Contacts of the helix formed by residues 58 - 72 (chain T) 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 T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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171Q ASN* 3.2 27.7 + - - +
172Q GLN* 3.7 5.6 - - - +
177S GLU* 3.4 26.8 + - - +
180S ASN* 4.9 0.9 + - - -
181S MET* 4.3 12.8 - - - -
56T PRO* 3.0 18.6 + - - +
57T ILE* 1.3 75.4 + - - +
59T GLU* 1.3 68.6 + - - +
60T MET 3.3 2.2 - - - -
61T GLY 3.0 2.9 + - - -
62T PHE* 2.9 24.0 + - - -
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Residues in contact with GLU 59 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138Q VAL* 5.9 0.7 - - - +
172Q GLN* 3.6 14.4 + - - +
177S GLU* 4.5 0.2 + - - -
28T GLU* 2.7 26.1 - - - +
57T ILE* 3.8 7.8 - - - +
58T SER* 1.3 77.9 + - - +
60T MET* 1.3 67.6 + - - +
61T GLY 3.0 0.9 + - - -
62T PHE* 3.6 21.3 - - + -
63T ALA* 3.1 24.6 + - - +
80T PHE* 4.2 14.8 - - + -
81T MET 6.2 0.2 - - - +
85T PHE* 3.4 47.7 - - + +
88T GLN* 3.6 17.6 + - + +
89T ALA* 4.4 2.7 - - + -
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Residues in contact with MET 60 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60R MET* 6.2 2.0 - - + -
88R GLN* 3.6 37.5 - - + +
172S GLN* 5.8 0.2 - - - +
174S GLN* 3.3 37.9 - - + +
177S GLU* 3.7 11.2 + - - +
58T SER 3.3 0.6 - - - -
59T GLU* 1.3 80.8 - - - +
61T GLY* 1.3 60.4 + - - +
64T GLY* 3.3 14.7 + - - -
88T GLN* 3.4 38.3 + - + +
89T ALA* 4.3 5.4 - - - +
91T ASP* 3.8 21.3 - - + +
92T GLN* 3.7 24.1 + - - +
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Residues in contact with GLY 61 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143S PRO* 3.6 17.1 - - - +
174S GLN 4.9 0.9 - - - -
177S GLU* 2.6 30.2 + - - -
181S MET* 3.4 12.5 - - - +
58T SER 3.0 1.6 + - - -
60T MET* 1.3 75.5 - - - +
62T PHE* 1.3 58.1 + - - -
65T ILE* 2.9 31.9 + - - +
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Residues in contact with PHE 62 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181S MET* 3.5 22.6 - - - +
26T LEU* 4.0 10.0 - - + +
27T GLY* 4.2 7.4 - - - -
28T GLU* 3.7 21.1 - - + -
55T THR* 3.6 35.4 - - + -
56T PRO 3.8 7.9 - - - -
58T SER* 2.9 28.2 + - - -
59T GLU* 3.6 29.4 - - + -
61T GLY* 1.3 70.0 - - - -
63T ALA* 1.3 69.1 + - - +
65T ILE* 3.6 4.3 - - - +
66T ALA* 2.9 24.4 + - - +
78T CYS* 3.8 17.7 - - - -
79T GLU 3.6 25.1 - - - -
80T PHE* 4.2 9.2 - + - -
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Residues in contact with ALA 63 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59T GLU 3.1 16.9 + - - +
60T MET 4.2 1.6 - - - +
62T PHE* 1.3 78.6 - - - +
64T GLY* 1.3 56.3 + - - +
66T ALA* 3.2 4.7 + - - +
67T VAL* 2.8 34.3 + - - +
78T CYS* 4.0 11.4 - - - -
80T PHE* 3.8 16.4 - - + -
89T ALA* 3.6 24.2 - - + +
92T GLN* 4.4 7.6 - - + -
112T ILE* 4.4 0.7 - - - +
114T PHE* 4.4 7.6 - - + -
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Residues in contact with GLY 64 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143S PRO* 3.4 11.6 - - - +
144S LEU* 3.4 11.1 - - - +
60T MET 3.3 9.4 + - - -
61T GLY 3.7 3.4 - - - -
63T ALA* 1.3 78.6 - - - +
65T ILE* 1.3 61.5 + - - +
67T VAL* 4.3 3.8 - - - -
68T GLY 3.2 16.5 + - - -
92T GLN* 3.3 34.1 - - - +
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Residues in contact with ILE 65 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143S PRO* 3.5 17.9 - - + +
146S ALA* 3.9 20.6 - - + +
147S GLY* 3.3 11.9 - - - -
150S LEU* 3.8 29.6 - - + -
178S ALA* 5.3 2.0 - - + -
181S MET* 3.5 45.8 - - + -
185S TRP* 3.9 9.2 - - + -
187S LEU* 5.1 2.2 - - + -
26T LEU* 4.3 10.3 - - + -
61T GLY 2.9 17.8 + - - +
62T PHE* 3.6 5.6 - - - +
63T ALA 3.2 0.2 - - - -
64T GLY* 1.3 72.9 - - - +
66T ALA* 1.3 69.2 + - - +
68T GLY 2.9 12.8 + - - -
69T ALA* 2.9 10.9 + - - +
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Residues in contact with ALA 66 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24T PHE* 4.9 0.7 - - - -
26T LEU* 3.7 27.4 - - + -
62T PHE 2.9 16.6 + - - +
63T ALA 3.5 7.6 - - - +
65T ILE* 1.3 76.8 - - - +
67T VAL* 1.3 64.8 + - - +
69T ALA* 3.1 5.4 + - - +
70T ALA 3.0 16.5 + - - -
76T PRO* 3.2 19.2 - - + +
78T CYS* 4.0 6.7 - - + -
112T ILE* 3.6 17.7 - - + -
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Residues in contact with VAL 67 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144S LEU* 3.4 17.7 - - + -
63T ALA 2.8 21.8 + - - +
64T GLY* 3.7 8.1 - - - +
65T ILE 3.1 0.4 - - - -
66T ALA* 1.3 78.0 - - - +
68T GLY* 1.3 55.5 + - - +
70T ALA* 3.2 5.5 + - - +
71T MET* 2.9 31.4 + - - +
92T GLN* 4.7 10.1 - - + +
96T SER* 4.3 19.1 - - - +
97T ALA* 4.2 10.8 - - + -
110T VAL* 4.1 15.0 - - + +
112T ILE* 3.7 19.7 - - + -
114T PHE* 4.2 11.7 - - + -
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Residues in contact with GLY 68 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144S LEU* 3.2 33.8 - - - +
147S GLY 3.8 6.3 - - - -
148S ILE* 3.7 6.0 - - - +
64T GLY 3.2 6.3 + - - -
65T ILE 2.9 9.4 + - - -
67T VAL* 1.3 69.7 - - - +
69T ALA* 1.3 67.3 + - - +
70T ALA 3.1 0.7 + - - -
71T MET* 3.3 7.7 + - - +
72T ALA* 3.1 21.8 + - - +
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Residues in contact with ALA 69 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147S GLY 3.6 17.6 - - - +
150S LEU* 4.8 6.3 - - + -
151S ALA* 4.4 5.1 - - - +
24T PHE* 3.8 32.8 - - + -
65T ILE 2.9 10.5 + - - +
66T ALA* 3.1 10.1 + - - +
68T GLY* 1.3 75.1 - - - +
70T ALA* 1.3 61.9 + - - +
72T ALA* 3.1 11.8 + - - +
74T LEU* 3.1 29.3 + - + +
76T PRO* 4.5 0.4 - - + -
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Residues in contact with ALA 70 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66T ALA 3.0 6.5 + - - +
67T VAL 3.3 9.0 - - - +
68T GLY 3.1 0.2 - - - -
69T ALA* 1.3 71.8 - - - +
71T MET* 1.3 65.0 + - - +
72T ALA 2.8 6.1 + - - -
73T GLY* 2.9 13.3 + - - -
74T LEU 3.1 16.7 - - - +
76T PRO* 3.7 22.9 - - + +
109T PRO 4.6 0.2 - - - +
110T VAL* 3.9 17.3 - - + -
111T PRO* 3.9 23.0 - - - +
112T ILE* 4.1 4.5 - - + -
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Residues in contact with MET 71 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127S TYR* 3.8 31.4 - - + +
132S TYR* 3.6 35.2 - - + +
135S ASN* 4.7 7.0 - - - +
144S LEU* 4.2 30.7 - - + -
148S ILE* 5.3 1.6 - - + -
67T VAL* 2.9 16.2 + - - +
68T GLY* 3.5 10.5 - - - +
70T ALA* 1.3 75.5 - - - +
72T ALA* 1.3 57.7 + - - +
73T GLY 3.4 1.1 + - - -
96T SER 4.8 3.8 - - - +
100T THR* 4.0 11.7 - - + +
108T GLN* 3.1 42.3 + - + +
109T PRO 4.0 2.9 - - - -
110T VAL* 3.9 17.2 - - + +
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Residues in contact with ALA 72 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84S HIS* 5.6 4.7 - - + -
132S TYR* 3.9 18.1 + - - +
148S ILE* 4.4 12.8 - - + -
151S ALA* 3.5 27.5 - - + +
155S ASN* 5.1 5.4 + - - -
68T GLY 3.1 9.4 + - - +
69T ALA 3.1 10.5 + - - +
70T ALA 2.8 1.6 + - - -
71T MET* 1.3 75.2 - - - +
73T GLY* 1.3 57.9 + - - +
74T LEU* 3.6 2.7 + - - +
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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