Contacts of the helix formed by residues 58 - 72 (chain N) 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 N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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177M GLU* 3.6 22.6 - - - +
180M ASN* 5.4 0.2 + - - -
181M MET* 3.4 25.2 - - - +
56N PRO* 2.9 15.2 + - - +
57N ILE* 1.3 74.4 + - - +
59N GLU* 1.3 61.6 + - - +
60N MET 3.5 1.8 - - - -
61N GLY 3.0 2.1 + - - -
62N PHE* 2.8 29.1 + - - -
171O ASN* 3.1 30.5 + - - +
172O GLN* 3.9 1.6 - - - +
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Residues in contact with GLU 59 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177M GLU* 4.6 0.2 + - - -
28N GLU* 2.6 30.7 - - - +
57N ILE* 3.5 11.9 - - - +
58N SER* 1.3 70.7 - - - +
60N MET* 1.3 64.0 + - - +
62N PHE* 3.6 14.6 - - + -
63N ALA* 2.9 29.8 + - - +
80N PHE* 4.5 7.0 - - + -
85N PHE* 3.5 45.0 - - + +
88N GLN* 3.2 21.3 + - + +
89N ALA* 3.9 6.3 - - + -
172O GLN* 3.1 22.4 + - - +
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Residues in contact with MET 60 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143M PRO* 4.5 0.5 - - - +
172M GLN* 4.9 0.4 - - - +
174M GLN* 3.5 48.0 - - + +
177M GLU* 3.8 7.0 + - - +
58N SER 3.5 0.4 - - - -
59N GLU* 1.3 76.8 - - - +
61N GLY* 1.3 59.4 + - - +
64N GLY* 2.9 26.0 + - - -
88N GLN* 3.5 24.8 + - + +
89N ALA* 3.8 13.9 - - - +
91N ASP* 4.3 16.8 - - - +
92N GLN* 3.9 20.8 + - + +
60P MET* 6.4 3.4 - - + -
88P GLN* 3.5 34.5 - - + +
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Residues in contact with GLY 61 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143M PRO* 3.6 19.6 - - - +
174M GLN* 4.9 1.8 - - - +
177M GLU* 2.7 34.3 + - - -
178M ALA* 5.8 0.2 - - - -
181M MET* 4.0 5.2 - - - -
58N SER 3.0 2.3 + - - -
60N MET* 1.3 78.4 - - - +
62N PHE* 1.3 60.9 + - - -
64N GLY* 3.1 5.2 + - - -
65N ILE* 3.0 19.8 + - - +
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Residues in contact with PHE 62 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181M MET* 3.6 24.4 - - - +
26N LEU* 3.9 11.4 - - + +
27N GLY* 4.6 2.9 - - - -
28N GLU* 3.6 23.3 - - + -
55N THR* 3.4 37.5 - - + -
56N PRO 3.6 12.6 - - - -
58N SER* 2.8 30.8 + - - -
59N GLU* 3.6 27.1 - - + -
61N GLY* 1.3 69.6 - - - -
63N ALA* 1.3 62.8 + - - +
65N ILE* 2.9 7.5 + - - +
66N ALA* 2.8 27.4 + - - +
78N CYS* 3.9 16.6 - - - -
79N GLU 3.8 22.7 - - - -
80N PHE* 4.4 9.0 - + - -
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Residues in contact with ALA 63 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59N GLU 2.9 18.8 + - - +
60N MET 4.2 0.2 - - - +
62N PHE* 1.3 77.6 - - + +
64N GLY* 1.3 66.4 + - - +
66N ALA* 3.2 3.0 + - - +
67N VAL* 2.9 28.0 + - - +
78N CYS* 4.2 8.5 - - - -
80N PHE* 4.1 19.3 - - + -
89N ALA* 3.7 21.5 - - + -
92N GLN* 4.5 5.6 - - + -
93N VAL* 5.5 0.2 - - + -
114N PHE* 4.3 9.6 - - + -
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Residues in contact with GLY 64 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143M PRO* 3.9 12.1 - - - -
144M LEU* 3.5 9.9 - - - +
60N MET 2.9 16.6 + - - -
61N GLY 3.4 4.7 - - - -
63N ALA* 1.3 78.3 - - - +
65N ILE* 1.3 55.2 + - - +
67N VAL* 3.1 2.3 + - - -
68N GLY* 2.8 24.4 + - - -
92N GLN* 3.8 26.3 - - - +
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Residues in contact with ILE 65 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143M PRO* 3.5 20.0 - - + +
146M ALA* 3.8 21.1 - - + +
147M GLY* 3.6 12.5 - - - -
150M LEU* 4.0 24.2 - - + -
178M ALA* 5.3 4.0 - - - -
181M MET* 3.7 41.3 - - + -
185M TRP* 4.2 11.2 - - + -
187M LEU* 5.3 1.6 - - + -
26N LEU* 4.5 5.6 - - + -
61N GLY 3.0 14.5 + - - +
62N PHE* 2.9 9.4 + - - +
64N GLY* 1.3 72.9 - - - +
66N ALA* 1.3 69.9 + - - +
69N ALA* 2.9 24.1 + - - +
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Residues in contact with ALA 66 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24N PHE* 5.3 0.9 - - - -
26N LEU* 3.8 13.9 - - + +
62N PHE 2.8 12.0 + - - +
63N ALA 3.5 8.5 - - - +
65N ILE* 1.3 79.9 - - - +
67N VAL* 1.3 65.0 + - - +
69N ALA* 3.7 2.4 - - - +
70N ALA* 2.9 24.3 + - - +
76N PRO* 3.5 13.5 - - + +
78N CYS* 3.7 21.8 - - + -
112N ILE* 3.6 18.8 - - + -
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Residues in contact with VAL 67 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144M LEU* 3.7 17.7 - - + -
63N ALA 2.9 16.2 + - - +
64N GLY* 3.1 6.9 + - - +
66N ALA* 1.3 76.1 - - - +
68N GLY* 1.3 61.5 + - - +
70N ALA* 3.3 4.0 + - - +
71N MET* 3.1 25.8 + - - +
92N GLN* 4.1 15.5 - - + +
96N SER* 4.1 5.4 - - - +
97N ALA* 4.0 20.2 - - + +
110N VAL* 3.8 18.8 - - + -
112N ILE* 3.8 6.7 - - + -
114N PHE* 3.7 25.6 - - + -
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Residues in contact with GLY 68 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144M LEU* 3.3 31.4 - - - +
147M GLY 3.9 6.5 - - - -
148M ILE* 3.8 6.2 - - - +
64N GLY 2.8 11.6 + - - -
65N ILE 3.1 2.0 + - - -
67N VAL* 1.3 74.4 - - - +
69N ALA* 1.3 65.4 + - - +
70N ALA 3.0 1.1 - - - -
71N MET* 3.0 18.2 + - - +
72N ALA* 3.1 12.8 + - - +
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Residues in contact with ALA 69 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147M GLY 3.4 22.1 + - - +
150M LEU* 4.5 7.2 - - + -
151M ALA* 4.5 1.6 - - - -
24N PHE* 4.0 28.9 - - + -
65N ILE 2.9 19.1 + - - +
66N ALA 3.7 3.1 - - - +
68N GLY* 1.3 70.0 - - - -
70N ALA* 1.3 63.9 + - - +
72N ALA* 3.0 15.4 + - - +
73N GLY 3.3 0.5 + - - -
74N LEU* 3.1 25.9 + - + +
76N PRO* 4.6 0.2 - - + -
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Residues in contact with ALA 70 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66N ALA 2.9 18.5 + - - +
67N VAL 3.5 6.1 - - - +
68N GLY 3.0 0.4 - - - -
69N ALA* 1.3 76.4 - - - +
71N MET* 1.3 58.1 + - - +
73N GLY* 2.9 18.5 + - - -
74N LEU 3.6 11.3 - - - +
76N PRO* 3.9 15.9 - - + -
109N PRO 4.6 0.2 - - - +
110N VAL* 4.3 4.5 - - + -
111N PRO* 3.4 28.7 - - + +
112N ILE* 4.1 18.2 - - + -
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Residues in contact with MET 71 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127M TYR* 4.2 8.3 - - + +
132M TYR* 3.9 44.1 - - + +
135M ASN* 5.5 0.9 - - - +
144M LEU* 4.2 29.2 - - + -
148M ILE* 5.4 2.0 - - + -
67N VAL* 3.1 20.9 + - - +
68N GLY* 3.0 10.4 + - - +
70N ALA* 1.3 77.5 - - - +
72N ALA* 1.3 56.4 + - - +
73N GLY* 3.0 3.9 + - - -
96N SER 4.9 7.6 - - - +
100N THR* 4.6 5.4 - - + +
108N GLN* 3.2 55.7 + - + +
109N PRO* 4.0 9.1 - - - +
110N VAL* 4.3 8.5 - - + -
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Residues in contact with ALA 72 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84M HIS* 5.5 5.0 - - + -
132M TYR* 4.0 17.7 - - - +
148M ILE* 4.3 15.5 - - + -
151M ALA* 3.6 23.8 - - + +
155M ASN* 5.0 4.9 + - - -
68N GLY 3.1 10.9 + - - +
69N ALA* 3.0 10.9 + - - +
70N ALA 3.0 0.6 - - - -
71N MET* 1.3 76.1 - - - +
73N GLY* 1.3 59.9 + - - +
74N LEU* 3.6 5.0 + - - +
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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