Contacts of the helix formed by residues 83 - 92 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78K LYS 4.6 7.4 - - - +
79K ASP 3.2 19.6 + - - +
80K THR* 4.2 7.1 - - - -
81K ASP 3.7 0.6 - - - -
82K SER* 1.3 78.9 - - - +
84K GLU* 1.3 61.7 + - - +
85K GLU 3.5 0.4 - - - -
86K ILE* 3.4 18.5 - - - +
87K ARG* 3.5 12.0 - - - +
143K VAL* 5.0 7.4 - - + +
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Residues in contact with GLU 84 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557J LYS* 6.1 5.6 - - - +
561J ARG* 6.1 2.9 - - - +
80K THR 4.7 10.6 + - - +
81K ASP 5.0 1.3 - - - +
82K SER* 4.5 0.4 - - - +
83K GLU* 1.3 77.3 - - - +
85K GLU* 1.3 60.1 + - - +
86K ILE 3.3 0.7 - - - -
87K ARG* 3.3 8.9 + - + +
88K GLU* 2.9 27.5 + - - +
91K ARG* 6.1 0.3 - - - -
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Residues in contact with GLU 85 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374J LEU* 3.7 13.0 - - + +
526J LYS* 3.6 36.6 - - + +
529J PHE* 3.8 8.4 - - + -
530J GLN* 4.7 7.6 - - - +
533J ARG* 5.5 5.4 - - - +
81K ASP 5.0 3.9 + - - +
82K SER* 4.2 10.8 - - - +
83K GLU 3.5 0.2 - - - -
84K GLU* 1.3 78.2 - - - +
86K ILE* 1.3 61.9 + - - +
88K GLU* 3.6 13.6 + - - +
89K ALA 3.6 7.1 + - - -
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Residues in contact with ILE 86 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374J LEU* 4.1 15.7 - - + +
375J ILE* 5.6 7.0 - - + -
378J ALA* 4.1 26.0 - - + -
522J TYR* 5.2 6.7 - - - +
82K SER 3.3 21.9 + - - +
83K GLU* 3.4 15.3 - - - +
85K GLU* 1.3 77.1 - - - +
87K ARG* 1.3 60.2 + - - +
88K GLU 3.2 0.2 - - - -
89K ALA* 3.0 23.1 + - + +
90K PHE* 3.6 19.3 - - + -
142K PHE* 5.0 10.3 - - + -
143K VAL* 4.6 13.2 - - + -
146K MET* 4.3 23.6 - - + -
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Residues in contact with ARG 87 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83K GLU 3.5 15.9 + - - +
84K GLU* 3.3 10.0 + - - +
86K ILE* 1.3 81.2 - - - +
88K GLU* 1.3 60.0 + - - +
89K ALA 3.3 0.2 - - - -
90K PHE* 3.7 13.4 + - - +
91K ARG* 3.3 34.8 + - - +
139K TYR* 5.5 10.6 - - + -
143K VAL* 4.9 11.4 - - + -
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Residues in contact with GLU 88 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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555G ARG* 5.9 3.4 - - - +
529J PHE* 4.3 15.5 - - + -
533J ARG* 5.6 7.9 - - - +
84K GLU 2.9 15.2 + - - +
85K GLU* 3.8 9.4 - - - +
86K ILE 3.2 0.4 - - - -
87K ARG* 1.3 77.4 - - - +
89K ALA* 1.3 61.2 + - - +
90K PHE 3.3 0.2 - - - -
91K ARG* 3.1 27.6 + - + +
92K VAL* 3.4 18.1 + - - +
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Residues in contact with ALA 89 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371J ALA* 3.8 23.7 - - + +
374J LEU* 4.3 15.3 - - + -
375J ILE* 4.6 14.6 - - + -
529J PHE* 4.5 3.3 - - + -
85K GLU 3.6 7.1 + - - +
86K ILE* 3.0 15.4 + - + +
88K GLU* 1.3 77.3 - - - +
90K PHE* 1.3 64.1 + - + +
92K VAL* 3.7 13.2 + - - +
93K PHE* 3.4 22.8 - - - -
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Residues in contact with PHE 90 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375J ILE* 3.9 26.5 - - + -
86K ILE* 3.6 22.4 + - + -
87K ARG* 4.0 10.1 - - - +
88K GLU 3.3 0.2 - - - -
89K ALA* 1.3 80.2 - - - +
91K ARG* 1.3 56.7 + - - +
93K PHE* 3.0 25.6 + + - +
94K ASP* 3.1 12.5 + - - +
101K ILE* 3.6 26.9 - - + +
106K LEU* 5.4 11.2 - - + -
137K VAL 5.1 4.3 - - - -
139K TYR* 3.5 45.0 - - + -
142K PHE* 3.6 41.7 - + + -
143K VAL* 4.4 10.3 - - + -
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Residues in contact with ARG 91 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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551G ASN* 5.9 4.7 - - - +
554G VAL* 4.8 25.8 - - + +
555G ARG* 3.2 48.5 - - - +
558G GLU* 3.5 37.1 + - - +
84K GLU 6.1 0.4 - - - -
87K ARG* 3.3 27.9 + - - +
88K GLU* 3.1 18.3 + - + +
90K PHE* 1.3 76.0 - - + +
92K VAL* 1.3 63.2 + - - +
93K PHE 3.2 0.4 + - - -
94K ASP* 3.7 21.0 + - + +
139K TYR* 5.4 16.7 + - + -
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Residues in contact with VAL 92 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364J PHE* 4.5 24.5 - - + -
367J GLN* 4.7 18.6 - - + +
368J ILE* 4.0 28.4 - - + +
371J ALA* 3.9 26.2 - - + -
529J PHE* 4.6 9.0 - - + -
88K GLU 3.4 16.2 - - - +
89K ALA* 4.0 7.2 - - - +
90K PHE 3.2 0.8 - - - -
91K ARG* 1.3 78.5 - - - +
93K PHE* 1.3 65.2 + - + +
94K ASP 3.5 2.1 + - - +
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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