Contacts of the helix formed by residues 38 - 57 (chain E) in PDB entry 1NZB
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 38 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37E PHE* 1.3 74.6 - - - +
39E GLU* 1.3 70.0 + - - +
40E HIS* 3.3 9.3 + - - +
41E THR* 2.8 18.2 + - - -
42E TRP* 3.0 11.5 + - - -
122F LYS* 3.1 15.0 - - - +
123G T 2.9 26.7 + - - -
124G A 2.7 28.3 + - - -
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Residues in contact with GLU 39 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37E PHE 3.8 1.4 + - - -
38E SER* 1.3 75.7 + - - +
40E HIS* 1.3 101.7 + - + +
42E TRP* 3.1 10.6 + - - +
43E LYS* 3.0 23.5 + - - +
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Residues in contact with HIS 40 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38E SER* 3.1 6.7 + - - +
39E GLU* 1.3 106.1 + - + +
41E THR* 1.3 60.9 + - - +
43E LYS* 3.2 31.2 + - - +
44E MET* 3.5 23.4 + - - +
123G T 4.4 1.3 - - + +
124G A 3.9 41.8 - + + +
125G T 3.3 31.6 + - + +
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Residues in contact with THR 41 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37E PHE* 4.3 9.4 - - + -
38E SER* 2.8 16.7 + - - -
40E HIS* 1.3 75.3 - - - +
42E TRP* 1.3 68.3 + - - +
43E LYS 3.0 0.7 + - - -
44E MET* 3.0 6.4 + - - +
45E LEU* 2.9 19.6 + - + +
94E GLN* 4.2 2.0 - - - +
97E MET* 3.8 30.1 - - + -
122G C 3.5 13.7 - - - +
123G T 2.6 52.8 + - + +
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Residues in contact with TRP 42 (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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30E MET* 3.8 17.0 - - + -
31E PHE* 3.4 38.1 - + - -
34E ARG* 2.5 62.9 + - + +
37E PHE* 3.6 34.2 - + + +
38E SER 3.0 10.0 + - - -
39E GLU* 3.4 10.8 - - - +
41E THR* 1.3 80.3 - - - +
43E LYS* 1.3 66.2 + - - +
45E LEU* 3.1 38.1 + - + +
46E LEU* 3.0 41.9 + - + +
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Residues in contact with LYS 43 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39E GLU 3.0 12.3 + - - +
40E HIS* 3.2 45.0 + - - +
42E TRP* 1.3 74.7 - - - +
44E MET* 1.3 60.5 + - - +
46E LEU* 2.9 16.1 + - + +
47E SER* 2.7 33.9 + - - -
50E ARG* 5.2 2.6 + - - +
124G A 5.9 0.2 + - - -
125G T 3.9 10.1 + - - -
126G A 4.6 2.4 - - - +
110H G 4.3 16.1 + - + +
111H T 3.3 43.9 + - + +
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Residues in contact with MET 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 HIS 3.7 12.1 - - - +
41E THR* 3.0 8.1 + - - +
43E LYS* 1.3 83.3 - - - +
45E LEU* 1.3 64.2 + - - +
47E SER* 3.5 16.8 - - - +
48E VAL* 2.7 30.5 + - + +
90E GLN* 4.5 18.2 - - + +
91E HIS* 5.5 9.0 - - + +
94E GLN* 4.1 11.4 - - - +
123G T 5.5 2.5 - - + -
124G A 4.0 15.9 - - - +
111H T 3.7 18.8 - - + -
112H A 3.4 42.8 - - + +
113H T 3.8 9.9 - - + +
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Residues in contact with LEU 45 (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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30E MET* 5.0 5.4 - - + -
37E PHE* 6.5 0.2 - - + -
41E THR 2.9 13.0 + - - +
42E TRP* 3.1 48.9 - - + +
43E LYS 3.0 0.2 + - - -
44E MET* 1.3 76.9 - - - +
46E LEU* 1.3 67.6 + - + +
48E VAL* 3.0 7.3 - - + +
49E CYS* 3.0 36.4 + - - -
94E GLN* 3.7 37.6 + - - +
97E MET* 4.4 19.7 - - - -
98E LEU* 4.3 18.6 - - + -
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Residues in contact with LEU 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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31E PHE* 6.3 2.0 - - + -
42E TRP* 3.0 38.5 + - + +
43E LYS* 2.9 12.9 + - + +
45E LEU* 1.3 77.2 - - + +
47E SER* 1.3 68.0 + - - +
49E CYS* 2.8 22.0 + - + +
50E ARG* 2.9 32.8 + - + +
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Residues in contact with SER 47 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43E LYS* 2.7 18.2 + - - -
44E MET* 3.5 17.9 - - - +
46E LEU* 1.3 73.7 - - - +
48E VAL* 1.3 61.1 + - - +
50E ARG* 3.4 23.6 - - - +
51E SER* 3.4 17.7 + - - -
111H T 2.8 53.1 + - - +
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Residues in contact with VAL 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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44E MET* 2.7 19.1 + - + +
45E LEU* 3.0 14.8 - - + +
47E SER* 1.3 69.1 - - - +
49E CYS* 1.3 85.5 + - - +
50E ARG 3.0 2.0 - - - -
51E SER* 2.8 8.8 + - - +
52E TRP* 2.8 21.5 + - + +
74E TYR* 4.5 3.1 - - + +
91E HIS* 3.3 61.2 - - + +
94E GLN* 3.2 31.6 - - + -
95E LEU* 4.8 9.0 - - + +
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Residues in contact with CYS 49 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45E LEU* 3.0 33.8 + - - +
46E LEU* 2.8 12.0 + - - +
48E VAL* 1.3 85.7 - - - +
50E ARG* 1.3 53.4 + - + +
52E TRP* 3.2 10.5 + - - +
53E ALA* 2.7 37.1 + - - +
63E TRP* 4.3 16.1 - - + -
94E GLN 5.9 0.4 - - - -
95E LEU* 5.7 4.3 - - - -
98E LEU* 4.1 26.2 - - - -
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Residues in contact with ARG 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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43E LYS* 5.2 3.2 + - - +
46E LEU* 2.9 33.0 + - + +
47E SER* 3.4 21.1 - - - +
48E VAL 3.0 0.2 - - - -
49E CYS* 1.3 73.5 - - + +
51E SER* 1.3 67.3 + - - +
53E ALA* 3.2 7.4 + - - +
54E ALA* 2.9 25.6 + - - +
110H G 3.4 29.0 + - - +
111H T 2.4 39.0 + - - +
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Residues in contact with SER 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 SER 3.4 8.1 + - - -
48E VAL 2.8 10.3 + - - -
50E ARG* 1.3 75.5 - - - +
52E TRP* 1.3 66.4 + - - +
54E ALA* 3.6 5.3 - - - +
55E TRP* 3.2 22.2 + - - +
74E TYR* 3.1 22.7 + - - -
77E TYR* 5.4 1.0 - - - -
81E ARG* 3.8 21.8 + - - -
91E HIS* 4.1 12.2 - - - -
111H T 5.8 0.4 + - - -
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Residues in contact with TRP 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 VAL 2.8 11.2 + - - +
49E CYS* 3.3 10.5 - - - +
51E SER* 1.3 78.8 - - - +
53E ALA* 1.3 63.3 + - - +
55E TRP* 3.8 7.1 - + - +
56E CYS* 2.9 53.0 + - - +
62E LYS 4.6 1.6 - - - -
63E TRP* 2.5 53.7 + + + +
66E ALA* 3.2 28.4 - - + +
70E ASP* 4.0 9.2 - - + -
71E VAL* 3.8 27.1 - - + -
74E TYR* 3.2 54.0 + + + -
95E LEU* 3.8 28.0 - - + +
98E LEU* 6.0 0.2 - - + -
99E HIS* 5.7 0.6 - + - -
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Residues in contact with ALA 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 CYS 2.7 20.9 + - - +
50E ARG* 3.5 7.9 - - - +
52E TRP* 1.3 72.7 - - - +
54E ALA* 1.3 67.2 + - - +
56E CYS* 4.3 3.1 - - - -
57E LYS* 3.0 47.5 + - - +
63E TRP* 4.4 14.1 - - + -
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Residues in contact with ALA 54 (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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50E ARG 2.9 16.7 + - - +
51E SER* 3.6 7.6 - - - +
52E TRP 3.1 0.4 + - - -
53E ALA* 1.3 74.4 - - - +
55E TRP* 1.3 68.6 + - - +
56E CYS 2.7 2.1 + - - -
57E LYS* 2.7 25.8 + - - +
58E LEU* 3.7 5.5 + - + +
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Residues in contact with TRP 55 (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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51E SER 3.2 13.0 + - - +
52E TRP* 3.8 29.2 - + - +
54E ALA* 1.3 78.0 - - - +
56E CYS* 1.3 71.7 + - - +
58E LEU* 3.5 9.8 + - + +
59E ASN* 2.5 55.8 + - + +
61E ARG* 3.7 38.6 - - + -
70E ASP* 3.8 6.5 - - + -
73E ASP* 3.7 33.7 - - + -
74E TYR* 3.8 20.9 - + + -
77E TYR* 3.1 48.5 - + + +
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Residues in contact with CYS 56 (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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52E TRP* 2.9 63.9 + - - +
53E ALA 3.4 6.1 - - - +
54E ALA 2.7 4.0 + - - -
55E TRP* 1.3 84.7 - - - +
57E LYS* 1.3 59.4 + - + +
58E LEU 3.0 0.9 + - - -
59E ASN 3.1 0.2 + - - -
60E ASN 2.8 31.5 + - - -
61E ARG* 3.1 27.5 + - - +
62E LYS 4.2 2.0 - - - -
63E TRP* 3.7 15.0 - - + -
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Residues in contact with LYS 57 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53E ALA* 3.2 30.7 + - - +
54E ALA* 2.7 10.8 + - - +
56E CYS* 1.3 81.8 - - + +
58E LEU* 1.3 61.4 + - - +
60E ASN* 4.3 8.5 - - - +
61E ARG 4.0 11.9 - - - +
63E TRP* 4.1 27.8 - - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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