Contacts of the helix formed by residues 84 - 94 (chain D) in PDB entry 6VSU
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 84 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84A PHE* 6.0 0.2 - - - -
87A PRO* 3.7 43.7 - - + -
88A ARG* 3.9 30.1 - - - +
91A GLU* 3.6 35.9 - - + -
80D GLN* 4.9 2.0 - - + -
81D GLY* 2.8 18.8 + - - +
83D ALA* 1.3 89.2 - - + +
85D ALA* 1.3 63.1 + - - +
86D PRO* 3.6 2.2 - - - -
87D PRO* 3.5 13.4 - - - +
88D ARG* 3.7 14.8 + - - +
316D PRO* 4.0 5.8 - - + -
317D GLN* 3.7 24.0 - - + -
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Residues in contact with ALA 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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82D PRO 3.0 14.5 + - - +
84D PHE* 1.3 77.8 - - - +
86D PRO* 1.4 69.9 - - - +
88D ARG* 2.9 15.2 + - - +
89D ILE* 3.0 15.7 + - + +
158D GLY 3.2 15.5 - - - +
314D PHE* 3.4 37.0 - - + +
316D PRO* 3.9 9.6 - - - +
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Residues in contact with PRO 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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69D GLY* 4.2 0.2 - - - -
70D VAL 4.3 1.3 - - - +
71D PRO* 4.2 17.7 - - + -
82D PRO 3.9 4.9 - - - +
83D ALA 3.9 7.6 - - - +
84D PHE 3.6 0.9 - - - -
85D ALA* 1.4 93.6 - - + +
87D PRO* 1.3 70.0 - - + +
89D ILE* 3.4 4.4 + - + +
90D ARG* 3.2 43.5 + - - +
119D ASP* 3.6 9.0 - - - +
157D LEU* 3.6 40.1 - - + +
158D GLY 3.6 8.1 - - - +
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Residues in contact with PRO 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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84A PHE* 3.6 29.5 - - + -
71D PRO* 5.6 1.8 - - + -
83D ALA 5.3 0.9 - - - +
84D PHE* 3.5 12.3 - - - +
85D ALA 3.5 3.1 - - - -
86D PRO* 1.3 100.0 - - + +
88D ARG* 1.3 58.7 + - - +
89D ILE 3.3 0.2 - - - -
90D ARG* 3.5 13.0 + - - +
91D GLU* 3.3 21.5 + - - +
119D ASP* 4.0 12.8 - - - +
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Residues in contact with ARG 88 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A PHE* 3.5 41.6 - - - +
88A ARG* 2.6 40.3 - - - +
316A PRO* 4.0 19.2 - - - +
317A GLN* 3.9 22.9 - - - +
84D PHE* 3.7 17.5 + - - +
85D ALA 2.9 6.5 + - - +
87D PRO* 1.3 73.0 - - - +
89D ILE* 1.3 66.5 + - - +
91D GLU* 3.6 13.6 + - - +
92D ALA* 3.2 21.3 + - - +
314D PHE* 3.8 17.9 - - + -
316D PRO* 4.0 18.4 + - + +
326D ALA* 4.2 7.6 - - + +
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Residues in contact with ILE 89 (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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85D ALA* 3.0 16.5 + - + +
86D PRO 3.8 6.5 - - - +
88D ARG* 1.3 73.6 - - - +
90D ARG* 1.3 65.2 + - - +
92D ALA* 3.0 8.5 + - - +
93D ILE* 3.0 31.7 + - + +
157D LEU* 4.2 22.4 - - + -
158D GLY 4.3 16.8 - - - +
311D VAL* 4.7 11.2 - - + +
314D PHE* 3.7 25.6 - - + -
326D ALA 4.7 1.8 - - - +
329D ALA* 3.8 20.0 - - + -
330D ALA* 4.1 10.5 - - - +
333D VAL* 3.9 23.1 - - + -
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Residues in contact with ARG 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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123A GLN* 6.5 1.3 - - - -
124A GLU* 5.9 0.4 - - - -
67D LEU* 4.7 5.3 - - + +
68D LEU 4.5 0.2 - - - -
69D GLY* 3.7 8.9 - - - +
86D PRO* 3.2 28.1 + - - +
87D PRO* 3.8 11.0 - - - +
88D ARG 3.3 0.2 - - - -
89D ILE* 1.3 74.0 - - - +
91D GLU* 1.3 63.3 + - - +
93D ILE* 3.2 18.6 + - - +
94D TRP* 3.2 27.6 - - + +
116D ASP* 2.7 42.8 + - - +
118D GLY* 3.3 18.0 + - - -
119D ASP* 2.7 42.0 + - - -
157D LEU* 4.2 16.5 - - + +
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Residues in contact with GLU 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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84A PHE* 3.5 21.3 - - + -
317A GLN* 2.8 37.8 + - - +
87D PRO 3.3 14.1 + - - +
88D ARG* 3.7 10.8 - - - +
90D ARG* 1.3 79.8 - - - +
92D ALA* 1.3 56.3 + - - +
94D TRP* 3.3 6.4 + - - +
95D CYS* 3.0 27.5 + - + +
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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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88D ARG 3.2 9.7 + - - +
89D ILE 3.0 5.7 + - - +
91D GLU* 1.3 77.5 - - - +
93D ILE* 1.3 64.8 + - - +
94D TRP 3.2 0.7 + - - -
95D CYS* 3.3 17.5 + - - +
98D THR* 4.3 2.6 - - - +
326D ALA* 3.2 36.8 - - + +
327D MET* 3.8 24.6 - - - +
330D ALA* 3.4 10.6 - - + +
334D ARG* 5.3 0.5 + - - -
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Residues in contact with ILE 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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67D LEU* 3.9 20.4 - - + -
89D ILE* 3.0 26.6 + - + +
90D ARG* 3.2 12.8 + - - +
92D ALA* 1.3 75.8 - - - +
94D TRP* 1.3 90.9 - - + +
98D THR* 3.8 4.2 + - - -
108D LEU* 4.8 2.7 - - + -
114D LEU* 4.5 9.4 - - + -
330D ALA* 3.7 24.7 - - + +
333D VAL* 3.9 25.6 - - + -
334D ARG* 3.2 39.3 + - + +
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Residues in contact with TRP 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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67D LEU* 6.1 1.6 - - - +
90D ARG* 3.2 30.0 + - + +
91D GLU* 3.3 7.2 + - - +
92D ALA 3.2 0.4 - - - -
93D ILE* 1.3 93.3 - - + +
95D CYS* 1.3 67.7 + - - +
96D GLY* 3.4 2.6 + - - -
98D THR* 4.3 0.4 - - - -
100D SER* 4.7 7.4 - - - -
108D LEU* 3.5 41.1 - - + -
109D LYS* 4.3 25.8 - - + -
114D LEU* 4.0 21.0 - - + +
116D ASP* 5.8 2.0 + - - -
334D ARG* 6.1 0.2 - - - -
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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