Contacts of the helix formed by residues 58 - 72 (chain F) in PDB entry 3EXG
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 SER 58 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177E GLU* 3.5 27.2 + - - +
180E ASN* 5.0 0.7 + - - -
181E MET* 3.4 25.3 - - - +
56F PRO* 3.0 18.9 + - - +
57F ILE* 1.3 73.0 - - - +
59F GLU* 1.3 56.7 + - - +
60F MET 3.3 3.1 - - - -
61F GLY 2.8 19.9 + - - -
62F PHE* 2.8 15.2 + - - -
171G ASN* 3.0 22.2 + - - +
172G GLN* 4.2 0.9 - - - +
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Residues in contact with GLU 59 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28F GLU* 2.6 27.7 - - - +
57F ILE* 3.5 12.0 - - - +
58F SER* 1.3 71.4 + - - +
60F MET* 1.3 63.6 + - - +
62F PHE* 3.5 19.0 - - + -
63F ALA* 3.1 28.4 + - - +
80F PHE* 4.5 8.0 - - + -
81F MET 5.6 0.8 + - - +
85F PHE* 3.5 46.9 - - + +
88F GLN* 3.5 15.9 + - + +
89F ALA* 3.3 9.1 - - + +
172G GLN* 3.3 21.4 + - - +
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Residues in contact with MET 60 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143E PRO* 4.5 0.9 - - - +
174E GLN* 3.7 28.3 - - + +
177E GLU* 3.6 10.2 + - - +
58F SER 3.3 0.8 - - - -
59F GLU* 1.3 77.8 - - - +
61F GLY* 1.3 65.5 + - - +
64F GLY* 3.2 14.7 + - - -
88F GLN* 3.5 31.7 + - + +
89F ALA* 4.1 9.6 - - - -
91F ASP* 3.9 16.4 - - + +
92F GLN* 3.8 35.1 + - - +
60H MET* 6.0 3.8 - - + -
88H GLN* 3.8 48.5 - - + +
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Residues in contact with GLY 61 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143E PRO* 3.8 14.5 - - - +
174E GLN* 5.0 0.4 - - - -
177E GLU* 2.7 23.4 + - - -
178E ALA* 5.3 0.7 - - - -
181E MET* 3.8 14.6 - - - -
58F SER 2.8 4.8 + - - -
60F MET* 1.3 75.1 - - - +
62F PHE* 1.3 64.2 + - - -
64F GLY* 2.9 5.4 + - - -
65F ILE* 2.9 24.0 + - - +
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Residues in contact with PHE 62 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181E MET* 3.5 20.3 - - + +
26F LEU* 4.4 10.0 - - + +
27F GLY* 4.3 7.6 - - - -
28F GLU* 3.7 22.4 - - + -
55F THR* 3.6 36.3 - - + -
56F PRO 3.8 7.2 - - - -
58F SER* 2.8 29.5 + - - -
59F GLU* 3.5 28.9 - - + -
61F GLY* 1.3 72.8 - - - -
63F ALA* 1.3 57.7 + - - +
65F ILE* 3.2 8.5 + - - +
66F ALA* 2.7 28.9 + - - +
78F CYS* 3.8 16.8 - - - -
79F GLU 3.7 23.1 - - - -
80F PHE* 4.1 11.7 - + - -
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Residues in contact with ALA 63 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59F GLU 3.1 20.6 + - - +
60F MET 4.2 0.9 - - - +
62F PHE* 1.3 75.8 - - - +
64F GLY* 1.3 60.3 + - - +
66F ALA* 3.2 2.1 + - - +
67F VAL* 3.0 33.9 + - - +
78F CYS* 4.0 11.9 - - - -
80F PHE* 4.0 16.4 - - + -
89F ALA* 3.6 20.0 - - + +
92F GLN* 4.4 8.1 - - + -
93F VAL* 5.3 0.2 - - + -
114F PHE* 4.4 8.8 - - + -
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Residues in contact with GLY 64 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143E PRO* 3.8 10.8 - - - -
144E LEU* 3.4 12.6 - - - +
60F MET 3.2 4.4 + - - -
61F GLY 2.9 8.2 + - - -
63F ALA* 1.3 78.5 - - - +
65F ILE* 1.3 58.4 + - - +
67F VAL* 3.2 1.3 + - - -
68F GLY 2.8 23.9 + - - -
92F GLN* 3.6 32.5 - - - +
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Residues in contact with ILE 65 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143E PRO* 3.5 20.4 - - + +
146E ALA* 3.8 23.8 - - + +
147E GLY* 3.6 11.5 - - - +
150E LEU* 4.4 16.4 - - + -
178E ALA* 5.5 2.5 - - + -
181E MET* 4.0 22.4 - - + -
185E TRP* 3.9 23.8 - - + -
187E LEU* 4.9 2.2 - - + -
26F LEU* 4.3 16.6 - - + -
61F GLY 2.9 14.1 + - - +
62F PHE* 3.5 9.2 - - - +
64F GLY* 1.3 74.7 - - - +
66F ALA* 1.3 66.9 + - - +
68F GLY* 3.6 0.2 - - - -
69F ALA* 2.9 23.5 + - + +
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Residues in contact with ALA 66 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24F PHE* 5.5 0.7 - - - -
26F LEU* 3.8 15.0 - - + -
62F PHE 2.7 17.3 + - - +
63F ALA 3.5 6.3 - - - +
64F GLY 3.2 0.2 - - - -
65F ILE* 1.3 79.5 - - - +
67F VAL* 1.3 62.7 + - - +
69F ALA* 3.4 2.5 + - - +
70F ALA* 3.1 17.2 + - - +
76F PRO* 3.3 19.4 - - + +
78F CYS* 3.8 21.8 - - + -
112F ILE* 3.6 17.0 - - + -
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Residues in contact with VAL 67 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144E LEU* 3.7 17.3 - - + -
63F ALA 3.0 18.4 + - - +
64F GLY* 3.6 7.6 - - - +
65F ILE 3.1 0.2 - - - -
66F ALA* 1.3 77.7 - - - +
68F GLY* 1.3 61.8 + - - +
70F ALA* 3.0 4.5 + - - +
71F MET* 3.0 26.3 + - - +
92F GLN* 4.1 15.9 - - + +
96F SER 4.0 12.1 - - - +
97F ALA* 4.0 12.6 - - + -
110F VAL* 3.8 20.4 - - + -
112F ILE* 3.9 17.9 - - + -
114F PHE* 3.9 11.9 - - + -
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Residues in contact with GLY 68 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144E LEU* 3.4 32.2 - - - +
147E GLY 3.7 7.4 - - - -
148E ILE* 3.4 16.8 - - - +
64F GLY 2.8 13.6 + - - -
65F ILE 3.1 3.3 + - - -
67F VAL* 1.3 78.1 - - - +
69F ALA* 1.3 59.7 + - - +
71F MET* 3.5 4.9 + - - +
72F ALA* 3.3 15.4 + - - +
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Residues in contact with ALA 69 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147E GLY* 3.4 18.9 + - - +
150E LEU* 4.8 6.1 - - + -
151E ALA* 4.5 0.2 - - - -
24F PHE* 3.9 29.6 - - + -
65F ILE* 2.9 15.0 + - + +
66F ALA 3.8 4.0 - - - +
68F GLY* 1.3 75.7 - - - +
70F ALA* 1.3 59.6 + - - +
72F ALA* 3.0 19.2 + - - +
74F LEU* 3.0 29.4 + - + +
76F PRO* 4.8 0.2 - - + -
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Residues in contact with ALA 70 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66F ALA 3.1 13.2 + - - +
67F VAL 3.0 9.9 + - - +
69F ALA* 1.3 71.8 - - - +
71F MET* 1.3 68.2 + - - +
72F ALA 2.9 1.3 - - - -
73F GLY* 3.0 13.7 + - - -
74F LEU 3.7 10.1 - - - -
76F PRO* 4.0 7.6 - - + +
109F PRO 4.5 0.5 - - - +
110F VAL* 3.8 18.8 - - + -
111F PRO* 3.5 42.0 - - - +
112F ILE* 4.1 3.1 - - + -
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Residues in contact with MET 71 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127E TYR* 4.1 13.7 - - + +
132E TYR* 4.0 41.2 - - + +
135E ASN* 5.4 3.6 - - - +
144E LEU* 4.6 20.9 - - + -
148E ILE* 5.3 1.1 - - + -
67F VAL* 3.0 28.7 + - - +
68F GLY* 3.8 7.4 - - - +
70F ALA* 1.3 78.5 - - - +
72F ALA* 1.3 60.2 + - - +
73F GLY* 3.2 1.4 + - - -
96F SER 4.8 7.2 - - - +
100F THR* 4.3 6.3 - - + +
108F GLN* 3.5 53.0 + - + +
109F PRO 4.2 7.2 - - - +
110F VAL* 4.4 11.4 - - + -
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Residues in contact with ALA 72 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84E HIS* 5.6 5.5 - - + -
132E TYR* 4.2 16.2 + - - +
148E ILE* 4.4 11.4 - - + -
151E ALA* 3.3 29.6 - - + +
155E ASN* 5.2 6.4 + - - -
22F LYS* 5.1 1.4 + - - -
68F GLY 3.3 10.1 + - - +
69F ALA 3.0 11.4 + - - +
70F ALA 2.9 1.0 - - - -
71F MET* 1.3 79.9 - - - +
73F GLY* 1.3 55.1 - - - +
74F LEU* 3.7 0.4 - - - -
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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