 8.5 - - - +
45E TYR* 3.1 7.7 + - - +
47E LEU* 1.3 78.2 - - + +
49E VAL* 1.3 58.0 + - - +
51E LEU* 3.3 6.6 + - + +
52E ALA* 2.9 31.5 + - - +
82E LEU* 4.1 17.5 - - + -
87E TRP* 4.3 20.6 - - + +
88E VAL* 3.7 28.7 - - + -
104E LEU* 4.0 11.9 - - + +
108E GLY 4.5 3.6 - - - +
111E VAL* 5.3 1.1 - - + -
112E LEU* 3.6 29.5 - - + +
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Residues in contact with VAL 49 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45E TYR* 3.0 44.9 + - + +
46E GLY* 3.5 11.0 - - - +
47E LEU 3.3 0.2 - - - -
48E LEU* 1.3 76.0 - - - +
50E LYS* 1.3 62.1 + - - +
52E ALA* 3.5 2.1 + - - +
53E GLU* 3.1 29.9 + - + +
112E LEU* 3.9 15.7 - - + -
17F ARG* 4.4 22.0 - - - +
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Residues in contact with LYS 50 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46E GLY 3.0 16.4 + - - +
47E LEU* 3.2 4.7 + - - +
49E VAL* 1.3 77.1 - - - +
51E LEU* 1.3 56.1 + - - +
53E GLU* 3.4 27.0 + - - +
54E SER* 2.6 37.0 + - - +
59E LEU* 3.8 14.6 - - + -
64E LEU* 4.3 9.0 - - + -
67E TYR* 3.6 56.9 + - + -
17F ARG* 5.0 6.9 - - - +
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Residues in contact with LEU 51 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47E LEU* 3.1 17.5 + - + +
48E LEU* 3.7 6.5 - - + +
50E LYS* 1.3 73.0 - - - +
52E ALA* 1.3 58.6 + - - +
53E GLU 3.0 1.3 - - - -
54E SER* 2.7 25.0 + - - -
57E ARG* 3.2 27.0 - - - +
58E ARG 4.2 0.7 - - - -
59E LEU* 3.6 32.8 - - + +
64E LEU* 3.9 21.3 - - + -
88E VAL* 4.2 20.9 - - + -
102E ALA* 3.6 28.9 - - + +
104E LEU* 4.0 20.4 - - + +
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Residues in contact with ALA 52 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48E LEU 2.9 18.2 + - - +
49E VAL* 3.6 4.7 - - - +
51E LEU* 1.3 76.1 - - - +
53E GLU* 1.3 59.3 + - + +
54E SER 3.7 1.9 + - - +
57E ARG* 4.1 13.8 + - - +
104E LEU* 3.5 21.8 - - + +
109E TYR* 4.4 15.8 - - + -
112E LEU* 3.6 18.2 - - + -
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Residues in contact with GLU 53 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49E VAL* 3.1 23.6 + - + +
50E LYS* 3.5 31.7 + - + +
51E LEU 3.0 1.0 - - - -
52E ALA* 1.3 75.7 - - + +
54E SER* 1.3 62.3 - - - +
55E PRO* 4.5 1.6 - - - +
13F GLN* 4.3 5.9 - - - +
17F ARG* 2.9 41.3 + - - -
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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