Contacts of the helix formed by residues 89 - 99 (chain D) in PDB entry 3ELP
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 89 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87D PHE* 3.1 1.9 + - - +
88D ALA* 1.3 82.3 - - - +
90D GLY* 1.3 59.6 + - - +
91D LEU* 3.5 8.9 + - - +
92D ALA* 2.9 24.6 + - - +
93D ALA* 2.9 23.2 + - - -
221D VAL* 3.9 14.6 - - - -
222D MET 4.0 2.7 - - - -
223D GLY* 3.4 15.7 - - - +
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Residues in contact with GLY 90 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89D SER* 1.3 73.9 - - - +
91D LEU* 1.3 56.7 + - - +
93D ALA* 3.0 6.5 - - - +
94D THR* 2.8 30.8 + - - -
207D MET* 3.4 6.2 - - - +
209D SER* 3.3 34.4 + - - -
210D ALA 5.6 0.2 + - - -
221D VAL* 5.1 1.4 - - - +
222D MET 3.6 6.9 + - - -
223D GLY* 3.8 8.3 - - - -
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Residues in contact with LEU 91 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89D SER* 3.1 8.4 + - - +
90D GLY* 1.3 74.2 - - - +
92D ALA* 1.3 59.6 + - - +
94D THR* 3.0 15.0 + - + +
95D VAL* 2.8 41.4 + - + +
120D TYR* 3.7 42.6 - - + -
124D VAL* 5.9 3.8 - - + -
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Residues in contact with ALA 92 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87D PHE* 4.4 4.7 - - + -
88D ALA* 4.5 4.5 - - + +
89D SER* 2.9 29.0 + - - +
91D LEU* 1.3 73.9 - - - +
93D ALA* 1.3 64.3 + - - +
95D VAL* 3.8 8.3 - - - +
96D THR* 2.8 31.4 + - - -
245D ALA* 4.0 24.6 - - + +
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Residues in contact with ALA 93 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87D PHE* 4.0 14.8 - - + +
89D SER 2.9 12.1 + - - +
90D GLY* 3.0 15.9 - - - +
91D LEU 3.0 0.2 - - - -
92D ALA* 1.3 80.2 - - - +
94D THR* 1.3 63.9 + - - +
96D THR* 3.1 2.9 + - - -
97D ILE* 2.9 27.0 + - - +
207D MET* 4.2 9.6 - - + -
223D GLY* 4.0 11.9 - - - -
225D VAL* 3.8 22.7 - - + +
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Residues in contact with THR 94 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90D GLY 2.8 16.4 + - - -
91D LEU* 3.2 16.4 + - + +
93D ALA* 1.3 76.0 - - - +
95D VAL* 1.3 64.0 + - + +
97D ILE* 3.0 5.5 + - - +
98D THR* 3.0 25.1 + - + +
121D PHE* 3.6 31.1 - - + -
124D VAL* 6.2 4.0 - - + -
155D TRP* 3.5 29.3 - - + -
207D MET* 3.4 15.0 - - - +
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Residues in contact with VAL 95 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91D LEU* 2.8 34.0 + - + +
92D ALA* 3.8 8.3 - - - +
93D ALA 3.3 0.2 - - - -
94D THR* 1.3 71.0 - - - +
96D THR* 1.3 65.5 + - - +
98D THR* 2.6 27.5 + - - +
99D HIS* 2.9 37.0 + - + +
124D VAL* 4.2 22.7 - - + -
128D PHE* 4.0 15.7 - - + -
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Residues in contact with THR 96 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87D PHE* 3.6 38.2 - - + -
92D ALA 2.8 20.5 + - - -
93D ALA 3.4 4.5 - - - -
95D VAL* 1.3 79.2 - - - +
97D ILE* 1.3 64.4 + - - +
99D HIS* 3.2 26.4 + - + +
100D LEU 3.7 0.2 + - - -
236D LEU* 4.1 8.8 - - + +
239D LEU* 3.5 37.3 - - + +
240D GLN 4.7 0.4 - - - +
243D LEU* 5.1 4.9 - - + +
245D ALA* 4.7 6.8 - - - +
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Residues in contact with ILE 97 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93D ALA 2.9 22.4 + - - +
94D THR 3.0 7.1 + - - +
96D THR* 1.3 74.5 - - + +
98D THR* 1.3 59.8 + - - +
100D LEU* 2.8 37.6 + - + +
101D LEU* 5.2 0.7 - - - +
153D LEU* 4.3 13.9 - - + +
155D TRP* 3.9 29.4 - - + -
185D VAL* 4.1 15.9 - - + -
205D ILE* 3.8 24.7 - - + -
207D MET* 5.4 1.3 - - + -
225D VAL* 3.6 35.9 - - + -
236D LEU* 4.2 11.0 - - + -
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Residues in contact with THR 98 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94D THR* 3.0 21.7 + - + +
95D VAL* 2.6 19.5 + - - +
97D ILE* 1.3 72.7 - - + +
99D HIS* 1.3 57.5 + - - +
100D LEU 2.8 11.1 + - - -
101D LEU* 2.8 30.5 + - + +
107D ILE* 5.7 6.1 - - + -
121D PHE* 5.4 7.9 - - + -
124D VAL* 3.5 29.1 - - + +
128D PHE* 4.9 1.7 - - - -
130D LEU* 4.3 18.7 - - + +
153D LEU* 4.5 17.3 - - + -
155D TRP* 5.4 1.3 - - + -
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Residues in contact with HIS 99 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95D VAL* 2.9 32.0 + - + +
96D THR* 3.4 19.7 - - - +
97D ILE 3.2 0.4 - - - -
98D THR* 1.3 76.0 + - - +
100D LEU* 1.3 60.0 + - - +
101D LEU 3.2 8.7 - - - +
128D PHE* 3.4 45.7 - + - +
239D LEU* 3.9 20.6 - - + +
243D LEU* 3.4 31.2 - - + +
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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