Contacts of the helix formed by residues 82 - 88 (chain D) in PDB entry 3DUF
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 PHE 82 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36D VAL* 4.6 10.3 - - + -
37D PHE* 3.6 27.6 - + - -
80D ILE* 3.0 12.5 + - - +
81D GLN* 1.3 116.8 - - + +
83D PHE* 1.3 59.8 + - - +
84D GLY 3.1 11.2 + - - +
85D PHE* 3.1 31.3 + + + +
116D SER* 3.4 4.3 - - - -
117D PRO* 3.6 9.6 - - + -
124D THR* 5.1 4.3 - - + -
128D HIS* 3.5 54.3 - + + +
173D LEU* 3.7 24.9 - - + -
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Residues in contact with PHE 83 (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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80D ILE* 4.3 10.1 - - + -
82D PHE* 1.3 67.0 - - - +
84D GLY* 1.3 59.1 - - - +
85D PHE 3.0 6.9 + - - -
86D VAL* 3.2 43.7 - - + +
93D ILE* 5.5 0.7 - - + -
114D ILE* 5.7 0.2 - - + -
116D SER* 3.1 24.5 + - - +
117D PRO 2.9 17.5 + - - +
118D PHE* 3.9 17.0 - + + +
128D HIS 5.2 0.4 + - - -
130D ASP 5.1 2.5 - - - +
132D LEU* 3.6 45.6 - - + +
133D GLU* 4.0 4.5 - - - -
136D VAL* 3.9 26.9 - - + -
168D ILE* 4.3 12.3 - - + -
170D LEU* 3.7 26.5 - - + -
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Residues in contact with GLY 84 (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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143A ILE* 4.5 2.6 - - - +
82D PHE* 3.1 3.6 - - - +
83D PHE* 1.3 77.2 - - - +
85D PHE* 1.3 67.3 + - - +
86D VAL 3.3 1.9 + - - -
87D TYR* 3.9 18.7 - - - -
88D GLU* 4.8 0.5 - - - +
127D LEU* 3.4 35.2 + - - +
128D HIS 5.2 2.8 + - - -
130D ASP* 5.0 9.6 + - - -
132D LEU* 4.1 11.9 - - - -
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Residues in contact with PHE 85 (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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142A ILE* 4.6 2.2 - - + -
143A ILE* 3.6 28.0 - - + -
1370A R1T 3.3 55.2 - + + +
59D GLU* 3.9 17.9 - - + +
80D ILE* 4.1 11.0 - - + -
81D GLN* 4.3 4.3 - - + -
82D PHE* 3.5 39.7 - + + +
83D PHE 3.0 1.4 - - - -
84D GLY* 1.3 83.9 - - - +
86D VAL* 1.3 61.5 + - - +
87D TYR 3.2 3.4 - - - -
88D GLU* 3.4 29.1 + - - +
89D VAL 4.2 0.5 + - - -
127D LEU 3.8 13.9 - - - -
128D HIS* 3.7 26.0 - + - -
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Residues in contact with VAL 86 (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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80D ILE* 4.4 5.3 - - + +
82D PHE 4.5 0.2 + - - -
83D PHE* 3.2 54.6 + - + +
84D GLY 3.3 0.4 - - - -
85D PHE* 1.3 75.7 - - - +
87D TYR* 1.3 61.6 + - + +
88D GLU 3.0 2.9 - - - -
89D VAL* 2.7 29.2 + - + -
90D MET* 3.0 29.9 + - - +
93D ILE* 3.8 26.0 - - + -
132D LEU* 3.8 18.8 - - + -
135D LEU* 5.1 2.2 - - + -
136D VAL* 5.1 3.1 - - + -
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Residues in contact with TYR 87 (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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87B TYR 4.3 3.8 - - - +
88B GLU 6.0 0.3 - - - -
90B MET* 3.6 44.9 - - + +
91B ASP* 3.7 37.7 + - + +
94B CYS* 3.8 10.3 - - + +
95B GLY* 4.1 13.5 - - - -
99B ARG* 3.3 17.6 + - - -
139B GLN* 3.1 23.6 + - - -
84D GLY 3.9 15.3 - - - -
85D PHE 3.2 0.4 - - - -
86D VAL* 1.3 78.5 - - + +
88D GLU* 1.3 65.0 + - - +
89D VAL 3.2 1.0 + - - -
90D MET* 3.6 18.9 + - + +
127D LEU* 4.2 6.7 - - + -
132D LEU* 3.2 33.8 - - + +
135D LEU* 3.8 17.1 - - + +
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Residues in contact with GLU 88 (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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143A ILE* 3.3 26.6 - - - +
144A ILE 5.3 1.4 - - - +
178A GLN* 4.6 11.0 - - - +
180A ASP* 4.5 9.3 - - - +
1370A R1T 3.9 18.4 - - + +
91B ASP* 3.2 34.3 - - - +
59D GLU* 3.8 17.0 - - + +
60D SER* 3.8 19.8 + - - +
84D GLY 4.8 0.3 - - - +
85D PHE* 3.4 27.6 + - - +
86D VAL 3.0 0.2 - - - -
87D TYR* 1.3 81.5 - - - +
89D VAL* 1.3 57.3 + - - +
90D MET 3.7 0.2 - - - -
1326D MG 3.9 10.2 - - - -
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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