Contacts of the helix formed by residues 40 - 59 (chain B) in PDB entry 5NRO
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 ASP 40 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34B PRO* 4.3 12.5 - - - +
37B ASN* 3.7 2.9 + - - +
38B GLN 3.7 1.0 - - - -
39B GLY* 1.3 81.3 + - - +
41B LYS* 1.3 62.0 + - - +
42B GLU* 3.5 20.6 - - + +
43B ALA* 2.9 38.8 + - - +
44B GLU* 4.1 5.9 + - - -
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Residues in contact with LYS 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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40B ASP* 1.3 73.1 - - - +
42B GLU* 1.3 55.0 + - - +
43B ALA 3.2 1.1 - - - -
44B GLU* 3.2 32.8 + - - +
45B ALA* 2.7 38.0 + - + +
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Residues in contact with GLU 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 ASP* 3.3 20.3 - - + +
41B LYS* 1.3 79.0 - - - +
43B ALA* 1.3 57.6 + - - +
45B ALA* 3.7 7.3 - - - +
46B LYS* 2.9 41.5 + - - +
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Residues in contact with ALA 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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31B LYS 5.6 0.2 - - - +
32B TYR* 2.9 29.8 - - + +
34B PRO 4.4 1.3 - - - -
37B ASN* 3.2 32.3 - - - +
40B ASP* 2.9 17.0 + - - +
42B GLU* 1.3 73.8 - - - +
44B GLU* 1.3 54.9 + - - +
46B LYS* 3.3 5.4 + - - +
47B PHE 2.6 32.4 + - - -
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Residues in contact with GLU 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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419A PRO* 4.9 7.5 - - + +
479A ASP* 5.0 10.2 - - - +
480A ALA 5.5 0.5 + - - -
34B PRO* 3.4 39.3 - - + +
40B ASP 4.1 1.2 + - - -
41B LYS* 3.2 48.7 + - + +
43B ALA* 1.3 77.8 - - - +
45B ALA* 1.3 62.1 + - + +
47B PHE* 3.9 1.4 - - - +
48B LYS* 3.0 56.9 + - - +
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Residues in contact with ALA 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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421A LYS* 4.6 15.7 + - - +
41B LYS* 2.7 22.8 + - + +
42B GLU* 3.7 9.9 - - - +
44B GLU* 1.3 76.7 - - + +
46B LYS* 1.3 66.0 + - + +
48B LYS* 3.6 14.3 + - - +
49B GLU* 3.7 17.3 + - - +
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Residues in contact with LYS 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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4B GLN* 5.1 8.7 + - - -
32B TYR* 4.2 30.1 - - + -
42B GLU* 2.9 27.9 + - + +
43B ALA 3.7 3.1 - - - +
45B ALA* 1.3 73.6 - - + +
47B PHE* 1.3 65.9 + - - +
49B GLU* 2.9 27.8 + - - +
50B ILE* 3.1 21.8 + - + +
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Residues in contact with PHE 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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392A LEU* 5.3 3.1 - - + -
417A THR* 4.8 5.2 - - + -
418A ILE 4.4 5.2 - - - -
419A PRO* 3.8 40.8 - - + -
25B TYR* 4.0 19.3 - + - -
29B ALA* 3.5 46.7 - - + -
32B TYR* 3.2 15.4 - - + +
33B HIS* 4.1 21.3 - + - -
34B PRO* 4.2 7.0 - - + -
43B ALA 2.6 22.9 + - - +
44B GLU 3.9 3.6 - - - +
46B LYS* 1.3 71.1 - - - +
48B LYS* 1.3 67.9 + - + +
50B ILE* 3.0 16.0 + - + +
51B LYS* 2.9 28.7 + - + -
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Residues in contact with LYS 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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419A PRO* 3.8 38.4 - - + +
420A THR* 3.9 11.3 + - - -
421A LYS* 3.4 37.5 - - + +
477A ASP* 2.5 37.4 + - - +
478A ILE 4.6 2.3 + - - -
479A ASP* 5.8 1.0 - - - +
44B GLU* 3.0 47.0 + - - +
45B ALA* 3.8 5.8 - - - +
46B LYS 3.2 0.2 - - - -
47B PHE* 1.3 79.5 - - + +
49B GLU* 1.3 60.0 + - + +
51B LYS* 3.6 12.6 + - - +
52B GLU* 3.1 24.3 + - - +
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Residues in contact with GLU 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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4B GLN* 5.5 4.5 - - - +
6B TYR* 5.5 0.9 - - - -
9B ILE* 4.3 15.6 - - + +
45B ALA 3.7 13.2 + - - +
46B LYS* 2.9 21.7 + - - +
48B LYS* 1.3 77.5 - - + +
50B ILE* 1.3 60.6 + - + +
51B LYS 3.2 0.2 - - - -
52B GLU* 3.1 18.1 + - - +
53B ALA* 2.9 29.8 + - - +
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Residues in contact with ILE 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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9B ILE* 4.8 10.5 - - + +
10B LEU* 4.0 16.3 - - + +
25B TYR* 4.0 16.8 - - + -
28B LEU* 3.7 38.6 - - + -
29B ALA* 4.6 4.9 - - - +
32B TYR* 3.4 37.5 - - + -
46B LYS* 3.1 32.3 + - + +
47B PHE* 3.0 12.1 + - + +
49B GLU* 1.3 74.9 - - + +
51B LYS* 1.3 63.9 + - - +
53B ALA* 3.4 2.8 + - - +
54B TYR* 3.0 20.3 + - - +
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Residues in contact with LYS 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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416A THR* 4.4 1.8 - - - +
417A THR* 3.2 33.8 + - + +
419A PRO 3.4 20.0 - - - +
420A THR* 2.7 31.5 + - - +
421A LYS 4.9 1.6 + - - +
25B TYR* 3.6 27.2 - - + +
47B PHE* 2.9 17.2 + - + +
48B LYS* 3.6 15.6 + - - +
50B ILE* 1.3 76.3 - - - +
52B GLU* 1.3 51.8 + - - +
54B TYR* 2.6 25.6 + - + +
55B GLU* 2.8 55.7 + - + +
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Residues in contact with GLU 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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421A LYS 5.2 5.9 - - - +
6B TYR* 4.3 22.9 + - + +
48B LYS 3.1 12.3 + - - +
49B GLU* 3.1 22.0 + - - +
51B LYS* 1.3 79.5 - - - +
53B ALA* 1.3 58.2 + - - +
55B GLU* 3.6 16.0 + - - +
56B VAL* 3.0 26.8 + - + +
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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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6B TYR* 3.5 27.5 - - + +
9B ILE* 4.1 6.7 - - + -
10B LEU* 3.6 28.9 - - + -
49B GLU 2.9 14.2 + - - +
52B GLU* 1.3 75.0 - - - +
54B TYR* 1.3 64.7 + - - +
55B GLU 3.2 0.2 - - - -
56B VAL* 3.1 10.8 - - - +
57B LEU* 3.1 30.2 + - + +
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Residues in contact with TYR 54 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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217A GLU* 4.9 5.4 - - - -
10B LEU* 4.6 6.9 - - + +
18B GLU* 5.5 2.2 - - + +
21B ILE* 3.9 15.5 - - + -
22B ARG* 2.6 63.4 + - + +
25B TYR* 3.3 63.5 - + + -
50B ILE 3.0 6.1 + - - +
51B LYS* 2.6 16.5 + - + +
53B ALA* 1.3 73.1 - - - +
55B GLU* 1.3 67.0 + - + -
57B LEU* 4.2 0.3 - - - +
58B THR* 3.1 38.5 + - + +
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Residues in contact with GLU 55 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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416A THR* 4.1 14.0 - - - +
417A THR* 4.6 4.3 + - - -
51B LYS* 2.8 65.9 + - + +
52B GLU* 3.9 11.5 - - - +
54B TYR* 1.3 82.6 - - + +
56B VAL* 1.3 63.3 + - - +
58B THR* 3.2 20.4 - - - +
59B ASP* 3.7 9.4 + - - +
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Residues in contact with VAL 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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6B TYR* 3.5 41.1 - - + +
52B GLU 3.0 19.0 + - - +
53B ALA* 3.1 17.0 - - - +
55B GLU* 1.3 80.7 - - - +
57B LEU* 1.3 64.9 + - + +
59B ASP* 3.3 21.5 + - - +
62B LYS* 3.4 42.4 - - + +
63B ARG* 3.6 7.0 + - - -
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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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6B TYR* 3.9 26.7 - - + -
7B TYR* 3.4 47.8 - - + +
10B LEU* 4.8 6.3 - - + -
12B VAL* 4.8 1.6 - - + -
18B GLU* 5.4 3.7 - - - +
21B ILE* 3.9 37.4 - - + +
53B ALA 3.1 23.3 + - - +
54B TYR 4.4 0.4 - - - +
55B GLU 3.3 0.4 - - - -
56B VAL* 1.3 92.3 - - + +
58B THR* 1.3 61.0 + - - +
59B ASP 3.4 1.7 - - - +
60B SER* 5.6 0.2 - - - -
63B ARG* 3.5 30.9 + - + -
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Residues in contact with THR 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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18B GLU* 2.6 50.3 + - - +
21B ILE* 5.6 1.0 - - - +
54B TYR* 3.1 39.9 + - + +
55B GLU* 3.2 16.8 - - - +
57B LEU* 1.3 75.0 - - - +
59B ASP* 1.3 62.8 + - + +
60B SER* 3.6 2.9 + - - -
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Residues in contact with ASP 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 GLU 4.1 8.7 - - - +
56B VAL 3.3 9.2 + - - +
57B LEU 3.4 0.6 - - - -
58B THR* 1.3 82.2 - - + +
60B SER* 1.3 83.6 + - - +
61B GLN* 3.3 15.7 + - - +
62B LYS* 3.9 20.7 + - + +
63B ARG* 3.1 24.1 + - - +
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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
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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