Contacts of the helix formed by residues 83 - 92 (chain H) in PDB entry 6V01
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 GLU 83 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78H LYS* 4.6 7.2 - - - +
79H ASP 3.2 20.1 + - - +
80H THR* 4.2 7.5 - - - -
81H ASP 3.7 0.4 - - - -
82H SER* 1.3 78.7 - - - +
84H GLU* 1.3 60.7 + - - +
85H GLU 3.5 0.2 - - - -
86H ILE* 3.4 18.2 - - - +
87H ARG* 3.5 12.1 - - - +
143H VAL* 5.0 7.2 - - + +
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Residues in contact with GLU 84 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555D ARG* 6.3 0.7 - - - +
557G LYS* 6.0 6.3 - - - +
561G ARG* 6.0 4.3 - - - +
80H THR 4.7 10.6 + - - +
81H ASP 5.0 1.1 - - - +
82H SER* 4.5 0.6 - - - +
83H GLU* 1.3 76.7 - - - +
85H GLU* 1.3 61.9 + - - +
86H ILE 3.3 0.4 - - - -
87H ARG* 3.3 8.4 + - + +
88H GLU* 2.9 27.9 + - - +
91H ARG* 6.1 0.3 - - - -
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Residues in contact with GLU 85 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374G LEU* 3.8 7.1 - - + +
526G LYS* 3.7 33.9 - - + +
529G PHE* 3.8 14.6 - - + -
530G GLN* 4.7 8.3 - - - +
533G ARG* 5.4 6.5 - - - +
81H ASP 5.0 3.9 + - - +
82H SER* 4.2 11.4 - - - +
83H GLU 3.5 0.2 - - - -
84H GLU* 1.3 76.8 - - - +
86H ILE* 1.3 62.9 + - - +
88H GLU* 3.6 13.4 + - - +
89H ALA 3.6 6.9 + - - -
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Residues in contact with ILE 86 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374G LEU* 4.2 16.3 - - + +
375G ILE* 5.6 7.9 - - + -
378G ALA* 4.2 24.9 - - + -
522G TYR* 5.4 6.1 - - - +
82H SER 3.3 21.0 + - - +
83H GLU* 3.4 15.5 - - + +
85H GLU* 1.3 76.9 - - - +
87H ARG* 1.3 61.0 + - - +
88H GLU 3.2 0.2 - - - -
89H ALA* 3.0 23.1 + - + +
90H PHE* 3.6 19.1 - - + -
142H PHE* 5.0 10.3 - - + -
143H VAL* 4.6 13.2 - - + -
146H MET* 4.3 22.4 - - + -
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Residues in contact with ARG 87 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83H GLU 3.5 15.5 - - - +
84H GLU* 3.3 11.1 + - - +
86H ILE* 1.3 81.2 - - - +
88H GLU* 1.3 59.2 + - - +
89H ALA 3.3 0.4 + - - -
90H PHE* 3.7 13.0 + - - +
91H ARG* 3.3 36.0 + - - +
139H TYR* 5.5 10.3 - - + -
143H VAL* 4.9 11.0 - - + -
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Residues in contact with GLU 88 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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555D ARG* 6.0 3.4 - - - +
529G PHE* 4.5 13.7 - - + -
533G ARG* 5.6 8.3 - - - +
84H GLU 2.9 14.8 + - - +
85H GLU* 3.8 10.5 - - - +
86H ILE 3.2 0.4 - - - -
87H ARG* 1.3 77.7 - - - +
89H ALA* 1.3 62.0 + - - +
90H PHE 3.3 0.2 - - - -
91H ARG* 3.1 26.2 + - + +
92H VAL* 3.4 18.1 + - - +
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Residues in contact with ALA 89 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371G ALA* 3.9 21.4 - - + +
374G LEU* 4.4 15.0 - - + -
375G ILE* 4.8 13.7 - - + -
529G PHE* 4.6 6.0 - - + -
85H GLU 3.6 6.7 + - - +
86H ILE* 3.0 15.4 + - + +
88H GLU* 1.3 77.0 - - - +
90H PHE* 1.3 65.0 + - + +
92H VAL* 3.7 13.1 + - - +
93H PHE* 3.4 23.5 - - - -
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Residues in contact with PHE 90 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375G ILE* 4.0 26.9 - - + -
86H ILE* 3.6 22.2 + - + -
87H ARG* 3.7 10.5 + - - +
88H GLU 3.3 0.2 - - - -
89H ALA* 1.3 78.7 - - - +
91H ARG* 1.3 57.1 + - - +
93H PHE* 3.0 25.2 + + - +
94H ASP* 3.1 13.0 + - - +
101H ILE* 3.6 26.9 - - + +
106H LEU* 5.4 10.5 - - + -
137H VAL 5.1 4.0 - - - -
139H TYR* 3.5 45.5 - - + -
142H PHE* 3.6 42.6 - + + -
143H VAL* 4.4 9.9 - - + -
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Residues in contact with ARG 91 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551D ASN* 6.1 2.5 - - - +
554D VAL* 4.6 28.2 - - + +
555D ARG* 3.6 43.9 - - - +
558D GLU* 3.4 39.7 + - - +
84H GLU 6.1 0.4 - - - -
87H ARG* 3.3 28.3 + - - +
88H GLU* 3.1 18.1 + - + +
90H PHE* 1.3 74.0 - - + +
92H VAL* 1.3 64.2 + - - +
93H PHE 3.2 0.2 - - - -
94H ASP* 3.7 20.7 + - + +
139H TYR* 5.4 16.6 + - + -
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Residues in contact with VAL 92 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364G PHE* 4.4 25.5 - - + -
367G GLN* 4.7 20.0 - - + +
368G ILE* 4.2 26.0 - - + +
371G ALA* 4.2 24.0 - - + -
529G PHE* 4.7 8.7 - - + -
88H GLU 3.4 15.9 - - - +
89H ALA* 4.0 7.2 - - - +
90H PHE 3.2 0.6 - - - -
91H ARG* 1.3 78.0 - - + +
93H PHE* 1.3 64.4 + - + +
94H ASP 3.5 2.5 + - - +
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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