Contacts of the helix formed by residues 58 - 72 (chain Z) 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 Z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1711 ASN* 3.2 27.9 + - - +
1721 GLN* 3.9 0.2 - - - +
177Y GLU* 3.3 24.3 + - - +
180Y ASN* 5.1 0.5 + - - -
181Y MET* 3.5 22.9 - - - +
56Z PRO* 2.8 20.7 + - - +
57Z ILE* 1.3 74.2 + - - +
59Z GLU* 1.3 67.8 + - - +
60Z MET 3.4 1.8 - - - -
61Z GLY 2.8 13.0 + - - -
62Z PHE* 2.9 12.6 + - - -
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Residues in contact with GLU 59 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1721 GLN* 3.0 22.3 + - - +
177Y GLU* 4.3 0.2 + - - -
28Z GLU* 2.8 23.9 - - - +
57Z ILE* 3.4 11.9 - - - +
58Z SER* 1.3 74.4 - - - +
60Z MET* 1.3 63.4 + - - +
61Z GLY 3.1 0.2 + - - -
62Z PHE* 3.4 22.6 - - + -
63Z ALA* 2.9 28.8 + - - +
80Z PHE* 4.4 9.6 - - + -
81Z MET 6.3 0.2 - - - +
85Z PHE* 3.3 45.8 - - + +
88Z GLN* 3.2 18.9 + - + +
89Z ALA* 3.9 7.2 - - + -
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Residues in contact with MET 60 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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602 MET* 5.7 4.0 - - + -
882 GLN* 3.7 37.2 - - + +
143Y PRO* 4.6 0.9 - - - +
174Y GLN* 3.2 48.5 - - + +
177Y GLU* 3.9 6.8 + - - +
58Z SER 3.1 1.0 + - - -
59Z GLU* 1.3 76.4 - - - +
61Z GLY* 1.3 57.9 + - - +
63Z ALA* 4.0 0.2 - - - +
64Z GLY* 3.1 21.3 + - - -
88Z GLN* 3.3 36.2 + - + +
89Z ALA* 3.6 15.0 - - - +
91Z ASP* 4.0 11.7 - - + +
92Z GLN* 3.8 31.1 + - - +
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Residues in contact with GLY 61 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143Y PRO* 3.7 15.4 - - - +
174Y GLN 4.8 0.7 - - - -
177Y GLU* 2.9 21.0 + - - -
178Y ALA* 5.8 0.2 - - - -
181Y MET* 3.6 13.7 - - - -
58Z SER 2.8 8.7 + - - -
60Z MET* 1.3 74.2 - - - +
62Z PHE* 1.3 64.8 + - - -
63Z ALA 3.1 0.9 - - - -
64Z GLY* 3.1 4.3 + - - -
65Z ILE* 2.9 23.3 + - - +
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Residues in contact with PHE 62 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181Y MET* 3.3 24.3 - - - +
26Z LEU* 4.2 11.6 - - + +
27Z GLY* 4.5 4.3 - - - -
28Z GLU* 3.8 17.7 - - + -
55Z THR* 3.3 36.6 - - + -
56Z PRO 3.7 4.5 - - - -
58Z SER* 2.9 33.6 + - - -
59Z GLU* 3.4 36.3 - - + -
61Z GLY* 1.3 73.0 - - - -
63Z ALA* 1.3 59.5 + - - +
65Z ILE* 3.2 5.8 + - - +
66Z ALA* 2.9 27.4 + - - +
78Z CYS* 4.2 9.0 - - - -
79Z GLU 4.0 19.7 - - - -
80Z PHE* 4.1 20.4 - + - -
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Residues in contact with ALA 63 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59Z GLU 2.9 19.2 + - - +
60Z MET 4.0 1.1 - - - +
62Z PHE* 1.3 76.8 - - - +
64Z GLY* 1.3 67.0 + - - +
66Z ALA* 3.1 4.7 + - - +
67Z VAL* 3.0 26.3 + - - +
78Z CYS* 4.3 7.9 - - - -
80Z PHE* 4.1 18.4 - - + -
89Z ALA* 3.5 23.3 - - + +
92Z GLN* 4.4 7.6 - - + -
114Z PHE* 4.6 6.2 - - + -
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Residues in contact with GLY 64 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143Y PRO* 3.9 12.8 - - - -
144Y LEU* 3.7 6.7 - - - -
60Z MET 3.1 6.9 + - - -
61Z GLY 3.1 7.1 + - - -
63Z ALA* 1.3 81.4 - - - +
65Z ILE* 1.3 55.5 + - - +
67Z VAL* 3.2 4.2 + - - +
68Z GLY* 2.8 26.2 + - - -
92Z GLN* 3.7 30.0 - - - +
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Residues in contact with ILE 65 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143Y PRO* 3.3 21.5 - - + +
146Y ALA* 3.9 21.1 - - + +
147Y GLY* 3.6 11.5 - - - +
150Y LEU* 4.5 19.7 - - + -
178Y ALA* 5.1 3.4 - - - -
181Y MET* 3.9 40.4 - - + -
185Y TRP* 4.1 14.8 - - + -
187Y LEU* 5.1 2.7 - - + -
26Z LEU* 4.5 6.7 - - + -
61Z GLY 2.9 12.1 + - - +
62Z PHE* 3.4 9.6 - - - +
64Z GLY* 1.3 72.9 - - - +
66Z ALA* 1.3 69.0 + - - +
68Z GLY 3.2 0.2 + - - -
69Z ALA* 2.9 22.0 + - - +
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Residues in contact with ALA 66 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24Z PHE* 5.2 1.3 - - - -
26Z LEU* 3.8 14.1 - - + -
62Z PHE 2.9 13.5 + - - +
63Z ALA 3.1 6.7 + - - +
65Z ILE* 1.3 81.3 - - - +
67Z VAL* 1.3 62.9 + - - +
69Z ALA* 3.1 2.7 + - - -
70Z ALA* 3.0 18.4 + - - +
76Z PRO* 3.4 17.9 - - + +
78Z CYS* 3.8 20.0 - - + -
112Z ILE* 3.6 21.8 - - + -
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Residues in contact with VAL 67 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144Y LEU* 3.4 19.7 - - + -
63Z ALA 3.0 16.9 + - - +
64Z GLY* 3.2 8.9 + - - +
66Z ALA* 1.3 75.9 - - - +
68Z GLY* 1.3 61.1 + - - +
70Z ALA* 3.2 5.4 + - - +
71Z MET* 3.1 25.3 + - - +
92Z GLN* 3.8 19.3 - - + +
96Z SER* 3.9 24.5 - - - +
97Z ALA* 4.3 3.8 - - + -
110Z VAL* 4.0 13.7 - - + -
112Z ILE* 3.8 5.8 - - + +
114Z PHE* 3.9 21.1 - - + -
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Residues in contact with GLY 68 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144Y LEU* 3.4 30.9 - - - +
147Y GLY* 3.8 6.3 - - - -
148Y ILE* 3.8 11.6 - - - +
64Z GLY 2.8 16.1 + - - -
65Z ILE 3.6 3.1 - - - -
66Z ALA 3.1 0.4 - - - -
67Z VAL* 1.3 72.2 - - - +
69Z ALA* 1.3 65.7 + - - +
70Z ALA 3.2 0.5 + - - -
71Z MET* 3.2 13.7 + - - +
72Z ALA* 3.3 8.5 + - - +
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Residues in contact with ALA 69 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147Y GLY 3.5 17.7 + - - +
150Y LEU* 4.3 7.9 - - + -
151Y ALA* 4.5 1.1 - - + -
24Z PHE* 3.9 29.4 - - + -
65Z ILE 2.9 16.2 + - - +
66Z ALA 3.7 3.8 - - - +
68Z GLY* 1.3 74.0 - - - +
70Z ALA* 1.3 60.9 + - - +
72Z ALA* 3.1 14.2 + - - +
73Z GLY 3.2 0.5 + - - -
74Z LEU* 2.9 31.1 + - + +
76Z PRO* 4.6 0.2 - - + -
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Residues in contact with ALA 70 (chain Z).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66Z ALA 3.0 16.1 + - - +
67Z VAL 3.6 5.6 - - - +
68Z GLY 3.0 0.4 - - - -
69Z ALA* 1.3 75.6 - - - +
71Z MET* 1.3 61.2 + - - +
73Z GLY* 2.8 17.3 + - - -
74Z LEU 3.6 9.4 - - - -
76Z PRO* 3.9 7.4 - - + -
109Z PRO 4.5 0.5 - - - +
110Z VAL* 4.1 9.4 - - + -
111Z PRO* 3.2 50.1 - - + +
112Z ILE* 4.3 4.3 - - + -
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Residues in contact with MET 71 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127Y TYR* 4.3 7.2 - - + -
132Y TYR* 3.7 52.7 + - + +
135Y ASN* 5.7 0.9 - - - +
144Y LEU* 4.1 28.7 - - + -
148Y ILE* 5.4 2.9 - - + -
67Z VAL* 3.1 18.1 + - - +
68Z GLY* 3.2 8.3 + - - +
70Z ALA* 1.3 77.3 - - - +
72Z ALA* 1.3 58.0 + - - +
73Z GLY* 3.2 4.0 + - - -
96Z SER 4.6 8.5 - - - +
100Z THR* 4.6 5.2 - - + +
108Z GLN* 3.4 44.8 + - + +
109Z PRO 4.1 7.6 - - - +
110Z VAL* 4.3 9.6 - - + -
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Residues in contact with ALA 72 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84Y HIS* 5.6 4.4 - - + -
132Y TYR* 4.1 16.6 - - - +
148Y ILE* 4.5 13.5 - - + -
151Y ALA* 3.6 25.6 - - + +
155Y ASN* 5.1 4.5 + - - -
68Z GLY 3.3 8.6 + - - +
69Z ALA 3.1 10.0 + - - +
70Z ALA 3.0 0.8 - - - -
71Z MET* 1.3 77.2 - - - +
73Z GLY* 1.3 60.2 + - - +
74Z LEU* 3.6 4.0 - - - +
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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
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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