Contacts of the helix formed by residues 58 - 72 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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171I ASN* 3.6 12.8 + - - +
172I GLN* 4.5 0.2 - - - +
177K GLU* 3.5 30.6 - - - +
180K ASN* 4.3 2.3 + - - -
181K MET* 3.7 19.4 - - - +
56L PRO* 3.0 26.8 + - - +
57L ILE* 1.3 78.3 + - - +
59L GLU* 1.3 65.2 + - - +
60L MET 3.5 2.2 - - - -
61L GLY 3.0 1.0 + - - -
62L PHE* 2.9 23.6 + - - -
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Residues in contact with GLU 59 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172I GLN* 3.6 11.4 + - - +
177K GLU* 4.4 1.2 + - - -
28L GLU* 2.6 32.2 - - - +
57L ILE* 3.5 18.4 - - - +
58L SER* 1.3 67.4 - - - +
60L MET* 1.3 71.0 + - - +
61L GLY 2.9 1.0 + - - -
62L PHE* 3.5 14.4 - - + -
63L ALA* 3.1 25.5 + - - +
80L PHE* 4.1 11.7 - - + -
85L PHE* 3.5 47.4 - - + +
88L GLN* 3.8 15.9 - - + +
89L ALA* 3.9 8.1 - - + -
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Residues in contact with MET 60 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60J MET* 6.2 1.6 - - + -
88J GLN* 3.7 43.5 - - + +
174K GLN* 3.5 32.8 - - + +
177K GLU* 3.5 10.0 + - - +
58L SER 3.5 0.6 - - - -
59L GLU* 1.3 80.1 - - - +
61L GLY* 1.3 60.8 + - - +
64L GLY* 3.2 15.2 + - - -
88L GLN* 3.4 33.5 - - - +
89L ALA* 3.9 11.1 - - - +
91L ASP* 3.9 13.7 - - + +
92L GLN* 3.5 36.9 + - - +
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Residues in contact with GLY 61 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143K PRO* 3.6 17.9 - - - +
174K GLN* 4.9 0.4 - - - -
177K GLU* 2.5 35.1 + - - -
178K ALA* 5.2 1.1 - - - -
181K MET* 3.8 6.7 - - - -
58L SER 3.0 1.1 + - - -
59L GLU 2.9 1.8 + - - -
60L MET* 1.3 74.5 - - - +
62L PHE* 1.3 58.2 + - - -
64L GLY* 3.0 5.4 + - - -
65L ILE* 2.8 24.9 + - - +
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Residues in contact with PHE 62 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181K MET* 3.4 23.2 - - - +
26L LEU* 3.8 10.6 - - + +
27L GLY* 4.7 4.9 - - - -
28L GLU* 3.7 23.3 - - + -
55L THR* 3.9 28.5 - - + -
56L PRO 4.0 13.2 - - - -
58L SER* 2.9 30.2 + - - -
59L GLU* 3.5 28.3 - - + -
61L GLY* 1.3 71.3 - - - -
63L ALA* 1.3 57.8 + - - +
65L ILE* 3.0 9.7 + - + +
66L ALA* 2.8 27.5 + - - +
78L CYS* 3.7 25.8 - - - -
79L GLU 4.0 17.5 - - - -
80L PHE* 4.3 9.2 - + - -
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Residues in contact with ALA 63 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59L GLU 3.1 17.8 + - - +
62L PHE* 1.3 82.4 - - - +
64L GLY* 1.3 58.5 + - - +
66L ALA* 3.5 2.8 + - - +
67L VAL* 3.1 32.4 + - - +
78L CYS* 4.2 7.9 - - - -
80L PHE* 4.0 19.7 - - + -
89L ALA* 3.5 21.8 - - + -
92L GLN* 4.2 7.9 - - + -
114L PHE* 4.4 7.5 - - + -
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Residues in contact with GLY 64 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143K PRO* 3.8 8.1 - - - -
144K LEU* 3.4 17.7 - - - +
60L MET 3.2 5.5 + - - -
61L GLY 3.0 8.9 + - - -
63L ALA* 1.3 76.8 - - - +
65L ILE* 1.3 64.2 + - - +
67L VAL* 4.4 0.2 - - - -
68L GLY 3.1 17.5 + - - -
92L GLN* 3.6 31.3 - - - +
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Residues in contact with ILE 65 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143K PRO* 3.5 18.8 - - + +
146K ALA* 4.0 19.1 - - + +
147K GLY* 3.1 15.8 - - - -
150K LEU* 4.3 13.7 - - + -
178K ALA* 5.1 3.4 - - - -
181K MET* 3.6 48.5 - - + -
185K TRP* 4.1 16.2 - - + -
187K LEU* 5.1 2.7 - - + -
26L LEU* 4.2 13.9 - - + -
61L GLY 2.8 12.0 + - - +
62L PHE* 3.0 9.8 + - - +
64L GLY* 1.3 73.2 - - - +
66L ALA* 1.3 68.9 + - - +
68L GLY 2.9 11.4 + - - -
69L ALA* 2.9 10.7 + - - +
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Residues in contact with ALA 66 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24L PHE* 5.1 0.7 - - - -
26L LEU* 3.9 25.8 - - + +
62L PHE 2.8 15.9 + - - +
63L ALA 3.6 7.4 - - - +
65L ILE* 1.3 74.7 - - - +
67L VAL* 1.3 64.9 + - - +
69L ALA* 3.2 7.0 + - - +
70L ALA 3.0 17.5 + - - -
76L PRO* 3.3 15.9 - - + +
78L CYS* 4.0 9.2 - - + -
112L ILE* 3.6 19.5 - - + -
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Residues in contact with VAL 67 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144K LEU* 3.8 19.3 - - + -
63L ALA 3.1 20.9 + - - +
64L GLY* 3.9 4.7 - - - +
65L ILE 3.1 0.6 - - - -
66L ALA* 1.3 76.9 - - - +
68L GLY* 1.3 61.6 + - - +
70L ALA* 3.3 6.8 + - - +
71L MET* 3.2 27.1 + - - +
92L GLN* 4.5 8.1 - - + +
96L SER* 4.1 20.0 - - - +
97L ALA* 4.3 10.3 - - + -
110L VAL* 4.0 13.8 - - + +
112L ILE* 3.7 21.3 - - + -
114L PHE* 3.8 14.8 - - + -
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Residues in contact with GLY 68 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144K LEU* 3.2 32.7 - - - +
148K ILE* 3.6 18.0 - - - +
64L GLY 3.1 7.9 + - - -
65L ILE 2.9 5.2 + - - -
67L VAL* 1.3 75.2 - - - +
69L ALA* 1.3 64.3 + - - +
71L MET* 3.1 21.0 + - - +
72L ALA* 3.4 4.5 + - - +
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Residues in contact with ALA 69 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147K GLY* 3.3 21.9 - - - +
150K LEU* 4.9 4.7 - - + -
151K ALA* 4.3 3.7 - - - +
24L PHE* 3.8 31.2 - - + -
65L ILE 2.9 10.2 + - - +
66L ALA* 3.2 9.6 + - - +
68L GLY* 1.3 75.1 - - - +
70L ALA* 1.3 60.2 + - - +
72L ALA* 3.2 10.0 + - - +
74L LEU* 3.1 32.0 + - + +
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Residues in contact with ALA 70 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66L ALA 3.0 12.1 + - - +
67L VAL 3.5 9.6 - - - +
68L GLY 3.1 0.2 - - - -
69L ALA* 1.3 73.9 - - - +
71L MET* 1.3 61.7 + - - +
72L ALA 3.0 5.2 - - - -
73L GLY* 3.1 10.2 + - - -
74L LEU 3.0 13.9 - - - +
76L PRO* 3.6 17.7 - - + -
109L PRO 4.5 0.2 - - - +
110L VAL* 4.0 15.7 - - + -
111L PRO* 3.2 32.5 - - - +
112L ILE* 4.2 3.8 - - + -
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Residues in contact with MET 71 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127K TYR* 4.1 10.8 - - + +
132K TYR* 3.6 49.2 - - + +
135K ASN* 5.9 0.4 - - - +
144K LEU* 3.9 27.6 - - + -
148K ILE* 5.3 1.1 - - + -
67L VAL* 3.4 18.4 - - - +
68L GLY* 3.1 12.3 + - - +
70L ALA* 1.3 78.9 - - - +
72L ALA* 1.3 58.3 + - - +
73L GLY 3.2 1.5 + - - -
96L SER 5.3 2.5 - - - +
100L THR* 4.8 5.2 - - + -
108L GLN* 3.0 46.5 + - + +
109L PRO 4.3 1.3 - - - -
110L VAL* 4.1 18.2 - - + -
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Residues in contact with ALA 72 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84K HIS* 5.5 4.5 - - + -
132K TYR* 4.3 17.0 - - - +
148K ILE* 4.5 13.2 - - + -
151K ALA* 3.7 22.0 - - + -
155K ASN* 5.0 6.9 + - - -
68L GLY 3.9 7.0 - - - +
69L ALA 3.2 9.6 + - - +
70L ALA 3.0 1.2 - - - -
71L MET* 1.3 80.0 - - - +
73L GLY* 1.3 58.7 + - - +
74L LEU* 3.6 5.2 + - - +
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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