Contacts of the helix formed by residues 84 - 94 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80A GLN* 5.0 1.8 - - + -
81A GLY* 3.1 21.4 + - - +
83A ALA* 1.3 85.4 - - + +
85A ALA* 1.3 62.9 + - - +
86A PRO* 3.7 1.3 - - - -
87A PRO* 3.5 13.7 - - - +
88A ARG* 3.8 12.2 + - - +
316A PRO* 3.9 5.4 - - + -
317A GLN* 3.7 22.7 - - + -
84D PHE 6.0 0.2 - - - -
87D PRO* 3.6 38.8 - - + -
88D ARG* 3.5 37.0 - - - +
91D GLU* 3.5 33.9 - - + -
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Residues in contact with ALA 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A PRO 3.1 7.6 + - - +
84A PHE* 1.3 77.7 - - - +
86A PRO* 1.4 69.5 - - - +
88A ARG* 2.8 14.7 + - - +
89A ILE* 3.0 14.3 + - + +
158A GLY 3.4 18.8 - - - +
314A PHE* 3.4 42.2 - - + +
316A PRO* 3.8 11.3 - - + +
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Residues in contact with PRO 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A VAL 4.3 0.7 - - - +
71A PRO* 4.2 15.7 - - + -
82A PRO 3.9 2.2 - - - +
83A ALA 3.6 12.6 - - - +
85A ALA* 1.4 93.6 - - + +
87A PRO* 1.4 73.0 - - + +
89A ILE* 3.3 3.6 + - + +
90A ARG* 3.2 29.6 + - - +
119A ASP* 3.6 20.4 - - - +
157A LEU* 3.3 42.0 - - + +
158A GLY 3.4 8.3 - - - +
159A GLY 4.2 0.2 - - - +
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Residues in contact with PRO 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A PRO* 5.5 2.0 - - + -
83A ALA 5.0 1.1 - - - +
84A PHE* 3.5 17.7 - - - +
86A PRO* 1.4 97.5 - - + +
88A ARG* 1.3 57.7 + - - +
90A ARG* 3.5 14.9 + - + +
91A GLU* 3.2 17.8 + - - +
119A ASP* 3.9 14.6 - - - +
84D PHE* 3.7 32.1 - - + -
123D GLN* 6.5 0.9 - - + -
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Residues in contact with ARG 88 (chain A).
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* 3.8 15.3 + - - +
85A ALA 2.8 14.5 + - - +
87A PRO* 1.3 70.9 - - - +
89A ILE* 1.3 62.8 + - - +
91A GLU* 3.4 9.2 + - - +
92A ALA* 3.1 23.2 + - - +
314A PHE* 3.8 19.1 - - + -
316A PRO* 4.0 17.4 + - + +
326A ALA* 4.2 6.5 - - + +
84D PHE* 3.9 34.7 - - + +
88D ARG* 2.6 40.3 - - - +
316D PRO* 4.0 17.4 - - - +
317D GLN* 3.5 36.4 - - - +
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Residues in contact with ILE 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A ALA* 3.0 17.5 + - + +
86A PRO 3.7 5.6 - - - +
88A ARG* 1.3 74.0 - - - +
90A ARG* 1.3 65.0 + - - +
92A ALA* 3.2 4.7 + - - +
93A ILE* 3.0 25.9 + - + +
157A LEU* 3.8 36.1 - - + -
158A GLY 4.2 11.4 - - - +
311A VAL* 4.6 11.0 - - + +
314A PHE* 3.6 28.3 - - + -
326A ALA 4.6 5.8 - - - -
329A ALA* 4.0 14.4 - - + -
330A ALA* 4.0 14.1 - - - +
333A VAL* 3.9 20.4 - - + -
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Residues in contact with ARG 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A ARG* 5.4 1.5 - - - +
67A LEU* 5.0 4.0 - - + +
68A LEU* 4.5 0.6 - - - +
69A GLY* 3.5 10.5 - - - +
86A PRO* 3.2 23.0 + - - +
87A PRO* 3.7 13.5 - - - +
88A ARG 3.3 0.2 - - - -
89A ILE* 1.3 73.6 - - - +
91A GLU* 1.3 65.6 + - - +
93A ILE* 3.2 17.7 + - - +
94A TRP* 3.3 26.9 - - + +
116A ASP* 2.9 36.4 + - - +
118A GLY* 3.3 25.3 + - - -
119A ASP* 2.7 41.3 + - - -
157A LEU* 4.5 14.9 - - + +
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Residues in contact with GLU 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A PRO 3.2 11.8 + - - +
88A ARG* 3.7 11.9 - - - +
89A ILE 3.3 0.4 - - - -
90A ARG* 1.3 78.8 - - - +
92A ALA* 1.3 59.0 - - - +
94A TRP* 3.5 4.4 + - - +
95A CYS* 3.2 25.9 + - + -
80D GLN* 5.9 2.9 - - - +
84D PHE* 3.6 20.5 - - + -
317D GLN* 2.7 37.1 + - - +
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Residues in contact with ALA 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A ARG 3.1 13.0 + - - +
89A ILE 3.2 3.8 + - - +
91A GLU* 1.3 75.2 - - - +
93A ILE* 1.3 64.1 + - - +
94A TRP 3.2 1.2 + - - -
95A CYS* 3.4 15.8 + - - +
98A THR* 4.5 2.6 - - - +
326A ALA* 3.5 32.5 - - + +
327A MET* 3.6 34.3 - - - +
330A ALA* 3.7 7.6 - - + +
334A ARG* 5.3 0.7 + - - -
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Residues in contact with ILE 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A LEU* 3.9 19.5 - - + -
89A ILE* 3.0 27.4 + - + +
90A ARG* 3.2 13.6 + - - +
92A ALA* 1.3 75.6 - - - +
94A TRP* 1.3 90.0 + - + +
95A CYS 3.8 0.5 + - - -
98A THR* 3.8 3.1 + - - -
108A LEU* 4.7 2.5 - - + -
114A LEU* 4.4 8.5 - - + -
157A LEU* 5.2 0.4 - - + -
330A ALA* 3.6 23.3 - - + +
333A VAL* 3.8 28.5 - - + -
334A ARG* 3.1 39.4 + - + +
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Residues in contact with TRP 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A LEU* 5.9 1.8 - - - +
90A ARG* 3.3 29.0 + - + +
91A GLU* 3.6 5.2 - - - +
92A ALA 3.2 0.4 - - - -
93A ILE* 1.3 93.4 - - + +
95A CYS* 1.3 63.2 + - - +
96A GLY* 3.6 1.9 + - - -
98A THR* 4.9 0.4 - - - -
100A SER* 4.8 7.6 - - - -
108A LEU* 3.2 48.2 - - + -
109A LYS* 4.3 23.3 - - + -
114A LEU* 4.0 19.0 - - + +
116A ASP* 5.2 8.5 + - + +
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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