Contacts of the helix formed by residues 63 - 78 (chain A) in PDB entry 1VJZ
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 PHE 63 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A ALA* 4.1 13.5 - - + -
22A THR 5.0 1.8 - - - -
23A GLY* 4.6 6.3 - - - -
49A LEU* 3.7 47.6 - - + +
50A TRP* 3.5 42.2 - + + -
60A ARG* 3.4 14.3 + - + +
62A ASP* 1.3 84.0 + - - +
64A PHE* 1.3 66.3 + + + +
66A LYS* 3.0 59.6 + - + +
67A ILE* 3.9 22.7 - - + -
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Residues in contact with PHE 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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45A MSE 4.5 9.6 - - + -
50A TRP* 3.5 56.3 - + - -
59A ILE* 4.6 0.9 - - + -
60A ARG 4.4 6.3 - - - -
61A GLU 2.9 16.0 + - - +
63A PHE* 1.3 78.9 - + - +
65A GLU* 1.3 58.9 + - - +
66A LYS 3.1 1.3 - - - -
67A ILE* 3.0 22.3 + - + +
68A ASP* 2.8 33.4 + - - +
83A ILE* 5.8 0.2 - - + -
119A PHE* 3.5 25.6 - + - -
120A ILE* 4.1 28.3 - - + -
123A ARG* 3.4 24.0 - - - +
124A TYR* 3.6 18.6 + + - -
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Residues in contact with GLU 65 (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 ASP* 3.0 31.7 + - - +
64A PHE* 1.3 75.3 - - - +
66A LYS* 1.3 62.7 + - + +
68A ASP* 3.4 12.8 - - - +
69A ARG* 3.2 22.3 + - - +
123A ARG* 3.7 13.5 - - - +
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Residues in contact with LYS 66 (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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22A THR 3.1 28.1 + - - +
23A GLY* 3.4 26.6 - - - +
24A ASN* 3.5 18.9 + - - +
25A PHE* 4.4 2.6 - - - -
62A ASP 5.5 0.7 - - - +
63A PHE* 3.0 38.4 + - + +
65A GLU* 1.3 78.3 - - + +
67A ILE* 1.3 66.4 + - + +
69A ARG* 3.5 9.1 - - - +
70A VAL* 3.5 21.8 + - - +
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Residues in contact with ILE 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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16A ALA* 4.3 5.6 - - + -
25A PHE* 4.1 22.9 - - + -
43A ILE* 4.5 5.8 - - + -
45A MSE 3.6 24.0 - - - -
63A PHE* 3.9 28.3 - - + -
64A PHE* 3.0 23.2 + - + +
66A LYS* 1.3 74.0 - - + +
68A ASP* 1.3 65.7 + - - +
69A ARG 3.2 0.2 - - - -
70A VAL* 3.2 8.7 + - + +
71A ILE* 3.0 32.6 + - + +
83A ILE* 4.1 18.4 - - + -
124A TYR* 3.4 18.2 - - + +
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Residues in contact with ASP 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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64A PHE 2.8 17.2 + - - +
65A GLU* 3.4 14.2 - - - +
67A ILE* 1.3 72.1 - - - +
69A ARG* 1.3 51.1 + - - +
71A ILE* 3.2 5.0 + - - +
72A PHE* 2.8 34.9 + - - +
123A ARG* 2.8 33.5 + - - -
124A TYR* 2.5 39.5 + - - -
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Residues in contact with ARG 69 (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 GLU 3.2 9.5 + - - +
66A LYS* 3.5 13.2 - - - +
67A ILE 3.2 0.2 - - - -
68A ASP* 1.3 75.6 - - - +
70A VAL* 1.3 56.0 + - - +
72A PHE* 3.2 10.1 + - + +
73A TRP* 2.7 78.8 + - + +
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Residues in contact with VAL 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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25A PHE* 3.3 51.4 - - + -
30A PHE* 4.1 7.4 - - + -
43A ILE* 3.8 31.4 - - + -
66A LYS 3.5 7.6 + - - +
67A ILE* 3.2 12.5 + - + +
69A ARG* 1.3 76.2 - - - +
71A ILE* 1.3 57.4 + - + +
73A TRP* 3.1 13.9 + - + +
74A GLY 2.9 24.4 + - - -
81A ILE* 3.7 21.6 - - + +
83A ILE* 5.6 1.6 - - + -
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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 ILE* 3.0 23.5 + - + +
68A ASP* 3.7 6.5 - - - +
70A VAL* 1.3 76.8 - - + +
72A PHE* 1.3 63.2 + - - +
74A GLY* 3.3 1.9 + - - -
75A GLU* 3.2 22.1 + - + +
81A ILE* 4.1 19.5 - - + +
83A ILE* 4.7 1.3 - - + -
124A TYR* 3.4 44.2 - - + +
127A ILE* 3.8 34.8 - - + -
131A HIS* 5.6 3.7 - - + +
132A LEU* 4.0 29.8 - - + -
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Residues in contact with PHE 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 ASP 2.8 14.1 + - - +
69A ARG* 3.2 13.2 - - + +
71A ILE* 1.3 76.9 - - - +
73A TRP* 1.3 84.3 + + - +
75A GLU* 3.3 8.7 + - - +
76A LYS* 3.1 60.4 + - + +
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Residues in contact with TRP 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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25A PHE* 3.3 38.8 - - + -
26A LYS 3.9 0.4 - - - -
27A GLU* 3.5 58.8 + - + -
30A PHE* 3.7 36.1 - + + -
69A ARG* 2.7 57.9 + - + +
70A VAL* 3.6 8.5 - - + +
72A PHE* 1.3 95.1 - + - +
74A GLY* 1.3 59.7 + - - +
76A LYS* 3.2 2.9 + - + -
77A TYR* 2.8 42.5 + + + +
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Residues in contact with GLY 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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30A PHE* 4.2 2.5 - - - -
70A VAL 2.9 14.4 + - - -
71A ILE 3.3 4.0 + - - -
73A TRP* 1.3 76.3 - - - +
75A GLU* 1.3 61.9 + - - +
78A GLY* 2.9 6.9 + - - -
79A ILE* 2.9 51.0 + - - -
81A ILE* 3.9 11.2 - - - -
131A HIS* 5.4 2.1 - - - -
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Residues in contact with GLU 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 ILE 3.2 12.0 + - - +
72A PHE* 3.7 10.8 - - + +
73A TRP 3.3 0.4 - - - -
74A GLY* 1.3 76.2 - - - +
76A LYS* 1.3 84.2 + - - +
77A TYR 3.5 0.2 + - - -
78A GLY* 3.6 7.6 + - - -
131A HIS* 3.7 43.8 + - + +
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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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72A PHE* 3.1 55.0 + - + +
73A TRP* 3.7 6.5 - - + +
74A GLY 3.2 0.2 - - - -
75A GLU* 1.3 94.8 + - - +
77A TYR* 1.3 72.5 + - + +
78A GLY 3.8 0.2 + - - -
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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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27A GLU* 2.5 45.1 + - + +
30A PHE* 3.6 17.3 - - + -
31A LEU* 3.6 46.1 - - + +
34A ALA* 3.8 22.9 - - + +
38A PHE 5.4 0.3 - - - +
73A TRP* 2.8 34.9 + + + +
74A GLY 4.5 0.2 - - - +
76A LYS* 1.3 89.8 - - + +
78A GLY* 1.3 61.1 + - - +
79A ILE* 3.4 21.1 - - + +
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Residues in contact with GLY 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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38A PHE 4.5 1.0 - - - +
39A ASN* 3.8 18.7 - - - +
74A GLY 2.9 5.6 + - - -
75A GLU 3.6 6.0 + - - -
76A LYS 3.5 3.0 - - - -
77A TYR* 1.3 78.8 - - - +
79A ILE* 1.3 63.2 + - - +
80A HIS 4.1 0.4 - - - -
131A HIS* 6.4 1.1 - - - -
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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