Contacts of the helix formed by residues 84 - 94 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80C GLN* 5.2 3.1 - - + -
81C GLY* 3.0 17.0 + - - +
82C PRO 2.9 2.0 + - - -
83C ALA* 1.3 85.5 - - + +
85C ALA* 1.3 61.1 + - - +
86C PRO* 3.7 2.2 - - - -
87C PRO* 3.6 13.7 - - - +
88C ARG* 3.8 16.6 + - + +
316C PRO* 4.0 11.7 - - + -
317C GLN* 3.3 42.4 - - + -
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Residues in contact with ALA 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82C PRO 3.0 9.5 + - - +
84C PHE* 1.3 78.0 - - - +
86C PRO* 1.3 74.0 - - + +
87C PRO 3.4 0.2 - - - -
88C ARG* 3.1 4.3 + - - +
89C ILE* 3.0 24.4 + - + +
158C GLY 3.6 11.2 - - - +
314C PHE* 3.2 43.7 - - + +
316C PRO* 3.9 11.6 - - + +
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Residues in contact with PRO 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69C GLY* 4.2 0.4 - - - -
70C VAL 4.2 8.7 - - - +
71C PRO* 4.4 8.1 - - + -
82C PRO 4.0 4.3 - - - +
83C ALA 4.1 7.0 - - - +
84C PHE 3.7 0.9 - - - -
85C ALA* 1.3 94.4 - - + +
87C PRO* 1.3 70.1 - - + +
89C ILE* 3.3 4.0 + - + +
90C ARG* 3.1 40.7 + - - +
119C ASP* 3.7 10.5 - - - +
157C LEU* 3.6 32.0 - - + +
158C GLY 3.6 16.6 - - - +
159C GLY 4.3 0.2 - - - +
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Residues in contact with PRO 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71C PRO* 5.7 1.3 - - + -
83C ALA 5.4 0.9 - - - +
84C PHE* 3.6 12.8 - - - +
85C ALA 3.4 4.0 - - - -
86C PRO* 1.3 101.1 - - + +
88C ARG* 1.3 58.0 + - + +
90C ARG* 3.5 13.9 + - + +
91C GLU* 3.1 26.3 + - - +
119C ASP* 3.9 14.1 - - - +
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Residues in contact with ARG 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84C PHE* 3.8 19.4 + - - +
85C ALA 3.1 6.7 + - - +
87C PRO* 1.3 75.5 - - + +
89C ILE* 1.3 65.5 + - - +
91C GLU* 3.4 21.0 + - - +
92C ALA* 3.0 23.0 + - - +
314C PHE* 3.9 16.8 - - + -
316C PRO* 4.0 26.0 + - + +
326C ALA* 4.2 8.4 - - + +
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Residues in contact with ILE 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85C ALA* 3.0 20.4 + - + +
86C PRO 3.3 6.5 + - - +
88C ARG* 1.3 74.9 - - - +
90C ARG* 1.3 62.0 + - - +
92C ALA* 3.0 17.4 + - - +
93C ILE* 3.0 20.6 + - + +
157C LEU* 4.3 22.0 - - + -
158C GLY 4.5 8.3 - - - +
311C VAL* 4.9 9.6 - - + +
314C PHE* 3.5 26.5 - - + -
326C ALA 4.7 2.5 - - - -
329C ALA* 3.8 19.3 - - + -
330C ALA* 3.9 14.1 - - - +
333C VAL* 3.9 23.8 - - + -
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Residues in contact with ARG 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67C LEU* 4.7 6.0 - - + +
68C LEU 4.5 0.6 - - - -
69C GLY* 3.6 10.5 - - - +
86C PRO* 3.1 27.9 + - - +
87C PRO* 3.6 13.9 - - + +
89C ILE* 1.3 72.0 - - - +
91C GLU* 1.3 65.8 + - - +
93C ILE* 3.2 17.9 + - + +
94C TRP* 3.3 26.1 - - + +
116C ASP* 2.5 42.0 + - - +
118C GLY* 3.5 16.0 + - - -
119C ASP* 2.8 40.5 + - - -
157C LEU* 4.1 19.1 - - + +
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Residues in contact with GLU 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87C PRO 3.1 12.5 + - - +
88C ARG* 3.6 24.4 + - - +
90C ARG* 1.3 80.3 - - - +
92C ALA* 1.3 62.6 + - + +
94C TRP* 3.3 4.4 + - - +
95C CYS* 3.2 22.2 + - + +
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Residues in contact with ALA 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88C ARG 3.0 13.7 + - - +
89C ILE 3.0 4.2 + - - +
91C GLU* 1.3 74.7 - - + +
93C ILE* 1.3 65.2 + - - +
94C TRP 3.4 0.3 + - - -
95C CYS* 3.4 16.3 + - - +
98C THR* 4.5 2.6 - - - +
326C ALA* 3.3 36.8 - - + +
327C MET* 3.6 27.8 - - - +
330C ALA* 3.4 9.9 - - + +
334C ARG* 5.2 0.5 + - - -
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Residues in contact with ILE 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67C LEU* 3.9 28.9 - - + -
89C ILE* 3.0 25.0 + - + +
90C ARG* 3.2 15.2 + - + +
92C ALA* 1.3 77.5 - - - +
94C TRP* 1.3 90.2 + - + +
95C CYS 3.4 0.7 + - - -
98C THR* 3.9 2.8 + - - -
99C ASN 5.8 0.2 - - - -
108C LEU* 4.6 4.5 - - + -
114C LEU* 4.4 10.5 - - + -
330C ALA* 3.8 22.9 - - + +
333C VAL* 3.9 17.3 - - + -
334C ARG* 3.0 42.8 + - + +
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Residues in contact with TRP 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90C ARG* 3.3 28.3 + - + +
91C GLU* 3.3 6.9 + - - +
92C ALA 3.2 0.2 - - - -
93C ILE* 1.3 93.3 - - + +
95C CYS* 1.3 67.1 + - - +
96C GLY* 3.3 3.1 + - - -
98C THR* 4.4 0.4 - - - -
100C SER* 4.6 9.4 - - - -
108C LEU* 3.6 37.5 - - + -
109C LYS* 4.1 28.0 - - + -
114C LEU* 4.1 20.6 - - + +
116C ASP* 6.0 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