Contacts of the helix formed by residues 67 - 83 (chain A) in PDB entry 4U0J
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 67 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64A ASP* 2.9 26.5 + - + +
65A VAL 3.2 0.4 - - - -
66A GLN* 1.3 77.0 - - - +
68A GLU* 1.3 64.1 + - - +
69A GLU* 2.8 26.2 + - - +
70A HIS* 3.1 50.6 + - - +
71A LEU* 3.2 15.5 + - - +
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Residues in contact with GLU 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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65A VAL 5.6 0.2 - - - +
66A GLN 3.7 10.1 + - - +
67A ASN* 1.3 73.4 + - - +
69A GLU* 1.3 58.7 + - + +
71A LEU* 3.4 21.6 + - - +
72A ALA* 2.9 30.2 + - - +
121A HIS* 5.6 4.7 + - - -
125A TYR* 5.6 5.4 + - - -
132A LYS* 5.9 0.9 + - - -
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Residues in contact with GLU 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A ASN* 2.8 14.5 + - - +
68A GLU* 1.3 76.0 - - + +
70A HIS* 1.3 68.0 + - + +
72A ALA* 3.3 7.2 + - - +
73A SER* 3.1 26.2 + - - -
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Residues in contact with HIS 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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62A GLU* 3.5 41.8 + - + -
63A LEU* 3.9 19.2 - - + -
64A ASP* 3.1 32.4 + - + +
67A ASN* 3.1 38.3 + - - +
69A GLU* 1.3 79.6 - - + +
71A LEU* 1.3 58.1 + - - +
73A SER* 3.3 2.5 + - - -
74A LEU* 3.0 18.0 + - - +
77A ARG* 3.0 28.4 + - - +
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Residues in contact with LEU 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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63A LEU* 3.9 20.6 - - + -
65A VAL* 3.5 26.5 - - - +
67A ASN 3.2 12.4 + - - +
68A GLU* 3.7 25.4 - - - +
69A GLU 3.2 0.2 - - - -
70A HIS* 1.3 81.1 - - - +
72A ALA* 1.3 62.4 + - - +
74A LEU* 3.3 18.4 + - + +
75A ALA 4.6 1.0 + - - -
125A TYR* 6.1 0.2 - - + -
129A SER* 3.8 42.2 - - - +
130A MET* 4.6 10.3 - - + +
133A ALA* 3.8 20.6 - - + +
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Residues in contact with ALA 72 (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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68A GLU* 2.9 17.5 + - + +
69A GLU* 3.3 8.3 + - - +
71A LEU* 1.3 77.0 - - - +
73A SER* 1.3 58.7 + - - +
74A LEU 3.8 0.2 + - - -
75A ALA* 5.0 2.9 + - - +
76A GLY 5.5 0.5 + - - -
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Residues in contact with SER 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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69A GLU 3.1 16.4 + - - -
70A HIS* 3.3 5.5 + - - -
72A ALA* 1.3 76.8 - - - +
74A LEU* 1.3 65.9 + - - +
75A ALA 3.4 2.0 - - - -
76A GLY* 3.2 5.6 + - - -
77A ARG* 2.8 47.4 + - - +
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Residues in contact with LEU 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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11A LEU* 4.8 2.2 - - + -
39A THR* 4.4 17.3 - - + -
61A LEU* 4.6 4.9 - - + -
62A GLU 5.0 0.2 - - - +
63A LEU* 3.9 29.2 - - + -
70A HIS 3.0 16.6 + - - +
71A LEU* 3.3 15.2 + - + +
73A SER* 1.3 76.7 - - - +
75A ALA* 1.3 58.4 + - - +
77A ARG* 3.1 25.1 + - - +
78A VAL* 2.9 44.2 + - + +
130A MET* 5.3 2.5 - - + -
133A ALA* 4.2 10.5 - - + -
134A LEU* 3.8 34.8 - - + -
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Residues in contact with ALA 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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71A LEU 4.6 2.0 + - - -
72A ALA 5.0 2.6 + - - +
73A SER 3.4 0.8 - - - -
74A LEU* 1.3 78.3 - - - +
76A GLY* 1.3 57.9 + - - +
78A VAL* 3.3 2.7 + - - +
79A THR* 2.9 33.8 + - - -
133A ALA 3.5 23.7 + - - +
134A LEU* 4.6 2.0 - - - -
136A PRO* 5.8 2.2 - - + -
137A ILE* 3.7 31.8 - - + +
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Residues in contact with GLY 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A ALA 5.5 0.4 + - - -
73A SER 3.2 7.9 + - - -
75A ALA* 1.3 77.9 - - - +
77A ARG* 1.3 57.7 + - - +
79A THR* 3.4 6.7 + - - -
80A GLU* 3.0 28.9 + - - +
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Residues in contact with ARG 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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61A LEU* 3.9 29.7 - - + +
62A GLU* 2.7 45.2 + - - +
63A LEU* 4.8 0.4 - - - +
70A HIS* 3.0 37.1 + - - +
73A SER* 2.8 29.9 + - - +
74A LEU* 3.6 19.2 - - - +
76A GLY* 1.3 72.6 - - - +
78A VAL* 1.3 66.4 + - - +
80A GLU* 3.5 17.0 - - - +
81A ALA* 3.1 21.3 + - - +
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Residues in contact with VAL 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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11A LEU* 3.7 24.5 - - + -
37A VAL* 4.7 5.8 - - + -
61A LEU* 3.7 17.5 - - + -
74A LEU* 2.9 29.5 + - + +
75A ALA 3.7 4.7 - - - +
76A GLY 3.3 0.2 - - - -
77A ARG* 1.3 74.1 - - - +
79A THR* 1.3 60.3 + - - +
81A ALA* 2.9 5.6 + - - +
82A ILE* 2.9 36.0 + - + +
88A LEU* 4.0 26.0 - - + -
134A LEU* 4.3 5.2 - - + -
137A ILE* 3.7 17.9 - - + -
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Residues in contact with THR 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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75A ALA 2.9 18.2 + - - -
76A GLY* 3.8 7.1 - - - -
78A VAL* 1.3 75.3 - - - +
80A GLU* 1.3 54.2 + - - +
82A ILE* 3.9 9.1 - - - +
83A GLY* 2.6 39.7 + - - +
84A ALA* 3.7 24.6 + - + +
85A GLY 4.9 1.1 - - - +
86A ASN 4.8 8.5 + - - +
137A ILE* 3.9 20.6 - - - +
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Residues in contact with GLU 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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76A GLY 3.0 16.2 + - - +
77A ARG* 3.5 20.3 - - - +
79A THR* 1.3 79.4 - - - +
81A ALA* 1.3 61.5 + - - +
83A GLY* 3.7 6.6 + - - -
84A ALA 5.6 0.4 - - - +
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Residues in contact with ALA 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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37A VAL* 4.5 11.9 - - + -
59A PRO* 4.0 35.0 - - + +
61A LEU* 4.7 7.0 - - + -
77A ARG 3.1 12.9 + - - +
78A VAL* 2.9 11.9 + - - +
80A GLU* 1.3 77.7 - - - +
82A ILE* 1.3 62.5 + - - +
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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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9A ARG* 4.2 20.5 + - + +
37A VAL* 3.3 33.0 - - + -
78A VAL* 2.9 31.3 + - + +
79A THR* 3.8 8.7 - - - +
81A ALA* 1.3 76.5 - - - +
83A GLY* 1.3 59.0 + - - +
86A ASN* 2.8 54.1 + - + +
87A LYS* 3.8 18.4 - - - +
88A LEU* 4.1 7.9 - - + +
137A ILE* 5.6 1.6 - - + -
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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 THR* 2.6 20.1 + - - +
80A GLU 3.7 6.1 + - - -
81A ALA 3.5 2.2 - - - -
82A ILE* 1.3 72.9 - - - +
84A ALA* 1.3 70.3 + - - +
86A ASN* 3.0 28.0 + - - +
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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