Contacts of the helix formed by residues 52 - 68 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47A ILE* 3.1 3.3 + - - +
48A PHE* 2.8 26.9 + - - -
49A GLU 4.5 0.4 + - - -
50A GLU 3.8 0.6 - - - -
51A LEU* 1.3 75.9 - - - +
53A GLU* 1.3 68.2 + - - -
54A ASP* 3.1 3.6 - - - -
55A ASN 3.2 3.2 + - - -
56A PHE* 3.2 19.6 + - - +
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Residues in contact with GLU 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A PHE* 3.6 32.7 + - + -
52A GLY* 1.3 73.2 - - - -
54A ASP* 1.3 70.6 + - - +
56A PHE* 3.1 3.7 + - - +
57A ARG* 3.0 60.1 + - + +
84A MET* 5.0 2.8 - - - +
1001A OSA 3.5 11.8 + - - -
2001A TLA 2.8 36.8 + - - +
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Residues in contact with ASP 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A GLY 3.1 1.2 - - - -
53A GLU* 1.3 82.7 + - - +
55A ASN* 1.3 60.1 - - - +
57A ARG* 3.2 9.4 + - - +
58A MET* 3.1 26.7 + - - +
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Residues in contact with ASN 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A LEU* 3.1 42.3 + - + +
52A GLY 3.2 2.9 + - - +
53A GLU 3.1 0.6 - - - -
54A ASP* 1.3 79.6 - - - +
56A PHE* 1.3 58.9 + - - +
58A MET* 3.2 26.9 + - - +
59A PHE* 2.9 42.0 + - + -
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Residues in contact with PHE 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A ASP* 3.6 22.7 - - - -
36A ILE* 4.0 30.3 - - + -
44A VAL* 3.7 27.8 - - + -
47A ILE* 3.9 24.3 - - + +
48A PHE* 3.7 29.2 - + + -
52A GLY 3.2 10.6 + - - +
53A GLU 3.1 8.0 + - - +
55A ASN* 1.3 73.6 - - - +
57A ARG* 1.3 88.6 + - - +
59A PHE* 3.3 11.9 + - - +
60A GLU* 2.9 39.0 + - - +
79A GLY* 6.3 0.2 - - - -
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Residues in contact with ARG 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A PHE* 4.0 6.4 - - - -
53A GLU* 3.0 48.8 + - + +
54A ASP* 3.5 10.1 - - - +
56A PHE* 1.3 99.6 - - - +
58A MET* 1.3 57.9 + - - +
60A GLU* 3.0 28.7 + - - -
61A LYS* 2.8 26.7 + - - +
81A GLY* 3.6 20.8 - - - +
84A MET* 3.7 22.5 - - - -
85A HIS* 3.3 19.2 - - + -
1001A OSA 3.2 39.2 + - - -
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Residues in contact with MET 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A ASP 3.1 12.0 + - - +
55A ASN* 3.5 26.7 - - - +
57A ARG* 1.3 74.1 - - - +
59A PHE* 1.3 98.1 + - + +
60A GLU 3.1 1.1 - - - -
61A LYS* 4.5 5.4 - - - -
62A ASN* 2.9 43.2 + - - +
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Residues in contact with PHE 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A ILE* 4.0 30.3 - - + -
40A VAL* 4.0 16.4 - - + -
47A ILE* 4.2 6.5 - - + -
51A LEU* 3.6 33.2 - - + -
55A ASN* 2.9 23.8 + - + -
56A PHE* 3.3 12.5 + - - +
58A MET* 1.3 100.4 - - + +
60A GLU* 1.3 51.9 + - - +
62A ASN* 3.2 8.9 + - - +
63A LEU* 2.8 36.8 + - - +
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Residues in contact with GLU 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A THR* 4.7 4.9 + - - +
33A ASP* 4.5 1.6 - - - +
36A ILE* 4.0 20.4 - - + -
56A PHE* 2.9 30.2 + - + +
57A ARG* 3.0 36.4 + - - +
58A MET 3.1 0.2 - - - -
59A PHE* 1.3 76.1 - - - +
61A LYS* 1.3 63.4 + - - +
63A LEU* 3.1 5.1 + - + +
64A ILE* 3.0 26.1 + - - +
79A GLY* 4.4 12.6 + - - -
82A ILE* 3.8 36.1 + - + +
85A HIS* 2.8 22.2 + - - +
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Residues in contact with LYS 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A ARG 2.8 20.2 + - - +
58A MET* 3.8 6.7 - - - +
60A GLU* 1.3 68.5 - - - +
62A ASN* 1.3 73.8 + - - +
63A LEU 3.3 0.3 + - - -
64A ILE* 3.3 8.8 + - - -
65A ASP* 3.4 11.9 + - - +
85A HIS* 4.0 20.1 + - + +
87A ASN* 2.6 50.8 + - + +
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Residues in contact with ASN 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A MET* 2.9 37.2 + - - +
59A PHE* 3.4 12.0 - - - +
61A LYS* 1.3 84.4 - - - +
63A LEU* 1.3 60.8 + - - +
65A ASP* 3.0 24.1 + - - +
66A GLU* 3.2 13.7 + - - +
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Residues in contact with LEU 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A THR* 3.9 30.5 - - + +
35A ILE* 3.6 43.3 - - + -
36A ILE* 3.9 12.8 - - + -
39A ARG* 4.0 4.3 - - - +
59A PHE 2.8 19.5 + - - +
60A GLU* 3.1 8.0 + - + +
62A ASN* 1.3 69.6 - - - +
64A ILE* 1.3 66.3 + - - +
66A GLU* 3.0 31.4 + - - +
67A LEU* 3.0 38.9 + - + +
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Residues in contact with ILE 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A GLU 3.0 15.6 + - - +
61A LYS* 4.0 3.4 - - - -
62A ASN 3.3 0.2 - - - -
63A LEU* 1.3 74.4 - - - +
65A ASP* 1.3 65.5 + - - +
67A LEU* 3.0 20.6 + - + +
68A LYS* 3.1 17.4 + - - +
82A ILE* 3.5 38.4 - - + -
85A HIS* 4.3 7.2 - - + -
87A ASN* 3.4 40.4 - - + +
88A LEU* 4.0 25.1 - - + +
91A LEU* 4.1 20.2 - - + -
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Residues in contact with ASP 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A LYS* 3.4 14.0 + - - +
62A ASN* 3.0 18.9 + - - +
64A ILE* 1.3 80.4 - - - +
66A GLU* 1.3 61.5 + - - +
68A LYS* 3.2 22.5 + - - +
69A THR* 3.9 8.9 + - - +
87A ASN* 2.8 34.3 + - - +
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Residues in contact with GLU 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A ARG* 2.3 49.6 + - - -
62A ASN 3.2 12.3 + - - +
63A LEU* 3.0 20.4 + - + +
65A ASP* 1.3 75.6 - - - +
67A LEU* 1.3 60.9 + - + +
69A THR* 2.7 34.4 + - - -
70A LEU* 3.8 4.0 + - - +
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Residues in contact with LEU 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A HIS* 3.2 21.3 + - - -
30A LEU* 3.6 31.9 - - + -
32A THR* 4.1 19.1 - - + -
35A ILE* 5.4 4.7 - - + -
63A LEU* 3.0 42.8 + - + +
64A ILE* 3.0 10.5 + - + +
66A GLU* 1.3 76.9 - - + +
68A LYS* 1.3 57.4 + - - +
69A THR 3.0 9.5 + - - -
70A LEU* 3.4 19.8 + - + +
76A ILE* 4.0 19.1 - - + -
91A LEU* 3.7 16.4 - - + -
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Residues in contact with LYS 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A GLN* 4.4 17.3 + - - +
64A ILE* 3.1 18.1 + - - +
65A ASP* 3.5 15.1 + - - +
66A GLU 3.2 0.2 - - - -
67A LEU* 1.3 75.8 - - - +
69A THR* 1.3 60.9 + - + +
70A LEU 4.6 1.8 - - - -
87A ASN* 2.9 31.1 + - - +
89A LYS 2.8 27.3 + - - -
90A GLY* 4.1 8.1 - - - +
91A LEU* 3.7 28.3 - - + +
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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