Contacts of the helix formed by residues 72 - 90 (chain A) in PDB entry 3NC0
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 ASN 72 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28A LEU* 4.9 4.3 - - + -
66A ILE* 3.0 47.7 - - + +
71A GLN* 1.3 79.8 - - - +
73A MET* 1.3 80.3 + - - +
74A ASN 3.0 2.7 - - - -
75A THR* 2.8 25.5 + - - -
76A LYS* 2.9 22.4 + - - +
122A LYS* 3.6 23.9 + - - +
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Residues in contact with MET 73 (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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72A ASN* 1.3 89.8 + - - +
74A ASN* 1.3 67.5 + - - +
76A LYS* 3.0 16.8 + - - +
77A TYR* 2.7 36.6 + - + +
121A GLU 4.8 1.1 - - - +
122A LYS* 4.0 12.6 - - + -
123A GLU* 3.4 39.9 - - + -
125A VAL* 3.2 41.1 - - + -
126A TYR* 3.9 23.5 - - + +
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Residues in contact with ASN 74 (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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31A VAL* 4.2 11.0 - - + +
35A LEU* 3.6 32.2 - - + +
36A TYR* 4.5 13.9 + - - -
71A GLN* 4.8 19.4 + - - +
72A ASN 3.0 0.2 - - - -
73A MET* 1.3 97.2 - - - +
75A THR* 1.3 59.5 + - - +
77A TYR* 3.5 8.2 + - - +
78A TYR* 3.2 21.0 + - - +
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Residues in contact with THR 75 (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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24A ASP* 4.5 4.0 - - - +
27A LEU* 3.5 33.4 - - + -
28A LEU* 3.9 23.4 + - + +
31A VAL* 3.9 21.1 - - + +
62A ARG* 3.0 30.5 - - + -
66A ILE* 6.0 2.7 - - + -
71A GLN 3.7 13.5 + - - -
72A ASN* 2.8 13.0 + - - -
74A ASN* 1.3 75.9 - - - +
76A LYS* 1.3 62.2 + - + +
78A TYR* 3.5 6.7 - - + +
79A GLY 3.3 6.6 + - - -
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Residues in contact with LYS 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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62A ARG* 4.3 10.1 - - + +
63A VAL* 3.6 37.0 - - + +
66A ILE* 3.4 27.3 + - + +
72A ASN* 2.9 31.7 + - - +
73A MET* 3.0 17.1 + - - +
75A THR* 1.3 77.4 - - - +
77A TYR* 1.3 65.5 + - - +
79A GLY* 3.0 3.5 + - - -
80A LEU* 2.9 27.0 + - - +
122A LYS* 4.7 8.3 - - - +
126A TYR* 3.8 43.3 - - + +
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Residues in contact with TYR 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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73A MET* 2.7 22.1 + - + +
74A ASN* 3.5 11.0 - - - +
76A LYS* 1.3 71.6 - - - +
78A TYR* 1.3 64.0 + - - +
80A LEU* 3.0 22.1 + - - +
81A GLN* 3.2 40.1 + - + +
125A VAL* 3.5 37.0 - - + -
126A TYR* 4.6 4.8 - - + -
129A LYS* 3.3 42.7 + - + +
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Residues in contact with TYR 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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27A LEU* 4.5 15.3 - - + -
31A VAL* 5.1 9.6 - - + -
48A GLU* 2.6 58.9 + - + -
51A THR* 3.2 21.2 - - + -
52A HIS* 3.3 16.7 + + - -
62A ARG* 4.2 12.6 - - - -
74A ASN 3.2 10.2 + - - +
75A THR* 3.5 12.8 - - - +
76A LYS 3.1 0.6 - - - -
77A TYR* 1.3 79.9 - - - +
79A GLY* 1.3 67.0 + - - +
81A GLN* 3.1 35.7 + - - +
82A ILE* 3.5 26.8 + - + +
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Residues in contact with GLY 79 (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 ALA* 4.9 6.1 - - - +
62A ARG* 2.9 34.3 - - - -
63A VAL* 4.7 8.9 - - - +
75A THR 3.3 5.1 + - - -
76A LYS 3.0 6.9 + - - -
78A TYR* 1.3 79.6 - - - +
80A LEU* 1.3 62.2 + - - +
82A ILE* 3.2 8.7 + - - +
83A LEU* 3.2 18.7 + - - +
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Residues in contact with LEU 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* 4.6 15.2 - - + +
76A LYS 2.9 15.2 + - - +
77A TYR* 3.0 11.6 + - - +
79A GLY* 1.3 73.7 - - - +
81A GLN* 1.3 53.8 + - - +
83A LEU* 3.1 17.5 + - + +
84A GLU* 2.6 38.2 + - - +
109A LEU* 5.6 1.8 - - + -
126A TYR* 3.3 36.8 - - + -
129A LYS* 4.1 26.5 - - + -
130A LEU* 3.9 23.8 - - + +
133A ILE* 3.5 24.5 - - + +
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Residues in contact with GLN 81 (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 HIS* 5.0 13.7 - - + -
77A TYR* 3.2 33.9 + - + +
78A TYR* 3.1 31.2 + - - +
80A LEU* 1.3 75.7 - - - +
82A ILE* 1.3 57.5 + - + +
84A GLU* 3.2 15.0 + - - +
85A ASN* 2.9 30.3 + - - +
129A LYS* 4.7 9.2 - - - +
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Residues in contact with ILE 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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51A THR* 4.9 8.5 - - + +
52A HIS* 4.2 29.8 - - + +
55A GLU 4.4 8.3 - - - +
56A HIS* 3.3 31.4 - - + -
58A ASP* 6.0 0.4 - - + -
59A ALA* 5.6 1.3 - - + -
62A ARG* 3.4 29.4 - - - +
78A TYR* 3.5 32.8 - - + +
79A GLY 3.4 5.2 - - - +
80A LEU 3.2 0.2 - - - -
81A GLN* 1.3 75.7 - - - +
83A LEU* 1.3 62.4 + - - +
85A ASN* 3.2 9.1 + - + +
86A VAL* 3.0 27.2 + - + +
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Residues in contact with LEU 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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56A HIS* 4.5 19.2 - - + +
59A ALA* 5.0 9.4 - - + +
63A VAL* 6.0 2.5 - - + -
79A GLY 3.2 9.2 + - - +
80A LEU* 3.1 20.3 + - + +
82A ILE* 1.3 79.1 - - - +
84A GLU* 1.3 63.7 + - - +
86A VAL* 3.2 16.3 + - + +
87A ILE* 3.3 35.0 + - + +
102A ILE* 4.4 20.9 - - + -
105A TYR* 4.8 18.6 - - + -
106A VAL* 4.4 19.7 - - + -
109A LEU* 5.8 1.6 - - + -
130A LEU* 6.2 0.2 - - + -
133A ILE* 4.3 15.5 - - + -
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Residues in contact with GLU 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 LEU 2.6 20.3 + - - +
81A GLN* 3.3 13.8 + - - +
83A LEU* 1.3 73.1 - - - +
85A ASN* 1.3 61.6 + - - +
87A ILE* 3.3 20.7 + - - +
88A LYS* 3.3 21.0 + - + +
129A LYS* 3.3 36.1 + - - -
132A MET* 4.3 5.4 - - - +
133A ILE* 4.3 11.6 - - + +
136A GLN* 3.1 41.1 + - + +
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Residues in contact with ASN 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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52A HIS* 6.0 4.9 - - - +
81A GLN 2.9 13.1 + - - +
82A ILE* 3.2 11.8 + - + +
84A GLU* 1.3 78.6 + - - +
86A VAL* 1.3 65.6 + - - +
88A LYS* 3.1 7.1 + - - +
89A THR* 2.7 48.5 + - - +
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Residues in contact with VAL 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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55A GLU* 5.3 3.8 - - + -
56A HIS* 3.3 49.4 - - + +
82A ILE* 3.0 19.7 + - + +
83A LEU* 3.2 9.4 + - + +
85A ASN* 1.3 80.2 - - - +
87A ILE* 1.3 60.0 + - + +
89A THR* 4.6 2.7 - - - +
90A ARG* 3.1 34.1 + - + +
91A TRP* 3.3 5.7 + - - -
94A LEU* 4.5 21.3 - - + -
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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 LEU* 3.4 27.8 - - + +
84A GLU* 3.3 8.2 + - - +
85A ASN 3.2 0.4 - - - -
86A VAL* 1.3 77.3 - - + +
88A LYS* 1.3 59.6 + - - +
91A TRP* 3.1 45.2 - - + +
102A ILE* 4.3 2.9 - - + -
133A ILE* 3.4 32.8 - - + +
136A GLN* 3.9 12.3 - - + +
137A ILE* 3.5 46.0 - - + +
140A GLN* 3.7 12.2 - - + +
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Residues in contact with LYS 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 GLU* 3.3 21.8 + - + +
85A ASN* 3.1 7.2 + - - +
87A ILE* 1.3 78.6 - - + +
89A THR* 1.3 61.5 + - - +
136A GLN* 3.1 47.4 - - + +
139A LYS* 5.9 4.3 - - - +
140A GLN* 4.6 7.6 - - + +
185A GLN* 5.5 6.7 + - - -
1023A LYS 4.5 1.6 - - - +
1024A GLU* 3.4 27.3 - - - +
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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 ASN* 2.7 42.7 + - - +
86A VAL* 3.3 1.8 + - - -
87A ILE 3.4 0.2 - - - -
88A LYS* 1.3 80.3 - - - +
90A ARG* 1.3 76.9 + - - +
91A TRP 3.5 1.3 - - - -
92A LYS* 5.1 1.9 + - - +
1023A LYS 4.2 12.8 + - - +
1024A GLU* 4.0 3.5 - - - +
1025A PHE* 3.1 59.3 + - + +
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Residues in contact with ARG 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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54A LYS 5.6 3.8 + - - -
86A VAL* 3.1 14.8 + - + +
89A THR* 1.3 94.6 - - - +
91A TRP* 1.3 65.6 + - - +
92A LYS 3.2 3.1 - - - -
93A ILE* 3.0 42.1 + - + +
94A LEU* 3.2 21.5 + - + +
1025A PHE* 3.9 35.9 - - + -
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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