Contacts of the helix formed by residues 52 - 68 (chain B) in PDB entry 3N2E
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 GLY 52 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47B ILE* 3.2 9.8 + - - +
48B PHE* 3.3 19.0 + - - -
49B GLU 4.6 0.8 + - - -
50B GLU 3.8 0.6 - - - -
51B LEU* 1.3 82.2 - - - +
53B GLU* 1.3 66.6 + - - -
54B ASP* 3.3 4.0 + - - -
55B ASN* 3.4 0.3 + - - +
56B PHE* 3.2 17.8 + - - +
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Residues in contact with GLU 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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48B PHE* 3.5 34.0 + - + -
52B GLY* 1.3 72.0 - - - -
54B ASP* 1.3 59.4 + - - +
56B PHE* 2.8 24.5 + - - +
57B ARG* 2.8 52.4 + - + +
84B MET* 4.8 5.2 - - - +
1001B OSA 3.6 13.8 + - - +
2001B TLA 3.1 30.3 + - - +
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Residues in contact with ASP 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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130A GLU* 5.8 0.5 - - - +
52B GLY* 3.3 1.0 - - - -
53B GLU* 1.3 86.2 - - - +
55B ASN* 1.3 59.9 + - - +
57B ARG* 3.2 9.2 + - - +
58B MET* 3.0 27.8 + - - +
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Residues in contact with ASN 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B LEU* 2.5 49.3 + - + +
52B GLY 3.4 2.4 + - - +
53B GLU 3.2 0.4 - - - -
54B ASP* 1.3 79.9 - - - +
56B PHE* 1.3 59.0 - - - +
58B MET* 3.3 18.5 + - - +
59B PHE* 3.0 46.4 + - + -
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Residues in contact with PHE 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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33B ASP* 3.7 21.5 - - - -
36B ILE* 4.1 26.5 - - + -
44B VAL* 4.0 25.6 - - + -
47B ILE* 3.9 26.0 - - + +
48B PHE* 3.7 24.2 - + + -
52B GLY 3.2 9.1 + - - +
53B GLU 2.8 16.5 + - - +
55B ASN* 1.3 71.5 - - - +
57B ARG* 1.3 82.0 + - - +
59B PHE* 3.2 10.2 + - - +
60B GLU* 2.9 53.5 + - + +
79B GLY* 6.1 0.2 - - - -
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Residues in contact with ARG 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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48B PHE* 4.0 6.9 - - - -
53B GLU* 2.8 41.2 + - + +
54B ASP* 3.6 10.1 - - - +
56B PHE* 1.3 97.4 - - - +
58B MET* 1.3 58.8 + - - +
60B GLU* 2.9 26.0 + - - -
61B LYS* 2.8 26.4 + - - +
81B GLY* 3.5 21.0 - - - +
84B MET* 3.6 24.2 - - - -
85B HIS* 3.3 18.8 - - + -
1001B OSA 3.2 48.0 + - - -
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Residues in contact with MET 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 ASP 3.0 14.0 + - - +
55B ASN* 3.6 21.8 - - - +
56B PHE 3.1 0.2 - - - -
57B ARG* 1.3 74.6 - - - +
59B PHE* 1.4 76.7 + - - +
61B LYS* 3.4 7.8 + - + +
62B ASN* 3.0 46.5 + - - +
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Residues in contact with PHE 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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36B ILE* 3.8 33.9 - - + -
39B ARG* 5.6 1.2 + - - -
40B VAL* 3.8 17.7 - - + -
47B ILE* 4.4 6.7 - - + -
51B LEU* 3.7 32.3 - - + -
55B ASN* 3.0 28.8 + - + -
56B PHE* 3.5 10.3 - - - +
58B MET* 1.4 86.8 - - - +
60B GLU* 1.3 58.6 + - - +
62B ASN* 3.1 10.3 + - - +
63B LEU* 2.8 30.3 + - - +
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Residues in contact with GLU 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B THR* 4.6 4.0 + - - +
33B ASP* 4.0 8.7 - - - +
36B ILE* 3.7 19.1 - - + -
56B PHE* 2.9 42.1 + - + +
57B ARG* 2.9 28.5 + - - +
59B PHE* 1.3 77.5 - - - +
61B LYS* 1.3 61.4 + - - +
63B LEU* 3.2 4.0 + - - +
64B ILE* 3.0 28.3 + - - +
79B GLY* 4.3 6.4 + - - -
82B ILE* 3.6 29.8 + - + +
85B HIS* 2.9 24.1 + - + +
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Residues in contact with LYS 61 (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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57B ARG 2.8 14.8 + - - +
58B MET* 3.7 7.6 - - - +
60B GLU* 1.3 73.9 - - - +
62B ASN* 1.3 74.5 + - - +
64B ILE* 3.3 5.6 + - - -
65B ASP* 3.4 8.8 + - - +
85B HIS* 3.8 21.5 - - + +
86B GLU 6.2 0.2 - - - +
87B ASN* 2.6 53.6 + - + +
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Residues in contact with ASN 62 (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 ARG* 6.0 1.3 - - - +
58B MET* 3.0 40.2 + - - +
59B PHE* 3.5 8.7 - - - +
61B LYS* 1.3 86.4 - - - +
63B LEU* 1.3 62.1 + - - +
65B ASP* 3.0 22.7 + - - +
66B GLU* 3.1 25.4 + - - +
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Residues in contact with LEU 63 (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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32B THR* 3.9 21.1 - - + +
35B ILE* 3.6 40.4 - - + -
36B ILE* 3.8 21.1 - - + -
39B ARG* 4.1 22.0 - - - +
59B PHE 2.8 17.1 + - - +
60B GLU* 3.7 6.1 - - - +
62B ASN* 1.3 72.3 - - - +
64B ILE* 1.3 66.0 + - - +
66B GLU* 3.2 15.6 + - + -
67B LEU* 3.0 45.1 + - + +
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Residues in contact with ILE 64 (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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32B THR* 5.9 2.9 - - + -
60B GLU 3.0 17.7 + - - +
61B LYS 3.5 0.2 - - - +
62B ASN 3.1 0.2 - - - -
63B LEU* 1.3 77.9 - - + +
65B ASP* 1.3 56.5 + - - +
67B LEU* 2.9 27.3 + - + +
68B LYS* 3.2 19.8 + - - +
82B ILE* 3.0 38.4 - - + +
85B HIS* 3.8 27.6 - - + -
87B ASN* 3.4 39.3 - - - +
88B LEU* 4.1 14.6 - - + -
91B LEU* 4.2 14.0 - - + +
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Residues in contact with ASP 65 (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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61B LYS* 3.4 13.2 + - - +
62B ASN* 3.0 15.5 + - - +
64B ILE* 1.3 77.4 - - - +
66B GLU* 1.3 64.6 + - - +
67B LEU 3.5 0.2 + - - -
68B LYS* 3.5 23.2 + - - +
69B THR* 4.1 7.3 + - - -
87B ASN* 2.7 31.4 + - - +
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Residues in contact with GLU 66 (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 ARG* 2.9 41.1 + - - +
62B ASN* 3.1 29.4 + - - +
63B LEU* 3.2 16.8 + - + +
65B ASP* 1.3 79.2 - - - +
67B LEU* 1.3 58.9 + - + +
69B THR* 2.9 35.0 + - + +
70B LEU* 4.0 2.8 + - - +
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Residues in contact with LEU 67 (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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3B HIS* 3.4 15.2 + - - -
30B LEU* 3.7 28.0 - - + -
32B THR* 4.1 18.2 - - + -
35B ILE* 5.6 4.9 - - + -
63B LEU* 3.0 42.8 + - + +
64B ILE* 2.9 16.6 + - + +
66B GLU* 1.3 69.4 - - + +
68B LYS* 1.3 54.5 + - - +
69B THR 2.8 14.9 + - - -
70B LEU* 3.0 26.1 + - + +
76B ILE* 4.3 21.1 - - + -
91B LEU* 3.7 18.8 - - + -
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Residues in contact with LYS 68 (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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3B HIS* 4.9 3.6 - - - -
64B ILE* 3.2 12.9 + - - +
65B ASP* 3.7 18.8 - - - +
66B GLU 3.2 0.4 - - - -
67B LEU* 1.3 74.5 - - - +
69B THR* 1.3 58.1 + - - +
70B LEU 3.5 4.3 - - - +
87B ASN* 3.0 25.1 + - - +
89B LYS 2.9 24.5 + - - -
90B GLY* 3.8 8.2 - - - +
91B LEU* 3.7 36.8 - - + +
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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
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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