Contacts of the helix formed by residues 76 - 92 (chain A) in PDB entry 3N2Q
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 76 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A LYS* 3.4 29.3 - - - +
75A LEU* 1.3 78.4 - - - +
77A LEU* 1.3 64.5 + - - +
78A ALA 3.2 3.4 + - - -
79A GLU* 3.2 8.4 + - + -
80A TYR* 3.1 17.2 + - - +
190A PHE* 4.0 14.3 - - + -
193A GLU 4.9 1.4 + - - -
200A ASN* 3.5 24.2 + - - -
201A GLY* 2.8 29.0 + - - -
329A GLU* 4.9 2.6 - - - +
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Residues in contact with LEU 77 (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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59A LYS* 4.8 12.1 - - - +
61A GLN* 5.2 1.3 - - - +
63A VAL* 4.0 29.8 - - + -
75A LEU* 3.3 26.1 - - + +
76A ASP* 1.3 75.1 - - - +
78A ALA* 1.3 63.4 + - - +
80A TYR* 3.2 18.3 + - + +
81A GLU* 2.9 56.0 + - + +
126A ILE* 5.6 0.2 - - + -
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Residues in contact with ALA 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A ASP 3.2 1.0 + - - -
77A LEU* 1.3 76.6 - - - +
79A GLU* 1.3 59.7 + - - +
81A GLU* 4.0 5.5 - - - +
82A ASN* 2.9 48.2 + - - +
330A LYS* 6.5 1.3 - - + -
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Residues in contact with GLU 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A ASP* 3.2 14.6 + - + +
78A ALA* 1.3 80.3 - - - +
80A TYR* 1.3 59.4 + - - +
82A ASN* 4.9 2.5 - - - +
83A GLY* 2.9 32.9 + - - +
190A PHE* 3.7 11.4 - - + -
200A ASN* 4.2 18.4 - - + +
201A GLY 3.4 22.2 - - - +
202A THR* 5.1 2.7 - - - +
203A TYR* 3.8 4.3 - - - -
329A GLU* 5.9 0.2 - - - +
330A LYS* 2.8 49.2 + - - +
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Residues in contact with TYR 80 (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 VAL* 5.2 0.9 - - + -
75A LEU* 4.3 10.8 - - + +
76A ASP 3.1 16.3 + - - +
77A LEU* 3.6 21.3 - - + +
79A GLU* 1.3 76.2 - - - +
81A GLU* 1.3 61.6 + - - +
84A LEU* 3.7 1.0 + - - +
124A ASN* 3.0 41.3 + - + +
125A ILE 3.4 1.6 + - - -
126A ILE* 3.4 34.8 + - + +
147A GLY 2.7 32.4 + - - -
149A ALA* 3.9 11.4 - - + -
190A PHE* 3.6 39.4 - + + -
203A TYR* 2.8 45.6 + - - -
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Residues in contact with GLU 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A LYS* 4.6 7.1 + - - -
61A GLN* 3.4 28.4 + - - +
77A LEU* 2.9 49.2 + - + +
78A ALA* 4.0 4.9 - - - +
80A TYR* 1.3 75.5 - - - +
82A ASN* 1.3 69.7 + - - +
84A LEU* 3.1 10.9 + - - +
85A ILE* 3.2 14.3 + - + +
101A LEU* 5.9 0.3 - - - +
126A ILE* 4.1 10.5 - - + -
128A GLN* 3.4 19.4 + - - +
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Residues in contact with ASN 82 (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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78A ALA* 2.9 36.7 + - - +
79A GLU* 4.7 2.7 - - - +
81A GLU* 1.3 75.4 + - - +
83A GLY* 1.3 65.8 + - - +
85A ILE* 3.0 22.6 + - - +
86A ASN* 3.0 21.9 + - - +
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Residues in contact with GLY 83 (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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79A GLU* 2.9 23.2 + - - +
82A ASN* 1.3 75.9 - - - +
84A LEU* 1.3 59.8 + - - +
86A ASN* 3.1 17.9 + - - +
87A ILE* 3.2 17.5 + - - +
203A TYR* 3.7 17.7 - - - -
270A LYS* 5.9 5.2 - - - -
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Residues in contact with LEU 84 (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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80A TYR 3.7 1.3 - - - +
81A GLU 3.1 10.6 + - - +
83A GLY* 1.3 73.6 - - - +
85A ILE* 1.3 65.6 + - - +
87A ILE* 3.4 11.1 + - + +
88A ALA* 3.2 20.6 + - - +
126A ILE* 3.7 15.5 - - + -
128A GLN* 3.5 25.0 - - + +
145A MSE 3.9 30.5 - - + +
146A ILE 4.1 8.7 - - - +
147A GLY* 3.5 22.0 - - - +
186A THR* 5.1 1.1 - - + +
188A ALA* 4.0 26.7 - - + -
203A TYR* 3.5 18.7 - - - +
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Residues in contact with ILE 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A GLU* 3.2 11.2 + - + +
82A ASN* 3.0 28.7 + - - +
84A LEU* 1.3 75.6 - - - +
86A ASN* 1.3 62.7 + - - +
88A ALA* 3.2 16.5 + - - +
89A THR* 3.2 18.5 + - + +
94A THR* 5.9 2.0 - - + -
99A LEU* 4.3 15.9 - - + -
128A GLN* 3.6 23.1 - - - +
130A TYR* 3.6 16.6 - - + +
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Residues in contact with ASN 86 (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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82A ASN 3.0 11.6 + - - +
83A GLY* 3.1 13.4 + - - +
85A ILE* 1.3 79.2 - - - +
87A ILE* 1.3 62.2 + - + +
89A THR* 2.9 25.1 + - - -
90A GLN* 2.9 34.9 + - - +
270A LYS* 4.1 34.0 + - + +
271A LYS* 4.3 19.4 + - - +
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Residues in contact with ILE 87 (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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83A GLY 3.2 15.1 + - - +
84A LEU* 3.7 10.5 - - + +
86A ASN* 1.3 73.7 - - + +
88A ALA* 1.3 66.3 + - - +
90A GLN* 3.2 19.5 + - + +
91A GLN* 3.2 21.5 + - + +
145A MSE 4.8 4.9 - - - -
186A THR* 4.4 22.2 - - + -
188A ALA* 3.7 28.0 - - + -
203A TYR* 3.9 21.3 - - + -
206A SER* 4.6 10.1 - - - +
222A ILE* 4.0 30.3 - - + -
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Residues in contact with ALA 88 (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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84A LEU 3.2 7.0 + - - +
85A ILE 3.2 11.2 - - - +
87A ILE* 1.3 80.7 - - - +
89A THR* 1.3 62.9 + - + +
91A GLN* 3.0 13.2 + - - +
92A PHE* 3.0 16.4 + - + +
94A THR* 3.8 11.1 + - - +
130A TYR* 3.5 36.3 - - + +
145A MSE 3.9 20.6 - - + -
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Residues in contact with THR 89 (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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85A ILE* 3.2 22.1 + - + +
86A ASN* 2.9 19.8 + - - -
88A ALA* 1.3 72.3 - - - +
90A GLN* 1.3 64.2 + - - +
92A PHE 2.9 21.2 - - - +
93A ASP* 5.1 2.1 - - - +
94A THR* 3.8 24.5 - - + -
271A LYS* 3.1 28.4 + - - +
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Residues in contact with GLN 90 (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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86A ASN* 2.9 31.1 + - - +
87A ILE* 3.2 22.4 + - + +
88A ALA 3.2 0.2 - - - -
89A THR* 1.3 83.2 + - - +
91A GLN* 1.3 60.8 + - - +
92A PHE* 4.4 0.9 - - - -
222A ILE* 4.4 11.9 - - - +
223A ASP* 3.3 61.3 + - + +
270A LYS* 5.2 1.4 - - - +
271A LYS* 3.1 23.6 - - + +
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Residues in contact with GLN 91 (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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87A ILE* 3.2 8.7 + - + +
88A ALA 3.0 8.4 + - - +
90A GLN* 1.3 81.4 - - + +
92A PHE* 1.3 74.3 + - + +
145A MSE 3.6 18.8 - - + +
184A PRO* 4.3 23.0 - - - +
186A THR* 2.5 39.4 + - - +
208A THR* 4.0 10.3 - - - +
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Residues in contact with PHE 92 (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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88A ALA 3.0 7.0 + - - +
89A THR* 2.9 25.5 - - - +
90A GLN 3.5 1.5 - - - -
91A GLN* 1.3 92.4 - - + +
93A ASP* 1.3 58.3 + - - +
94A THR* 2.7 30.1 + - - -
97A HIS* 3.3 40.2 - + - +
130A TYR* 4.2 20.9 - + + -
142A SER* 4.4 11.0 - - - -
143A GLY* 4.4 16.4 - - - -
145A MSE 3.6 32.5 - - + -
184A PRO* 5.6 1.6 - - + -
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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
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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