Contacts of the helix formed by residues 66 - 88 (chain A) in PDB entry 4CEJ
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 66 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A THR* 2.9 18.4 + - - -
65A PHE* 1.3 97.2 - - + +
67A ASN* 1.3 63.6 + - - +
68A ALA* 3.6 9.2 + - - +
69A SER* 2.7 37.4 + - - +
70A ALA 3.3 0.2 + - - -
108A THR* 3.6 5.2 - - - -
797A LYS* 6.2 0.7 - - + -
55X T 5.3 10.8 - - - -
56X T 3.7 10.1 - - - +
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Residues in contact with ASN 67 (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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66A THR* 1.3 73.5 - - - +
68A ALA* 1.3 61.9 + - - +
70A ALA* 3.2 8.6 + - - +
71A ALA* 3.1 22.2 + - - +
107A SER* 4.9 3.3 - - - -
108A THR* 3.8 11.3 + - - +
111A SER* 3.9 14.7 + - - -
677B LYS* 5.2 10.4 - - + +
56X T 2.9 34.3 + - - +
57X T 2.5 30.8 + - - -
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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
----------------------------------------------------------
66A THR* 3.2 8.4 - - - +
67A ASN* 1.3 79.1 - - - +
69A SER* 1.3 56.8 + - - +
71A ALA* 3.3 7.3 + - - +
72A GLU* 2.9 30.0 + - - +
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Residues in contact with SER 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A THR* 3.8 16.8 - - - -
65A PHE* 4.8 2.1 + - - +
66A THR* 2.7 33.0 + - - +
68A ALA* 1.3 75.3 - - - +
70A ALA* 1.3 57.6 + - - +
72A GLU* 3.4 8.3 + - - +
73A MET* 2.9 37.8 + - - +
407A ASP* 6.2 0.4 - - - -
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Residues in contact with ALA 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A THR* 3.5 23.0 + - - +
66A THR 3.3 3.7 + - - +
67A ASN* 3.2 13.2 + - - +
68A ALA 3.2 0.6 - - - -
69A SER* 1.3 79.3 - - - +
71A ALA* 1.3 61.5 + - - +
73A MET* 3.2 5.4 + - - +
74A LYS* 3.0 21.9 + - - +
106A ILE* 3.3 31.7 - - - +
107A SER* 3.6 10.5 - - - -
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Residues in contact with ALA 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A ASN 3.1 9.9 + - - +
68A ALA* 3.6 9.6 - - - +
70A ALA* 1.3 78.2 - - - +
72A GLU* 1.3 63.7 + - - +
74A LYS* 3.0 20.9 + - - +
75A HIS* 3.1 17.5 + - - -
611B ASP* 5.7 1.8 - - - +
680B LEU* 3.8 25.4 - - + -
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Residues in contact with GLU 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A ALA 2.9 17.7 + - - +
69A SER* 3.5 9.6 - - - +
71A ALA* 1.3 77.2 - - - +
73A MET* 1.3 66.7 + - - +
75A HIS* 3.3 6.9 + - - +
76A ARG* 2.9 53.2 + - + +
680B LEU* 5.0 1.3 - - - +
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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
----------------------------------------------------------
37A THR* 4.5 18.4 - - + -
40A LEU* 3.6 30.1 - - + -
41A VAL* 4.2 24.5 - - + -
44A MET* 6.2 1.8 - - + -
62A VAL* 4.0 6.1 - - + -
64A THR* 3.5 25.4 - - + -
69A SER* 2.9 23.9 + - - +
70A ALA* 3.3 9.4 - - - +
72A GLU* 1.3 80.5 - - - +
74A LYS* 1.3 64.4 + - - +
76A ARG* 3.8 4.7 - - - +
77A ILE* 2.9 39.9 + - + +
106A ILE* 3.9 14.8 - - + -
407A ASP* 4.8 11.7 - - + +
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Residues in contact with LYS 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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70A ALA 3.0 13.2 + - - +
71A ALA* 3.2 13.7 - - - +
73A MET* 1.3 76.7 - - - +
75A HIS* 1.3 59.5 + - - +
77A ILE* 3.5 7.0 - - - +
78A ALA* 3.0 21.9 + - + +
101A LEU* 3.2 56.8 + - + +
102A ASN* 3.4 27.3 + - - +
104A ALA* 5.3 1.3 - - + +
106A ILE* 4.8 16.1 - - + +
611B ASP* 3.5 30.2 + - - +
612B GLY* 5.3 5.3 - - - +
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Residues in contact with HIS 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 ALA 3.1 10.2 + - - +
72A GLU* 3.8 10.3 - - - +
74A LYS* 1.3 76.0 - - - +
76A ARG* 1.3 64.0 + - + +
77A ILE 2.8 5.6 + - - -
78A ALA* 2.9 17.8 + - + +
79A GLU* 3.0 34.1 + - + +
611B ASP* 3.3 30.2 + - - -
680B LEU* 3.5 33.0 - - + +
681B PRO* 3.9 16.8 + - - +
682B SER 5.8 0.6 - - - -
686B LYS* 4.8 12.6 + - - -
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Residues in contact with ARG 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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37A THR* 5.7 1.0 - - - +
38A ALA* 4.3 25.1 - - - +
41A VAL* 4.2 26.5 - - + +
45A ILE* 4.2 6.8 - - - +
72A GLU* 2.9 45.1 + - + +
73A MET* 4.0 4.9 - - - +
75A HIS* 1.3 74.2 - - - +
77A ILE* 1.3 60.2 + - - +
79A GLU* 4.4 10.8 - - - +
80A ALA* 3.9 16.1 + - - +
2233A ANP 4.9 13.9 + - - -
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Residues in contact with ILE 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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41A VAL* 4.5 7.6 - - + -
44A MET* 3.6 35.7 - - + -
45A ILE* 4.5 21.6 - - + +
48A ILE* 5.4 8.5 - - + -
57A VAL* 5.4 0.4 - - + -
73A MET* 2.9 30.3 + - + +
74A LYS* 3.5 4.9 - - - +
75A HIS 2.8 1.2 + - - -
76A ARG* 1.3 77.4 - - - +
78A ALA* 1.3 66.4 + - - +
79A GLU 3.2 1.6 - - - -
80A ALA* 3.1 5.9 + - - +
81A LEU* 2.9 29.5 + - + +
101A LEU* 3.7 26.9 - - + -
106A ILE* 3.8 17.7 - - + -
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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
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74A LYS* 3.0 18.1 + - + +
75A HIS* 2.9 15.0 + - + +
77A ILE* 1.3 72.0 - - - +
79A GLU* 1.3 59.1 - - + +
81A LEU* 3.3 9.1 + - - +
82A GLU* 3.0 31.5 + - + +
98A LEU* 3.7 10.0 - - + +
101A LEU* 3.6 17.9 - - + -
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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
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75A HIS* 3.0 32.8 + - + +
76A ARG* 4.5 9.0 - - - +
78A ALA* 1.3 75.2 - - + +
80A ALA* 1.3 65.4 + - - +
82A GLU* 3.0 18.8 + - - +
83A LYS* 3.0 29.6 + - - +
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Residues in contact with ALA 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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45A ILE* 3.7 40.6 - - + -
76A ARG 3.9 6.3 + - - +
77A ILE 3.1 10.1 + - - +
79A GLU* 1.3 78.8 - - - +
81A LEU* 1.3 63.3 + - - +
83A LYS* 3.3 11.0 + - - +
84A GLU* 3.0 29.9 + - + +
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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
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45A ILE* 6.3 0.7 - - + -
48A ILE* 4.5 5.2 - - + -
49A THR* 3.8 22.0 - - + -
57A VAL* 5.2 1.1 - - + -
77A ILE* 2.9 20.8 + - + +
78A ALA* 3.3 8.7 - - - +
79A GLU 3.2 0.2 - - - -
80A ALA* 1.3 77.0 - - - +
82A GLU* 1.3 57.2 + - - +
84A GLU* 3.5 6.2 + - - +
85A LEU* 3.0 27.6 + - - +
94A ILE* 3.6 28.5 - - + +
97A GLN* 3.9 19.5 - - + -
98A LEU* 3.7 33.7 - - + +
101A LEU* 3.8 30.5 - - + -
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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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78A ALA* 3.0 18.3 + - + +
79A GLU* 3.0 11.7 + - - +
81A LEU* 1.3 74.8 - - - +
83A LYS* 1.3 61.2 + - + +
85A LEU* 3.0 14.3 + - - +
86A VAL* 2.8 37.2 + - + +
98A LEU* 3.8 26.3 - - + +
300B ARG* 5.6 3.6 + - - -
690B GLU* 5.1 12.5 - - - +
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Residues in contact with LYS 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* 3.0 29.5 + - - +
80A ALA* 3.7 11.3 - - - +
82A GLU* 1.3 75.0 - - + +
84A GLU* 1.3 65.2 + - + +
86A VAL* 3.2 9.4 + - - +
87A GLN* 3.1 23.8 + - - +
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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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45A ILE* 5.4 4.0 - - + +
49A THR* 4.0 30.8 + - + +
80A ALA* 3.0 22.3 + - + +
81A LEU* 3.6 7.2 - - - +
83A LYS* 1.3 76.8 - - - +
85A LEU* 1.3 56.0 + - - +
87A GLN* 3.6 18.1 + - - +
88A ARG* 2.9 46.6 + - - +
94A ILE* 3.6 19.9 - - + +
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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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81A LEU 3.0 14.8 + - - +
82A GLU* 3.0 18.4 + - - +
84A GLU* 1.3 76.7 - - - +
86A VAL* 1.3 66.6 + - + +
88A ARG 3.1 31.5 - - - +
89A PRO* 3.2 20.3 - - + +
91A SER 4.5 9.9 - - - +
94A ILE* 4.3 15.0 - - + +
95A ARG* 4.7 10.1 - - + +
98A LEU* 3.7 25.8 - - + -
300B ARG* 4.6 29.6 - - + +
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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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82A GLU* 2.8 23.1 + - + +
83A LYS* 3.2 10.7 + - - +
85A LEU* 1.3 77.0 - - + +
87A GLN* 1.3 63.0 + - - +
89A PRO* 4.0 8.0 - - - +
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Residues in contact with GLN 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 LYS 3.1 15.5 + - - +
84A GLU* 3.9 19.9 - - - +
86A VAL* 1.3 80.2 - - - +
88A ARG* 1.3 69.6 + - + +
89A PRO* 3.5 6.3 - - - +
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Residues in contact with ARG 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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49A THR* 4.5 14.5 + - - +
50A ALA 4.9 1.2 - - - +
51A GLU* 3.3 47.9 + - - +
84A GLU* 2.9 24.8 + - - +
85A LEU* 3.1 19.5 - - - +
87A GLN* 1.3 91.7 - - + +
89A PRO* 1.3 65.5 - - - +
90A GLY 3.4 2.2 + - - -
91A SER* 3.2 38.4 + - - +
94A ILE* 3.3 27.0 - - - +
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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
------------------------------------------------------------
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