Contacts of the helix formed by residues 69 - 90 (chain A) in PDB entry 1N3G
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 69 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A HIS* 3.1 11.6 - - + +
68A GLU* 1.3 95.0 - - + +
70A MET* 1.3 69.1 + - - +
71A TYR* 5.0 6.3 - - - +
72A THR* 2.9 33.4 + - + +
73A ALA* 2.9 24.9 + - - +
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Residues in contact with MET 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ILE* 4.0 18.4 - - + -
48A PHE* 3.0 49.5 - - + -
68A GLU 3.7 7.9 + - - +
69A ASP* 1.3 78.6 - - - +
71A TYR* 1.3 86.0 + - + +
73A ALA* 3.1 8.7 + - - +
74A ILE* 2.7 31.0 + - - +
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Residues in contact with TYR 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ALA* 2.8 54.7 + - + +
16A ILE* 3.9 7.9 - - + -
19A HIS* 3.1 42.2 + + - +
69A ASP* 3.3 6.9 - - - +
70A MET* 1.3 98.1 - - + +
72A THR* 1.3 57.0 + - - +
74A ILE* 3.5 7.7 + - + +
75A ASN* 2.6 36.8 + - - +
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Residues in contact with THR 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A HIS* 3.0 35.7 - - + +
69A ASP* 2.9 36.3 + - - +
71A TYR* 1.3 75.9 - - - +
73A ALA* 1.3 61.5 + - - +
75A ASN* 3.9 7.2 - - + +
76A GLU* 2.9 37.9 + - + +
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Residues in contact with ALA 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A PHE* 3.8 23.1 - - + -
50A ALA* 3.7 12.0 - - + +
65A GLY* 3.5 24.5 - - - +
67A HIS* 4.3 7.8 - - - +
69A ASP 2.9 11.7 + - - +
70A MET 3.1 9.6 + - - +
72A THR* 1.3 76.3 - - - +
74A ILE* 1.3 62.5 + - + +
76A GLU* 4.7 0.4 - - - -
77A LEU* 2.9 31.4 + - - +
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Residues in contact with ILE 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ILE* 3.8 12.3 - - + -
19A HIS* 3.5 31.0 - - + +
20A VAL* 3.8 39.9 - - + +
23A ARG* 4.8 9.0 + - + +
41A LEU* 3.6 28.9 - - + -
50A ALA* 5.2 2.2 - - + -
70A MET 2.7 26.5 - - - +
71A TYR* 3.5 5.6 - - + +
73A ALA* 1.3 77.9 - - + +
75A ASN* 1.3 62.1 + - - +
77A LEU* 3.4 11.7 - - + +
78A ILE* 3.2 22.2 + - - +
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Residues in contact with ASN 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A HIS* 4.0 15.6 + - - -
23A ARG* 2.6 33.3 + - - +
71A TYR* 2.6 29.3 + - - +
72A THR* 3.9 6.5 - - + +
73A ALA 3.3 0.2 - - - -
74A ILE* 1.3 73.1 - - - +
76A GLU* 1.3 66.5 + - + +
77A LEU 3.0 1.3 - - - -
78A ILE* 2.7 29.7 - - - +
79A ASN* 3.0 14.7 - - - +
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Residues in contact with GLU 76 (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 GLY* 4.5 12.1 - - - -
66A LYS 5.4 2.9 - - - +
67A HIS* 5.0 10.1 - - + +
72A THR* 2.9 33.9 + - + +
73A ALA* 4.3 3.1 - - - +
75A ASN* 1.3 74.1 - - + +
77A LEU* 1.3 60.6 + - - +
79A ASN* 2.7 30.6 + - - +
80A LYS* 3.2 42.2 + - + +
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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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20A VAL* 6.2 4.3 - - + -
39A ILE* 5.3 9.2 - - + -
50A ALA* 3.2 38.8 - - + +
51A ASP 4.6 0.2 - - - -
52A ALA* 3.5 20.2 - - + +
63A ALA* 3.3 40.2 - - + +
64A SER 4.5 1.3 - - - -
65A GLY* 4.1 9.8 - - - +
73A ALA 2.9 19.6 + - - +
74A ILE* 3.4 12.3 - - + +
75A ASN 3.0 0.2 - - - -
76A GLU* 1.3 78.4 - - - +
78A ILE* 1.3 72.6 + - + +
79A ASN 3.2 0.7 + - - -
80A LYS* 3.4 1.9 + - - +
81A LEU* 3.2 17.1 + - + -
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Residues in contact with ILE 78 (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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23A ARG* 3.8 52.9 - - + +
27A LEU* 3.4 25.1 - - + -
74A ILE 3.2 6.8 + - - +
75A ASN* 2.7 30.3 - - - +
77A LEU* 1.3 87.8 - - + +
79A ASN* 1.3 63.9 + - - +
81A LEU* 4.0 4.0 - - - -
82A GLU* 2.8 68.4 + - - +
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Residues in contact with ASN 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A ARG* 5.4 1.6 + - - -
75A ASN* 3.0 22.0 + - - +
76A GLU* 2.7 35.3 + - - +
77A LEU 3.1 0.6 - - - -
78A ILE* 1.3 82.6 - - - +
80A LYS* 1.3 69.9 + - + +
82A GLU* 3.2 17.1 + - - +
83A ARG* 3.2 22.1 + - - +
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Residues in contact with LYS 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A VAL 5.8 1.1 - - - +
63A ALA* 5.3 0.7 - - - -
64A SER* 3.6 28.2 + - - +
65A GLY* 5.5 0.2 - - - -
76A GLU* 3.2 30.7 + - + +
77A LEU 4.1 2.9 - - - +
79A ASN* 1.3 78.3 - - + +
81A LEU* 1.3 63.3 + - - +
83A ARG* 3.4 16.9 + - - +
84A GLN* 3.1 24.5 + - - +
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Residues in contact with LEU 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A LEU* 5.2 7.9 - - + -
54A ILE* 4.2 16.6 - - + -
61A LEU* 3.2 36.1 - - + +
62A VAL 3.4 0.4 - - - -
63A ALA* 3.2 46.8 - - + +
77A LEU* 3.2 8.0 + - + +
78A ILE* 3.9 7.4 - - + +
79A ASN 3.2 0.4 - - - -
80A LYS* 1.3 80.0 - - - +
82A GLU* 1.3 58.4 + - - +
84A GLN* 3.3 22.4 + - - +
85A LEU* 2.8 41.2 + - + +
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Residues in contact with GLU 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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27A LEU* 3.1 18.9 - - - +
30A TRP* 3.3 34.4 - - + -
78A ILE* 2.8 54.8 + - - +
79A ASN* 3.2 9.3 + - - +
81A LEU* 1.3 76.0 - - - +
83A ARG* 1.3 60.2 + - + +
85A LEU* 3.0 9.3 + - - +
86A ASN* 2.6 36.3 + - - +
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Residues in contact with ARG 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 ASN* 3.2 19.7 + - - +
80A LYS* 3.8 17.9 - - - +
81A LEU 3.3 0.2 - - - -
82A GLU* 1.3 76.7 - - + +
84A GLN* 1.3 63.8 + - - +
85A LEU 3.2 0.5 + - - -
86A ASN* 3.2 19.9 + - - +
87A LYS* 3.3 12.8 + - - +
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Residues in contact with GLN 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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60A VAL 4.0 4.3 - - - +
61A LEU* 3.0 29.1 - - - +
62A VAL 3.5 17.7 + - - +
80A LYS 3.1 14.4 + - - +
81A LEU* 3.3 31.2 - - - +
83A ARG* 1.3 78.8 - - - +
85A LEU* 1.3 60.2 + - - +
87A LYS* 3.6 20.8 + - - +
88A LEU* 3.3 35.9 + - - +
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Residues in contact with LEU 85 (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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27A LEU* 4.5 9.2 - - + -
30A TRP* 3.1 45.8 - - + -
31A GLN 3.6 3.4 - - - +
32A THR* 2.7 32.1 - - + +
34A LEU* 5.1 0.2 - - + -
61A LEU* 3.5 18.1 - - + +
81A LEU* 2.8 33.2 + - + +
82A GLU* 3.0 11.2 + - - +
84A GLN* 1.3 75.6 - - - +
86A ASN* 1.3 65.0 + - - +
87A LYS 3.2 0.2 + - - -
88A LEU* 3.2 4.4 + - + +
89A GLN* 3.0 44.6 + - + +
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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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30A TRP* 3.2 27.9 - - - -
82A GLU* 2.6 36.3 + - - +
83A ARG* 3.2 9.9 + - - +
85A LEU* 1.3 75.0 - - - +
87A LYS* 1.3 57.1 + - - +
89A GLN* 3.2 7.2 + - - +
90A HIS* 2.8 29.0 + - - +
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Residues in contact with LYS 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 ARG 3.3 9.1 + - - +
84A GLN* 3.7 26.6 + - - +
85A LEU 3.2 0.6 - - - -
86A ASN* 1.3 79.6 - - - +
88A LEU* 1.3 77.2 + - - +
90A HIS* 2.8 33.0 + - + +
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Residues in contact with LEU 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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56A THR* 4.7 14.8 - - + +
58A ASN* 3.0 54.5 + - + +
59A GLY* 5.1 0.7 - - - +
60A VAL 5.4 3.8 - - - +
61A LEU* 4.9 3.8 - - + -
84A GLN* 3.3 27.0 + - - +
85A LEU* 3.2 9.3 + - + +
87A LYS* 1.3 98.0 - - + +
89A GLN* 1.3 71.4 + - - +
90A HIS 4.6 2.1 - - - +
91A LYS* 5.8 0.5 - - - +
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Residues in contact with GLN 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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30A TRP* 5.9 0.9 - - + -
31A GLN* 2.5 46.0 + - + +
32A THR* 3.6 6.5 + - - +
56A THR* 5.4 2.1 + - - -
58A ASN* 4.8 12.8 + - - +
61A LEU* 5.8 0.3 - - - +
85A LEU* 3.0 30.7 + - + +
86A ASN* 3.6 8.3 - - - +
87A LYS 3.0 0.8 - - - -
88A LEU* 1.3 85.2 + - - +
90A HIS* 1.3 67.2 + - - +
91A LYS* 2.9 12.4 + - - +
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Residues in contact with HIS 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A ASN 2.8 13.6 + - - +
87A LYS* 2.8 21.4 + - + +
88A LEU 4.6 2.3 - - - +
89A GLN* 1.3 74.8 - - - +
91A LYS* 1.3 64.3 + - - +
92A GLY* 3.9 14.9 + - - -
93A GLU* 5.2 10.3 + - + -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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