Contacts of the helix formed by residues 56 - 75 (chain A) in PDB entry 3UON
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 THR 56 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A HIS 4.4 7.9 - - - +
54A LEU 3.3 3.4 + - - -
55A GLN* 1.3 84.9 - - - +
57A VAL* 1.3 59.5 + - - +
58A ASN* 3.5 16.0 + - - +
59A ASN* 2.8 29.3 + - - +
60A TYR* 2.8 35.4 + - - -
137A THR* 6.3 0.4 - - - -
1061A ASP* 3.3 39.7 - - + +
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Residues in contact with VAL 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A THR* 1.3 72.8 - - - +
58A ASN* 1.3 68.0 + - - +
60A TYR* 3.1 21.3 + - - +
61A PHE* 3.2 23.7 + - + -
120A ASP* 5.1 0.2 - - - +
135A ARG* 3.1 55.2 - - + +
136A THR 3.7 32.1 - - - +
137A THR* 4.1 13.2 - - + +
140A ALA* 4.3 8.7 - - + -
1065A LYS* 6.3 0.2 - - - +
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Residues in contact with ASN 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A THR* 3.5 19.3 + - - +
57A VAL* 1.3 85.3 - - - +
59A ASN* 1.3 63.0 + - - +
61A PHE* 3.2 29.2 + - + +
62A LEU* 3.2 17.2 + - + +
120A ASP* 4.1 4.9 - - - +
121A ARG* 3.6 16.5 + - - -
135A ARG* 4.0 9.8 + - - +
385A VAL* 3.6 33.6 - - + +
1061A ASP* 5.2 2.4 + - - -
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Residues in contact with ASN 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A ILE* 3.0 23.9 - - + +
53A HIS 4.9 0.4 + - - -
54A LEU* 2.4 53.7 + - - +
56A THR* 2.8 21.6 + - - +
58A ASN* 1.3 77.7 - - - +
60A TYR* 1.3 61.7 + - - +
62A LEU* 3.6 21.5 - - - +
63A PHE* 2.8 23.2 + - - +
444A ASN* 5.2 6.2 + - - +
447A PHE* 3.9 11.3 - - - -
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Residues in contact with TYR 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A ILE* 5.0 9.4 - - + -
55A GLN* 4.2 18.8 + - + +
56A THR* 2.8 36.1 + - - -
57A VAL* 3.1 13.9 + - - +
59A ASN* 1.3 77.2 - - + +
61A PHE* 1.3 60.4 + - - +
63A PHE* 3.1 10.2 + + + +
64A SER 3.0 22.9 + - - -
137A THR* 3.4 44.1 - - + +
140A ALA* 4.1 19.7 - - + -
141A GLY* 5.2 2.2 - - - -
144A ILE* 3.7 23.3 - - + +
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Residues in contact with PHE 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A VAL* 3.7 18.4 - - + -
58A ASN* 3.2 14.3 + - - +
60A TYR* 1.3 77.7 - - - +
62A LEU* 1.3 57.3 + - - +
64A SER* 3.1 8.1 + - - -
65A LEU* 2.9 32.0 + - - +
113A ASN* 4.3 8.8 - - + +
116A ILE* 3.5 33.9 - - + -
117A ILE* 3.7 35.0 - - + -
120A ASP* 4.1 28.9 - - + -
135A ARG* 5.3 1.6 - - - -
140A ALA* 4.6 18.6 - - + -
143A MET* 5.1 2.0 - - + -
144A ILE* 4.2 23.8 - - + -
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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
----------------------------------------------------------
44A VAL* 4.6 0.8 - - + +
48A ILE* 4.7 6.7 - - + -
58A ASN* 3.2 14.4 + - + +
59A ASN* 3.7 25.1 - - - +
61A PHE* 1.3 77.6 - - - +
63A PHE* 1.3 57.0 + - - +
65A LEU* 3.6 15.0 - - + +
66A ALA* 2.9 29.1 + - - +
117A ILE* 4.9 11.7 - - + -
388A THR* 4.2 19.1 - - + +
389A ILE* 6.5 0.7 - - + -
392A ILE* 4.9 3.8 - - + -
440A TYR* 3.9 44.7 + - + +
447A PHE* 3.9 17.7 - - + -
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Residues in contact with PHE 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A VAL* 5.5 0.2 - - - -
45A MET* 3.4 53.2 - - + -
48A ILE* 4.2 19.7 - - + +
49A LYS* 3.9 27.4 - - + -
59A ASN 2.8 15.0 + - - +
60A TYR* 3.2 16.2 - + + +
62A LEU* 1.3 75.5 - - - +
64A SER* 1.3 65.9 + - - +
66A ALA* 3.2 7.7 + - - +
67A CYS* 3.0 45.9 + - - -
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Residues in contact with SER 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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60A TYR 3.0 11.4 + - - -
61A PHE 3.4 5.6 - - - -
63A PHE* 1.3 79.3 - - - +
65A LEU* 1.3 62.4 + - - +
67A CYS* 3.0 20.2 + - - +
68A ALA* 3.1 11.3 + - - +
113A ASN* 2.9 28.0 + - - -
144A ILE* 3.7 17.8 - - - +
148A TRP* 2.8 31.1 + - - +
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Residues in contact with LEU 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A PHE 2.9 11.6 + - - +
62A LEU* 3.6 18.8 - - + +
64A SER* 1.3 75.1 + - - +
66A ALA* 1.3 56.9 + - - +
68A ALA* 3.4 6.2 + - - +
69A ASP* 2.9 39.0 + - - +
110A SER* 4.0 20.2 - - - +
113A ASN* 3.4 34.1 - - + +
114A LEU* 4.7 8.5 - - + +
117A ILE* 5.1 6.1 - - + -
392A ILE* 4.2 22.0 - - + -
436A ASN* 4.0 15.3 - - - +
440A TYR* 3.6 20.9 - - - +
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Residues in contact with ALA 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A ASN* 3.3 29.3 - - - +
44A VAL* 4.2 13.2 - - + -
45A MET* 3.7 21.0 - - + +
62A LEU 2.9 18.5 + - - +
63A PHE* 3.4 7.0 - - - +
65A LEU* 1.3 73.9 - - - +
67A CYS* 1.3 60.0 + - - +
69A ASP* 4.6 0.2 - - - -
70A LEU* 2.8 30.7 + - - +
440A TYR* 4.9 4.0 + - + -
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Residues in contact with CYS 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A MET* 3.7 28.5 - - - -
63A PHE* 3.0 40.3 + - - -
64A SER* 3.0 11.3 + - - +
66A ALA* 1.3 74.1 - - - +
68A ALA* 1.3 66.3 + - - +
70A LEU* 3.0 14.7 + - - +
71A ILE* 3.1 20.4 + - + +
148A TRP* 4.1 12.8 - - + -
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Residues in contact with ALA 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A SER 3.1 6.2 + - - +
65A LEU* 3.6 9.2 - - - +
67A CYS* 1.3 78.2 - - - +
69A ASP* 1.3 63.5 + - - +
71A ILE* 3.3 7.2 + - - +
72A ILE* 3.1 25.8 + - - +
106A VAL* 4.0 16.4 - - + +
109A ALA* 5.2 0.2 - - + -
110A SER* 3.5 26.9 - - - +
113A ASN* 6.2 0.7 - - - +
148A TRP* 3.8 23.6 - - + -
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Residues in contact with ASP 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A THR* 3.5 11.8 - - - +
41A ASN* 3.2 24.8 - - - +
65A LEU* 2.9 23.9 + - - +
68A ALA* 1.3 74.5 - - - +
70A LEU* 1.3 64.0 + - - +
72A ILE* 3.5 4.3 + - - +
73A GLY 3.2 15.8 + - - -
110A SER* 4.5 9.9 + - - -
432A ASN* 5.5 1.2 - - - +
433A SER* 2.8 36.4 + - - +
436A ASN* 2.6 36.1 + - - +
440A TYR* 4.8 0.2 + - - -
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Residues in contact with LEU 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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37A THR 5.2 0.7 - - - -
38A ILE* 3.4 45.5 - - + +
41A ASN* 4.0 8.5 - - + +
42A ILE* 3.5 26.2 - - + -
45A MET* 4.1 20.9 - - + -
66A ALA 2.8 20.0 + - - +
67A CYS* 3.0 7.4 + - - +
69A ASP* 1.3 75.0 - - - +
71A ILE* 1.3 67.8 + - + +
73A GLY* 3.0 12.0 + - - -
74A VAL* 3.0 19.0 + - + +
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Residues in contact with ILE 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 CYS* 3.1 14.9 + - + +
68A ALA 3.3 7.6 + - - +
70A LEU* 1.3 78.1 - - + +
72A ILE* 1.3 57.5 + - + +
74A VAL* 3.2 8.9 - - + +
75A PHE* 2.8 38.9 + - + +
76A SER* 5.7 1.3 - - - +
102A LEU* 3.6 42.4 - - + -
106A VAL* 4.2 22.4 - - + -
148A TRP* 5.1 9.4 - - + -
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Residues in contact with ILE 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 ALA* 3.1 16.0 + - + +
69A ASP* 3.6 8.7 - - - +
70A LEU 3.2 0.2 - - - -
71A ILE* 1.3 76.3 - - + +
73A GLY* 1.3 60.1 + - - +
76A SER* 3.2 25.7 + - - +
77A MET* 2.9 35.5 + - + +
103A ASP* 3.9 10.8 - - - +
106A VAL* 3.7 24.5 - - + -
107A SER* 4.7 4.3 - - - +
429A CYS 5.5 0.2 - - - +
430A TYR* 3.9 31.2 - - + +
433A SER* 3.8 26.9 - - - +
1162A QNB 6.0 0.4 - - - -
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Residues in contact with GLY 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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34A SER* 2.3 31.4 + - - -
37A THR* 3.8 24.5 - - - -
38A ILE* 3.6 8.1 - - - -
69A ASP 3.2 6.5 + - - -
70A LEU 3.0 7.5 + - - -
72A ILE* 1.3 80.0 - - - +
74A VAL* 1.3 58.1 + - - +
77A MET* 4.0 12.4 - - - +
78A ASN* 3.6 1.6 + - - -
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Residues in contact with VAL 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A ILE* 3.6 13.4 - - + +
70A LEU* 3.0 22.4 + - + +
71A ILE* 3.2 17.3 - - + +
73A GLY* 1.3 78.6 - - - +
75A PHE* 1.3 89.7 + - + +
78A ASN* 2.7 29.0 + - - +
79A LEU* 5.1 1.0 - - - +
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Residues in contact with PHE 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A ILE* 2.8 25.3 + - + +
74A VAL* 1.3 111.4 - - + +
76A SER* 1.3 66.8 + - - +
77A MET 3.4 1.8 - - - -
78A ASN 3.4 1.4 + - - -
79A LEU* 3.0 42.7 + - + +
99A TRP* 4.0 10.5 - + + -
102A LEU* 3.7 31.9 - - + -
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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
------------------------------------------------------------
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