Contacts of the helix formed by residues 56 - 71 (chain A) in PDB entry 3NTV
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 56 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44A ARG* 3.8 6.5 + - - +
54A ILE 3.5 5.3 + - - +
55A VAL* 1.3 78.5 - - - +
57A ARG* 1.3 59.9 + - - +
58A LEU 3.4 0.4 - - - -
59A THR* 3.3 4.7 + - - +
60A LEU* 2.9 28.1 + - - +
175A ASP* 5.2 2.1 + - - +
222A ASP* 3.3 39.8 - - + +
223A ASP* 3.0 27.7 - - - +
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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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30A ILE* 4.1 34.4 - - + +
33A HIS* 3.0 33.5 + - + +
34A GLN* 3.4 16.4 - - - +
36A GLN* 4.0 13.9 + - - +
37A ASN* 2.9 28.7 - - - +
41A GLU* 3.5 32.7 + - - +
44A ARG* 3.4 22.1 - - - +
56A ASP* 1.3 72.3 - - - +
58A LEU* 1.3 59.1 + - - +
60A LEU* 3.3 5.2 + - - +
61A ASP* 2.8 57.3 + - - +
84A TYR* 4.3 4.7 - - - -
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Residues in contact with LEU 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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26A LYS* 4.0 20.6 - - + +
29A LEU* 3.9 29.6 - - + -
30A ILE* 3.9 24.6 - - + +
33A HIS* 3.7 31.0 - - + +
56A ASP* 3.4 0.8 - - - +
57A ARG* 1.3 76.4 - - - +
59A THR* 1.3 62.3 + - - +
61A ASP* 3.4 3.1 + - - +
62A LEU* 3.1 23.7 + - - +
221A ILE* 4.6 4.7 - - + -
222A ASP* 3.8 11.7 + - - +
217B ASN* 5.1 0.3 + - - -
218B PHE 3.7 13.9 - - - +
219B LEU* 4.2 9.0 - - + +
220B ASN* 3.5 24.9 - - - +
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Residues in contact with THR 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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55A VAL* 3.9 17.3 - - + -
56A ASP* 3.5 8.7 - - - -
58A LEU* 1.3 74.7 - - - +
60A LEU* 1.3 67.1 + - - +
62A LEU* 3.3 4.2 + - - +
63A ILE* 3.0 36.1 + - + +
175A ASP* 4.2 13.6 + - - +
221A ILE* 3.6 19.5 + - - +
222A ASP* 2.6 36.0 + - - +
224A GLY 5.8 0.3 + - - -
225A LEU* 3.9 22.2 - - + +
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Residues in contact with LEU 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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55A VAL* 4.1 12.8 - - + -
56A ASP 2.9 18.1 + - - +
57A ARG* 3.3 9.2 + - - +
59A THR* 1.3 77.1 - - - +
61A ASP* 1.3 69.9 + - - +
63A ILE* 3.1 7.5 + - - +
64A LYS* 2.9 31.6 + - + +
84A TYR* 3.5 29.4 - - + +
85A SER* 4.3 15.0 - - - -
88A GLN* 3.7 41.3 - - + +
89A PHE* 3.8 24.5 - - + -
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Residues in contact with ASP 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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33A HIS* 2.6 41.7 + - + +
36A GLN* 3.9 14.9 + - - +
57A ARG* 2.8 46.2 + - - +
58A LEU 3.4 1.8 + - - +
59A THR 3.3 0.2 - - - -
60A LEU* 1.3 80.6 - - - +
62A LEU* 1.3 60.2 + - - +
64A LYS* 3.5 25.2 + - - +
65A GLN* 3.1 21.8 + - - +
68A ARG* 4.7 1.9 + - - -
217B ASN* 4.1 6.9 - - + +
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Residues in contact with LEU 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 LEU 3.1 13.8 + - - +
59A THR* 3.6 7.9 - - - +
60A LEU 3.3 0.2 - - - -
61A ASP* 1.3 77.5 - - - +
63A ILE* 1.3 56.9 + - - +
65A GLN* 3.0 9.1 + - + +
66A LEU* 2.9 44.6 + - + +
219A LEU* 3.5 32.3 - - + -
221A ILE* 4.2 1.6 - - + -
225A LEU* 3.7 17.9 - - + -
227A ILE* 4.4 5.8 - - + -
62B LEU* 5.2 4.9 - - + -
217B ASN* 3.6 24.6 - - - +
219B LEU* 3.9 15.9 - - + -
227B ILE* 4.0 20.6 - - + -
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Residues in contact with ILE 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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55A VAL* 4.9 0.7 - - + -
59A THR* 3.0 33.1 + - + +
60A LEU* 3.1 7.6 + - - +
62A LEU* 1.3 74.9 - - - +
64A LYS* 1.4 57.9 + - - +
66A LEU* 3.1 11.1 + - + +
67A ILE* 2.9 27.5 + - + +
89A PHE* 3.5 27.8 - - + -
145A MSE 3.9 25.8 - - + -
147A PHE* 3.7 38.1 - - + -
173A ILE* 3.8 21.5 - - + -
225A LEU* 4.5 7.6 - - + -
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Residues in contact with LYS 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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36A GLN 5.1 6.7 + - - -
38A SER* 4.7 6.3 + - - -
60A LEU* 2.9 30.9 + - + +
61A ASP* 3.7 26.5 + - - +
63A ILE* 1.4 74.3 - - - +
65A GLN* 1.4 62.1 + - - +
67A ILE* 3.3 6.5 + - - +
68A ARG* 3.1 47.2 + - - +
88A GLN* 3.1 40.3 + - + +
89A PHE* 4.4 9.6 - - + -
91A SER* 4.0 5.7 + - - -
92A ILE* 3.7 29.3 - - + +
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Residues in contact with GLN 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 ASP 3.1 12.6 + - - +
62A LEU* 3.0 12.9 + - + +
64A LYS* 1.4 73.8 - - - +
66A LEU* 1.3 59.2 + - - +
68A ARG* 3.1 29.4 + - - +
69A MSE 3.0 37.5 + - + +
215B THR* 3.1 23.1 + - - +
216B THR 5.1 0.2 - - - -
217B ASN* 3.0 24.7 + - - +
227B ILE* 2.9 38.2 - - + +
229B ILE* 3.4 29.3 - - + +
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Residues in contact with LEU 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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62A LEU* 2.9 31.2 + - + +
63A ILE* 3.1 17.9 + - + +
65A GLN* 1.3 72.5 - - + +
67A ILE* 1.3 66.4 + - - +
69A MSE 3.4 6.9 + - - -
70A ASN* 2.9 32.6 + - - +
145A MSE 4.2 10.8 - - + -
171A LEU* 4.2 5.2 - - + -
173A ILE* 3.9 22.4 - - + -
225A LEU* 5.6 0.4 - - + -
227A ILE* 3.7 26.0 - - + -
66B LEU* 4.3 15.3 - - + -
69B MSE 3.8 30.5 - - + -
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Residues in contact with ILE 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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63A ILE* 2.9 19.5 + - + +
64A LYS* 3.4 6.5 - - - +
66A LEU* 1.3 74.8 - - - +
68A ARG* 1.3 56.4 + - - +
71A ASN* 3.0 26.0 + - - -
72A VAL* 3.0 35.5 + - + +
75A ILE* 3.8 9.9 - - + -
89A PHE* 3.5 40.4 - - + -
92A ILE* 3.7 26.9 - - + -
96A ILE* 3.8 21.3 - - + -
145A MSE 3.8 18.6 - - + -
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Residues in contact with ARG 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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36A GLN* 5.4 8.1 - - - +
61A ASP 4.7 1.8 + - - -
64A LYS* 3.1 40.8 + - - +
65A GLN* 3.1 50.4 + - - +
67A ILE* 1.3 79.5 - - - +
69A MSE 1.4 62.9 + - - +
71A ASN* 3.4 16.9 + - - +
92A ILE* 4.1 26.4 - - + +
169B GLN* 5.0 8.2 + - - -
215B THR* 3.6 23.8 - - - +
217B ASN* 6.3 0.4 - - - +
229B ILE* 3.8 13.0 - - + -
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Residues in contact with MSE 69 (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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65A GLN* 3.0 28.6 + - - +
66A LEU* 3.8 12.3 - - - +
68A ARG* 1.4 76.3 - - - +
70A ASN* 1.3 60.8 + - - +
71A ASN* 3.7 7.8 + - - -
66B LEU* 3.8 22.9 - - + +
69B MSE 3.6 31.2 - - + +
70B ASN* 2.5 54.9 - - - +
171B LEU* 4.3 15.0 - - + -
227B ILE* 5.0 3.6 - - - -
229B ILE* 3.8 19.3 - - + -
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Residues in contact with ASN 70 (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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66A LEU 2.9 28.7 + - - +
69A MSE 1.3 79.6 - - - +
71A ASN* 1.4 72.0 + - - +
72A VAL* 3.3 16.1 + - + +
144A ASP* 5.9 0.2 - - - +
167A LYS* 4.8 10.2 + - - -
169A GLN 4.8 6.2 - - - +
171A LEU* 3.6 28.4 - - + +
69B MSE 3.6 44.6 - - - +
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Residues in contact with ASN 71 (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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67A ILE 3.0 8.0 + - - -
68A ARG 3.4 10.8 + - - +
69A MSE 4.1 8.7 + - - -
70A ASN* 1.4 79.2 - - - +
72A VAL* 1.3 66.3 + - - +
73A LYS* 3.4 29.2 + - - +
144A ASP* 4.5 2.6 - - - +
167A LYS* 5.4 2.3 + - - -
169B GLN* 4.9 10.4 + - - +
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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