Contacts of the helix formed by residues 58 - 72 (chain X) 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 X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171U ASN* 3.2 18.8 + - - +
172U GLN* 3.9 2.7 - - - +
177W GLU* 2.7 44.8 - - - +
180W ASN* 4.7 0.9 + - - -
181W MET* 3.8 9.8 - - - +
28X GLU* 4.2 0.8 + - - -
56X PRO* 2.9 26.5 + - - +
57X ILE* 1.3 74.9 - - - +
59X GLU* 1.3 59.9 + - - +
62X PHE* 3.1 21.2 + - - -
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Residues in contact with GLU 59 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172U GLN* 3.3 21.0 + - - +
177W GLU* 3.7 0.2 + - - -
28X GLU* 2.5 34.0 - - - +
57X ILE* 3.8 5.4 - - - +
58X SER* 1.3 69.1 - - - +
60X MET* 1.3 68.6 + - - +
61X GLY 3.0 0.2 + - - -
62X PHE* 3.6 15.4 - - + -
63X ALA* 2.9 28.2 + - - +
80X PHE* 3.9 18.5 - - + -
81X MET 5.6 0.3 + - - -
85X PHE* 3.6 41.1 - - + +
88X GLN* 3.5 16.7 + - + +
89X ALA* 3.9 2.9 - - + -
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Residues in contact with MET 60 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60V MET* 5.9 6.3 - - + -
88V GLN* 3.1 52.0 - - + +
174W GLN* 3.4 35.9 - - + +
177W GLU* 3.6 11.5 + - - +
58X SER 3.5 0.6 - - - -
59X GLU* 1.3 78.3 - - - +
61X GLY* 1.3 57.6 + - - +
64X GLY* 3.0 22.2 + - - -
88X GLN* 3.3 32.0 + - + +
89X ALA* 4.1 7.4 - - - +
91X ASP* 4.4 10.3 - - + +
92X GLN* 3.5 28.4 + - - +
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Residues in contact with GLY 61 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143W PRO* 3.6 14.9 - - - +
174W GLN 4.9 1.1 - - - -
177W GLU* 2.9 25.7 + - - -
178W ALA* 5.3 0.9 - - - -
181W MET* 3.9 12.6 - - - -
60X MET* 1.3 76.9 - - - +
62X PHE* 1.3 53.3 + - - +
64X GLY* 3.1 2.8 + - - -
65X ILE* 2.7 38.9 + - - +
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Residues in contact with PHE 62 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181W MET* 3.6 19.4 - - - +
185W TRP* 5.3 0.2 - - + -
26X LEU* 4.0 22.9 - - + +
27X GLY* 4.1 8.3 - - - -
28X GLU* 3.9 18.4 - - - -
55X THR* 3.7 24.5 - - + -
56X PRO 4.1 4.0 - - - -
58X SER* 3.1 26.6 + - - -
59X GLU* 3.6 33.0 - - + -
61X GLY* 1.3 69.9 - - - +
63X ALA* 1.3 68.1 + - - +
65X ILE* 3.6 6.7 - - + +
66X ALA* 2.8 24.9 + - - +
78X CYS* 3.6 25.6 - - - -
79X GLU 3.7 20.4 - - - -
80X PHE* 4.3 8.5 - + - -
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Residues in contact with ALA 63 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59X GLU 2.9 18.1 + - - +
60X MET 3.9 1.8 - - - +
62X PHE* 1.3 75.5 - - - +
64X GLY* 1.3 65.3 + - - +
66X ALA* 2.9 15.1 + - - +
67X VAL* 2.9 16.6 + - - +
78X CYS* 4.1 11.4 - - - -
80X PHE* 4.2 12.3 - - + -
89X ALA* 3.5 24.0 - - + +
92X GLN* 4.2 8.5 - - + -
93X VAL* 5.4 0.2 - - + -
114X PHE* 4.5 8.5 - - + -
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Residues in contact with GLY 64 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143W PRO* 3.5 20.6 - - - -
144W LEU* 3.5 12.7 - - - +
60X MET 3.0 9.7 + - - -
61X GLY 3.4 3.4 - - - -
63X ALA* 1.3 77.2 - - - +
65X ILE* 1.3 62.3 + - - +
67X VAL* 3.3 1.4 + - - -
68X GLY 3.0 18.7 + - - -
92X GLN* 3.6 23.5 - - - +
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Residues in contact with ILE 65 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143W PRO* 3.6 20.4 - - + +
146W ALA* 4.0 20.4 - - + +
147W GLY* 3.2 14.2 - - - -
150W LEU* 4.0 22.7 - - + -
178W ALA* 5.1 4.3 - - - -
181W MET* 3.9 36.6 - - + -
185W TRP* 4.0 16.4 - - + -
187W LEU* 5.2 1.3 - - + -
26X LEU* 4.7 5.8 - - + -
61X GLY* 2.7 21.1 + - - +
62X PHE* 3.6 6.5 - - - +
63X ALA 3.2 0.2 - - - -
64X GLY* 1.3 74.5 - - - +
66X ALA* 1.3 64.1 + - - +
68X GLY 3.2 0.3 + - - -
69X ALA* 3.0 20.8 + - - +
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Residues in contact with ALA 66 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24X PHE* 5.2 1.3 - - - -
26X LEU* 4.0 14.3 - - + +
62X PHE 2.8 17.5 + - - +
63X ALA 3.3 8.1 - - - +
65X ILE* 1.3 72.5 - - - +
67X VAL* 1.3 65.9 + - - +
69X ALA* 3.1 8.0 + - - +
70X ALA 2.9 18.4 + - - -
76X PRO* 3.6 15.7 - - + +
78X CYS* 3.8 21.3 - - + -
112X ILE* 3.5 19.5 - - + -
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Residues in contact with VAL 67 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144W LEU* 3.6 19.1 - - + -
63X ALA 2.9 17.3 + - - +
64X GLY* 3.7 8.1 - - - +
66X ALA* 1.3 76.6 - - - +
68X GLY* 1.3 64.5 + - - +
70X ALA* 3.0 15.0 + - - +
71X MET* 3.0 17.8 + - - +
92X GLN* 4.2 16.4 - - + +
96X SER* 4.0 19.7 - - - +
97X ALA* 4.5 3.1 - - + -
110X VAL* 4.0 16.6 - - + -
112X ILE* 3.8 19.7 - - + -
114X PHE* 4.1 12.3 - - + -
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Residues in contact with GLY 68 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144W LEU* 3.5 30.7 - - - +
148W ILE* 3.3 23.4 - - - +
64X GLY 3.0 12.4 + - - -
65X ILE 3.8 1.6 - - - -
66X ALA 3.2 0.2 - - - -
67X VAL* 1.3 76.9 - - - +
69X ALA* 1.3 61.1 + - - +
71X MET* 3.2 8.1 + - - +
72X ALA 3.2 15.4 + - - -
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Residues in contact with ALA 69 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147W GLY 3.5 17.5 - - - +
150W LEU* 4.5 6.1 - - + -
151W ALA* 4.3 4.0 - - - -
24X PHE* 4.0 26.5 - - + -
65X ILE 3.0 13.0 + - - +
66X ALA 3.4 8.3 - - - +
68X GLY* 1.3 71.7 - - - +
70X ALA* 1.3 67.0 + - - +
72X ALA* 2.9 14.0 + - - +
74X LEU* 3.1 30.3 + - + +
76X PRO* 4.8 0.2 - - + -
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Residues in contact with ALA 70 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66X ALA 2.9 12.5 + - - +
67X VAL 3.0 9.2 + - - +
69X ALA* 1.3 75.7 - - - +
71X MET* 1.3 58.8 + - - +
73X GLY* 2.9 18.9 + - - -
74X LEU 3.3 17.5 - - - +
76X PRO* 3.7 18.6 - - + +
109X PRO 4.6 0.2 - - - +
110X VAL* 3.9 20.6 - - + -
111X PRO* 3.6 23.2 - - - +
112X ILE* 4.2 2.7 - - + +
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Residues in contact with MET 71 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127W TYR* 4.3 9.4 - - + +
132W TYR* 3.5 54.0 - - + +
135W ASN* 5.8 1.1 - - - +
144W LEU* 4.6 15.9 - - + -
148W ILE* 5.2 1.3 - - + -
67X VAL* 3.0 27.1 + - - +
68X GLY* 3.6 13.9 - - - +
69X ALA 3.1 0.4 - - - -
70X ALA* 1.3 76.9 - - - +
72X ALA* 1.3 57.2 + - - +
73X GLY 3.0 4.4 + - - -
96X SER 4.9 4.9 - - - +
100X THR* 4.6 4.7 - - + +
108X GLN* 3.3 46.9 + - + +
109X PRO 4.3 0.9 - - - -
110X VAL* 4.2 17.3 - - + -
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Residues in contact with ALA 72 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84W HIS* 5.4 5.6 - - + -
132W TYR* 4.2 10.3 - - - +
148W ILE* 4.3 16.6 - - + -
151W ALA* 3.5 26.0 - - + -
155W ASN* 4.7 9.1 + - - +
68X GLY 3.2 9.4 + - - +
69X ALA 2.9 10.7 + - - +
71X MET* 1.3 76.6 - - - +
73X GLY* 1.3 59.5 + - - +
74X LEU* 3.3 5.3 + - - +
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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