Contacts of the helix formed by residues 38 - 59 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B ALA 4.1 0.6 + - - -
37B PHE* 1.3 76.7 - - - +
39B GLU* 1.3 68.6 + - - +
40B HIS* 3.2 13.7 + - - +
41B THR* 3.1 16.5 + - - -
42B TRP* 3.5 6.2 + - - -
199B ARG* 6.0 0.9 - - - -
123D T 3.0 36.3 + - - +
124D A 2.7 29.2 + - - -
122E LYS* 3.2 14.3 - - - +
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Residues in contact with GLU 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B PHE 3.7 1.2 + - - -
38B SER* 1.3 75.3 + - - +
40B HIS* 1.3 72.9 + - + +
42B TRP* 2.8 26.3 + - + +
43B LYS* 3.0 17.0 + - + +
122E LYS* 3.9 6.0 - - - +
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Residues in contact with HIS 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B SER* 3.2 5.8 + - - +
39B GLU* 1.3 89.6 + - + +
41B THR* 1.3 62.6 + - - +
43B LYS* 3.7 27.0 + - - +
44B MET* 3.5 24.8 + - - +
123D T 4.8 2.2 - - + +
124D A 3.8 47.5 + + + +
125D T 3.3 38.9 + - + +
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Residues in contact with THR 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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37B PHE* 4.3 10.8 - - + -
38B SER* 3.1 14.7 + - - -
39B GLU 3.0 1.2 + - - -
40B HIS* 1.3 80.7 - - - +
42B TRP* 1.3 62.8 + - + +
44B MET* 3.4 3.6 + - - +
45B LEU* 3.1 23.5 + - + +
94B GLN* 3.6 3.7 + - - +
97B MET* 3.6 33.9 - - + -
122D T 3.5 15.2 - - - +
123D T 2.7 41.8 + - + +
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Residues in contact with TRP 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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27B LEU* 6.4 1.3 - - + -
30B MET* 3.7 27.6 - - + -
31B PHE* 4.0 25.4 - + + -
34B ARG* 3.1 61.7 + - + +
37B PHE* 3.8 16.7 - + + +
38B SER 3.7 12.8 - - - -
39B GLU* 2.8 10.7 + - - +
41B THR* 1.3 77.9 - - + +
43B LYS* 1.3 65.5 + - - +
44B MET 2.6 7.2 + - - -
45B LEU* 3.0 37.6 + - + +
46B LEU* 3.2 38.0 + - + +
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Residues in contact with LYS 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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39B GLU* 3.0 18.3 + - + +
40B HIS* 3.7 29.5 + - - +
41B THR 3.6 0.2 - - - -
42B TRP* 1.3 74.6 - - - +
44B MET* 1.3 65.2 + - - +
46B LEU* 3.9 8.9 - - - +
47B SER* 3.1 24.8 + - - -
50B ARG* 4.5 5.1 + - - +
110C G 4.6 16.0 + - + +
111C T 3.5 36.3 + - + +
125D T 3.5 21.3 + - - -
126D A 4.1 5.5 - - - +
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Residues in contact with MET 44 (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 HIS 3.5 12.5 + - - +
41B THR 3.4 4.7 + - - +
42B TRP 2.6 5.1 + - - -
43B LYS* 1.3 78.7 - - - +
45B LEU* 1.3 68.1 + - - +
46B LEU 2.9 2.4 + - - -
47B SER* 2.9 13.1 + - - -
48B VAL* 2.7 33.4 + - - +
90B GLN* 4.5 11.2 - - - +
94B GLN* 3.4 22.2 - - + +
111C T 3.7 18.6 - - + +
112C A 2.9 51.6 - - - +
113C T 3.4 12.3 - - - +
123D T 5.7 0.9 - - + -
124D A 4.0 13.2 - - - +
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Residues in contact with LEU 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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30B MET* 4.6 9.4 - - + -
41B THR* 3.1 11.9 + - + +
42B TRP* 3.0 45.0 + - + +
44B MET* 1.3 76.8 - - - +
46B LEU* 1.3 60.6 + - + +
48B VAL* 3.5 1.9 + - - +
49B CYS* 2.9 54.8 + - - -
94B GLN* 3.9 28.6 - - + +
97B MET* 4.8 13.5 - - - -
98B LEU* 3.6 31.2 - - + -
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Residues in contact with LEU 46 (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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42B TRP* 3.4 42.4 - - + +
43B LYS* 3.9 4.7 - - - +
44B MET 2.9 0.8 + - - -
45B LEU* 1.3 77.6 - - + +
47B SER* 1.3 65.7 + - - +
48B VAL 2.7 5.7 + - - -
49B CYS* 2.9 6.3 + - + +
50B ARG* 2.8 50.1 + - - +
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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
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43B LYS 3.1 17.5 + - - -
44B MET* 2.9 14.3 + - - -
46B LEU* 1.3 79.2 - - - +
48B VAL* 1.3 60.2 + - - +
50B ARG* 3.6 17.9 - - - +
51B SER* 3.5 19.6 + - - -
91B HIS* 5.6 1.8 + - - -
111C T 3.5 48.0 + - - +
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Residues in contact with VAL 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 MET* 2.7 30.3 + - - +
45B LEU 3.7 3.4 - - - +
46B LEU 2.7 3.8 + - - -
47B SER* 1.3 74.4 - - - +
49B CYS* 1.3 67.5 + - - +
50B ARG 3.0 1.5 + - - -
51B SER* 3.0 6.4 + - - -
52B TRP* 2.8 21.1 + - + +
74B TYR* 5.0 2.0 - - - +
90B GLN* 4.5 2.0 - - + +
91B HIS* 3.7 55.4 - - + +
94B GLN* 3.6 26.5 - - + -
95B LEU* 4.6 13.7 - - + +
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Residues in contact with CYS 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 LEU* 2.9 50.0 + - - +
46B LEU* 3.9 7.2 - - + +
48B VAL* 1.3 73.4 - - - +
50B ARG* 1.3 66.8 + - - +
52B TRP* 3.5 8.6 - - - +
53B ALA* 2.8 25.9 + - - +
63B TRP* 3.7 20.6 - - + -
94B GLN* 6.3 0.4 - - - -
95B LEU* 5.2 7.0 - - - -
98B LEU* 3.7 23.6 - - - -
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Residues in contact with ARG 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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43B LYS* 4.5 5.5 + - - +
46B LEU* 2.8 43.0 + - - +
47B SER* 3.6 20.5 - - - +
49B CYS* 1.3 81.6 - - - +
51B SER* 1.3 54.0 + - - +
53B ALA* 3.7 3.4 - - - +
54B ALA* 2.8 32.7 + - - +
110C G 4.3 22.6 + - - +
111C T 2.9 35.4 + - - +
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Residues in contact with SER 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 3.5 10.7 + - - -
48B VAL 3.0 6.4 + - - -
50B ARG* 1.3 79.8 - - - +
52B TRP* 1.3 62.9 + - - +
54B ALA* 3.6 8.1 - - - +
55B TRP* 3.3 19.1 + - - +
74B TYR* 3.1 18.6 + - - -
77B TYR* 5.5 1.7 - - - -
81B ARG* 4.2 15.9 + - - -
91B HIS* 4.1 15.3 - - - -
112C A 5.7 1.1 + - - -
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Residues in contact with TRP 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 VAL* 2.8 20.7 + - + +
49B CYS* 3.5 4.9 - - - +
51B SER* 1.3 68.4 - - - +
53B ALA* 1.3 67.2 + - - +
54B ALA 3.0 0.7 - - - -
55B TRP* 2.7 30.8 + + - +
56B CYS* 2.7 33.6 + - - +
62B LYS 4.5 2.9 - - - -
63B TRP* 2.9 47.8 + + + +
66B ALA* 3.5 27.6 - - + +
70B ASP* 3.9 8.5 - - + -
71B VAL* 3.7 25.8 - - + -
74B TYR* 3.3 57.1 + + + +
95B LEU* 3.7 29.7 - - + +
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Residues in contact with ALA 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 CYS 2.8 20.3 + - - +
50B ARG* 3.7 2.9 - - - +
52B TRP* 1.3 73.5 - - - +
54B ALA* 1.3 64.0 + - - +
56B CYS* 3.4 10.9 - - - +
57B LYS* 2.7 27.4 + - - +
63B TRP* 4.3 23.6 - - + -
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Residues in contact with ALA 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 ARG 2.8 21.9 + - - +
51B SER* 3.6 10.8 - - - +
53B ALA* 1.3 77.2 - - - +
55B TRP* 1.3 63.1 + - - +
57B LYS* 3.1 21.6 + - - +
58B LEU* 3.2 12.9 + - - +
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Residues in contact with TRP 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 SER 3.3 9.8 + - - +
52B TRP* 2.7 44.6 + + - +
54B ALA* 1.3 76.3 - - - +
56B CYS* 1.3 65.0 + - - +
58B LEU* 3.6 4.4 + - - -
59B ASN* 3.0 56.6 + - - +
61B ARG* 3.1 43.5 - - + -
70B ASP 3.4 17.7 - - - -
73B ASP* 4.1 9.4 - - + -
74B TYR* 3.8 27.4 - + + -
77B TYR* 3.2 44.9 - + + +
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Residues in contact with CYS 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 TRP* 2.7 59.6 + - - +
53B ALA* 3.1 11.6 + - - +
55B TRP* 1.3 81.2 - - - +
57B LYS* 1.3 66.6 + - - +
59B ASN 3.3 0.5 + - - -
60B ASN 3.1 4.0 + - - -
61B ARG* 2.9 41.3 + - - +
62B LYS 2.9 20.9 - - - +
63B TRP* 3.9 8.5 - - + -
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Residues in contact with LYS 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 ALA 2.7 19.1 + - - +
54B ALA* 3.6 13.3 + - - +
56B CYS* 1.3 76.2 - - - +
58B LEU* 1.3 76.4 + - - +
60B ASN* 3.3 14.7 + - - -
61B ARG 4.8 0.7 - - - -
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Residues in contact with LEU 58 (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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54B ALA 3.2 12.2 + - - +
55B TRP* 4.2 4.0 - - + +
57B LYS* 1.3 90.6 - - - +
59B ASN* 1.3 75.4 + - - +
60B ASN* 3.3 1.8 + - - +
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Residues in contact with ASN 59 (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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55B TRP* 3.0 55.3 + - + +
56B CYS 3.3 0.2 + - - -
57B LYS 3.2 0.2 - - - -
58B LEU* 1.3 94.9 - - - +
60B ASN* 1.3 69.1 + - - +
61B ARG* 3.1 35.1 + - - +
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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