Contacts of the helix formed by residues 51 - 68 (chain E) in PDB entry 7V3X
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 GLY 51 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49E GLY* 3.5 2.8 - - - -
50E THR* 1.3 78.4 - - - +
52E LYS* 1.3 61.2 + - - +
53E THR* 3.5 2.0 - - - -
54E LEU* 3.8 10.3 - - - +
55E PHE* 2.9 29.8 + - - +
207E LEU* 3.4 8.7 - - - +
239E ILE* 4.2 16.4 - - - -
244E ILE* 3.9 5.6 - - - +
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Residues in contact with LYS 52 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44E VAL* 3.9 13.9 - - + +
45E SER 4.4 0.2 - - - -
46E GLY 2.8 30.0 + - - +
47E THR 3.0 19.6 + - - -
48E SER* 3.9 7.5 - - - +
49E GLY 4.7 1.8 - - - +
50E THR* 3.7 11.0 - - - +
51E GLY* 1.3 73.4 - - - +
53E THR* 1.3 62.7 + - - +
55E PHE* 3.2 6.0 + - - +
56E SER* 3.0 29.6 + - - -
145E ASP* 4.1 1.3 - - - -
179E VAL* 5.5 0.2 - - - +
181E THR* 3.5 27.8 + - + +
182E THR 3.1 27.6 + - - +
183E GLU* 4.5 12.7 + - - +
207E LEU* 3.6 15.7 - - + -
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Residues in contact with THR 53 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51E GLY* 4.6 0.6 - - - -
52E LYS* 1.3 78.1 - - - +
54E LEU* 1.3 55.7 + - - +
56E SER* 2.4 19.3 + - - +
57E ILE* 2.8 34.8 + - + +
73E PHE* 4.5 4.7 - - + -
78E GLU* 4.1 20.3 + - - +
83E ILE* 5.8 1.6 - - + -
86E ASN* 6.3 0.4 - - - +
145E ASP* 2.9 32.7 + - - +
181E THR* 5.4 0.2 - - - +
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Residues in contact with LEU 54 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51E GLY* 3.7 14.0 + - - +
52E LYS 3.3 0.2 - - - -
53E THR* 1.3 78.6 - - - +
55E PHE* 1.3 54.2 + - - +
57E ILE* 3.3 5.7 + - + +
58E GLN* 2.8 54.3 + - - +
90E PHE* 3.2 49.8 - - + -
92E TRP* 3.9 13.9 - - + -
239E ILE* 3.4 29.2 - - + -
244E ILE* 3.8 18.6 - - + +
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Residues in contact with PHE 55 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23E THR* 5.1 10.5 - - + -
25E ILE* 5.8 4.3 - - + -
28E PHE* 3.7 46.2 - + - -
42E THR* 6.2 1.3 - - + -
44E VAL* 4.0 26.5 - - + -
51E GLY 2.9 20.4 + - - +
52E LYS* 3.2 8.7 + - - +
54E LEU* 1.3 74.2 - - - +
56E SER* 1.3 59.7 + - - +
58E GLN* 3.5 5.1 + - - +
59E PHE* 3.0 32.5 + + + +
179E VAL* 4.7 13.0 - - + -
205E VAL* 4.1 11.2 - - + -
207E LEU* 4.2 12.6 - - + -
220E LEU* 3.9 12.6 - - + -
244E ILE* 3.9 16.3 - - + +
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Residues in contact with SER 56 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52E LYS 3.0 10.7 + - - -
53E THR* 2.4 28.4 + - - -
55E PHE* 1.3 74.3 - - - +
57E ILE* 1.3 63.8 + - - +
59E PHE* 3.4 11.9 - - - +
60E LEU* 3.6 3.6 + - - +
73E PHE* 3.5 11.6 - - - -
143E SER* 2.9 39.5 + - - -
145E ASP* 3.6 4.9 + - - -
179E VAL* 4.0 18.8 - - - -
181E THR* 4.2 7.9 - - - -
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Residues in contact with ILE 57 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53E THR* 2.8 31.9 + - + +
54E LEU* 3.9 5.6 - - + +
56E SER* 1.3 69.9 + - - +
58E GLN* 1.3 66.8 + - - +
60E LEU* 3.1 7.7 + - + +
61E TYR* 3.0 22.7 + - + +
73E PHE* 3.4 31.6 - - + -
83E ILE* 3.7 28.0 - - + -
87E ALA* 4.8 3.6 - - + -
92E TRP* 4.3 21.8 - - + -
94E LEU* 4.2 29.9 - - + +
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Residues in contact with GLN 58 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23E THR 5.1 0.2 - - - -
25E ILE* 3.9 27.6 - - + +
54E LEU* 2.8 20.7 + - - +
55E PHE* 3.6 5.8 - - - +
57E ILE* 1.3 77.7 - - - +
59E PHE* 1.3 62.7 + - - +
61E TYR* 4.5 4.9 - - - -
62E ASN* 3.2 42.9 + - - +
92E TRP* 3.3 27.6 - - + -
242E HIS 4.6 4.0 + - - -
243E GLY* 3.4 7.8 - - - -
244E ILE* 2.8 52.9 + - - +
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Residues in contact with PHE 59 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21E MET* 3.9 15.9 - - + -
23E THR* 4.2 32.3 - - + -
36E LEU* 4.5 13.2 - - + -
55E PHE* 3.0 19.8 + + + +
56E SER 3.4 10.5 - - - +
57E ILE 3.1 0.4 - - - -
58E GLN* 1.3 76.5 - - - +
60E LEU* 1.3 64.7 + - + +
62E ASN* 4.1 0.9 - - - +
63E GLY 3.3 3.8 + - - -
141E ARG* 2.7 69.8 + - + -
142E VAL 3.8 11.0 - - - -
143E SER* 3.9 10.8 - - - -
177E THR* 4.0 15.9 - - - -
178E THR 5.7 0.2 - - - -
179E VAL* 3.3 31.9 - - + -
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Residues in contact with LEU 60 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56E SER 3.6 2.4 + - - +
57E ILE* 3.1 7.2 + - + +
59E PHE* 1.3 76.8 - - + +
61E TYR* 1.3 55.7 + - - +
63E GLY* 2.9 4.5 + - - -
64E ILE* 2.8 35.4 + - - +
69E GLU 4.7 1.7 - - - +
71E GLY* 4.0 9.8 - - - -
72E VAL 3.3 32.8 - - - +
73E PHE* 3.7 20.2 - - + +
94E LEU* 6.4 1.6 - - + -
103E LEU* 4.3 12.3 - - + -
141E ARG* 3.4 44.6 - - + +
142E VAL 3.9 2.5 - - - +
143E SER* 3.7 22.9 - - - +
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Residues in contact with TYR 61 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57E ILE* 3.0 23.2 + - + +
58E GLN* 3.9 6.3 - - - +
60E LEU* 1.3 75.5 - - - +
62E ASN* 1.3 66.0 + - - +
64E ILE* 3.3 5.1 + - + +
65E ILE* 2.8 72.5 + - + +
91E GLY 4.7 1.2 + - - -
92E TRP* 3.3 61.6 - + + +
93E ASP 4.8 9.3 + - - -
94E LEU* 4.6 18.8 - - + +
97E LEU* 6.1 4.7 - - + -
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Residues in contact with ASN 62 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23E THR 2.8 28.9 + - - +
24E MET* 3.1 35.0 + - + +
25E ILE* 3.6 4.8 - - - +
58E GLN* 3.2 29.4 + - - +
59E PHE 4.1 0.2 - - - +
61E TYR* 1.3 88.6 - - - +
63E GLY* 1.3 57.4 + - - +
65E ILE* 4.4 2.9 - - - +
66E GLU* 2.6 40.5 + - + +
67E PHE* 5.7 0.2 - - - -
92E TRP* 5.4 1.2 - - - -
141E ARG* 4.9 0.4 - - - +
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Residues in contact with GLY 63 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59E PHE 3.3 5.5 + - - -
60E LEU 2.9 7.6 + - - -
62E ASN* 1.3 77.7 - - - +
64E ILE* 1.3 51.8 + - - +
67E PHE* 3.5 9.0 + - - +
68E ASP 3.2 8.3 + - - -
69E GLU* 2.8 34.6 + - - +
141E ARG* 3.4 36.3 - - - +
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Residues in contact with ILE 64 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60E LEU 2.8 11.4 + - - +
61E TYR* 3.6 9.2 - - - +
63E GLY* 1.3 74.2 - - - +
65E ILE* 1.3 65.6 + - + +
68E ASP* 2.8 29.3 + - - +
69E GLU 3.5 15.1 + - - +
71E GLY 5.6 1.1 - - - +
97E LEU* 5.7 5.2 - - + -
102E LYS* 4.5 29.4 - - + +
103E LEU* 5.8 2.2 - - + -
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Residues in contact with ILE 65 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61E TYR* 2.8 65.3 + - + +
62E ASN* 4.1 3.1 - - - +
64E ILE* 1.3 77.9 - - + +
66E GLU* 1.3 63.5 + - + +
68E ASP* 4.4 1.4 + - - +
97E LEU* 6.4 1.6 - - + -
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Residues in contact with GLU 66 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24E MET* 4.3 18.6 - - + -
62E ASN* 2.6 23.0 + - - +
65E ILE* 1.3 77.6 - - + +
67E PHE* 1.3 80.3 + - + +
68E ASP 3.9 0.2 - - - -
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Residues in contact with PHE 67 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21E MET* 5.9 0.2 - - + -
22E ARG* 3.7 48.5 - - + -
24E MET* 4.1 17.5 - - + -
62E ASN 5.2 0.4 - - - -
63E GLY* 3.5 13.3 + - - +
66E GLU* 1.3 98.3 - - + +
68E ASP* 1.3 73.2 + - - +
69E GLU* 3.4 29.9 + - + +
141E ARG* 3.9 13.0 - - - -
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Residues in contact with ASP 68 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63E GLY 3.2 0.2 + - - -
64E ILE* 2.8 26.4 + - - +
65E ILE 4.4 1.4 + - - +
66E GLU 3.9 0.6 - - - -
67E PHE* 1.3 75.3 - - - +
69E GLU* 1.3 59.0 + - - +
70E PRO* 3.5 11.5 - - - +
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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