Contacts of the helix formed by residues 72 - 81 (chain Q) in PDB entry 5KZ5
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 ARG 72 (chain Q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77K ASN* 3.3 26.1 - - - +
79K ARG 4.9 1.1 - - - -
81K SER 3.4 27.4 - - - +
82K GLY* 3.8 9.1 - - - -
83K THR* 4.3 16.4 - - + -
86K HIS* 3.5 18.7 - - + -
70Q ASP* 3.0 22.9 + - - +
71Q PRO* 1.4 79.4 - - + +
73Q VAL* 1.4 57.0 + - + +
75Q ASP* 3.3 11.3 + - - +
76Q ALA 3.0 24.1 + - - -
82k LYS* 4.5 9.7 - - - +
83k GLY* 3.5 11.1 + - - -
84k LYS* 3.4 23.1 - - - +
111k GLY 3.1 24.9 + - - -
112k LYS* 3.7 0.4 - - - +
113k THR* 3.5 33.5 - - + +
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Residues in contact with VAL 73 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45J ASP* 4.4 6.7 - - - +
48J ALA* 3.8 19.1 - - + -
49J THR* 4.2 13.6 - - + +
79K ARG* 3.7 16.4 - - - +
86K HIS* 5.6 0.4 - - - -
208K LYS* 3.7 25.4 - - + +
209K ASP* 3.3 29.2 - - + +
210K ALA 4.1 7.2 - - - +
70Q ASP* 3.5 14.5 + - + +
71Q PRO 3.4 1.0 - - - -
72Q ARG* 1.4 75.1 - - + +
74Q LEU* 1.4 60.4 + - - +
76Q ALA* 3.5 6.7 + - - +
77Q MET* 3.4 24.1 + - - +
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Residues in contact with LEU 74 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171K LYS* 6.4 0.4 - - + -
172K ASN* 6.0 3.6 - - + -
203K LEU 3.2 26.2 - - - +
204K ALA* 3.3 22.2 - - - +
205K TYR* 4.3 1.6 - - + -
206K SER* 3.3 36.8 - - - +
208K LYS* 3.6 18.5 - - - +
209K ASP* 3.4 17.9 - - - +
70Q ASP 4.1 1.4 + - - -
71Q PRO* 3.2 12.0 + - + +
73Q VAL* 1.4 75.9 - - - +
75Q ASP* 1.3 69.8 + - - +
77Q MET* 3.2 5.5 + - - +
78Q LEU* 3.1 30.6 + - + -
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Residues in contact with ASP 75 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86K HIS* 3.7 7.7 - - + +
87K PRO* 3.4 38.1 - - + +
88K GLY 3.8 3.6 + - - -
171K LYS* 3.3 31.9 + - - +
71Q PRO* 3.2 24.0 - - - +
72Q ARG* 3.4 14.2 - - - +
74Q LEU* 1.3 84.1 - - - +
76Q ALA* 1.4 64.8 + - - +
78Q LEU* 3.2 21.3 + - - +
79Q PRO* 4.1 0.2 - - - +
164j ALA* 4.9 2.4 - - - +
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Residues in contact with ALA 76 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49J THR* 4.9 11.7 - - + +
50J CYS* 5.9 1.1 - - - -
54J ARG* 4.7 8.1 + - - +
86K HIS* 3.6 40.1 - - + +
72Q ARG 3.0 8.9 + - - +
73Q VAL* 3.5 12.8 - - - +
75Q ASP* 1.4 75.7 - - - +
77Q MET* 1.3 62.0 + - + +
78Q LEU 3.3 0.9 + - - -
79Q PRO* 3.9 3.5 - - - +
80Q TYR* 3.7 21.3 - - - -
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Residues in contact with MET 77 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49J THR* 3.6 18.6 - - + -
204K ALA* 5.1 0.2 - - - -
209K ASP* 3.4 28.5 - - - +
210K ALA 3.3 26.0 - - - +
73Q VAL 3.4 12.5 + - - +
74Q LEU 3.2 7.4 + - - +
75Q ASP 3.2 0.6 - - - -
76Q ALA* 1.3 76.5 - - + +
78Q LEU* 1.3 61.7 + - - +
79Q PRO 3.6 1.8 - - - -
80Q TYR* 4.4 8.5 - - + -
81Q LEU* 3.4 52.5 + - + +
299Q PRO* 4.0 13.7 - - + +
302Q VAL* 3.9 28.9 - - + -
303Q GLY 4.6 0.4 - - - +
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Residues in contact with LEU 78 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87K PRO* 4.3 14.8 - - + -
88K GLY 4.8 1.1 - - - +
91K ASP* 3.8 21.3 - - + +
171K LYS* 4.0 35.0 - - + +
204K ALA* 4.3 21.0 - - - +
205K TYR* 4.5 7.0 - - + -
74Q LEU* 3.1 19.4 + - + +
75Q ASP* 3.2 16.6 + - - +
77Q MET* 1.3 78.5 - - - +
79Q PRO* 1.3 66.3 - - + +
82Q ILE* 3.2 35.3 + - + +
166j LYS* 3.8 20.0 - - - +
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Residues in contact with PRO 79 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88K GLY* 4.1 8.7 - - - +
89K SER* 3.8 30.3 - - - +
90K LEU* 4.5 10.3 - - + +
91K ASP* 4.1 26.0 - - + +
75Q ASP 4.1 3.4 - - - +
76Q ALA 3.9 7.9 - - - +
77Q MET 3.8 1.6 - - - -
78Q LEU* 1.3 100.1 - - + +
80Q TYR* 1.4 71.9 + - + +
81Q LEU 3.3 0.7 + - - -
82Q ILE* 3.6 15.8 + - + +
83Q ASN* 3.0 19.2 + - - +
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Residues in contact with TYR 80 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120C PHE* 4.7 18.1 - + - -
121C GLU* 3.9 37.1 - - + +
122C ASP* 6.4 0.2 - - - -
54J ARG* 4.0 10.6 + - - -
89K SER* 3.5 17.2 + - - -
90K LEU* 3.7 20.2 - - + +
76Q ALA 3.7 24.0 - - - -
77Q MET* 4.5 5.2 - - + -
78Q LEU 3.6 0.2 - - - -
79Q PRO* 1.4 84.7 - - + +
81Q LEU* 1.3 72.6 + - + +
83Q ASN* 3.3 25.1 + - - +
84Q TYR* 3.8 12.8 - - + -
67j PRO* 4.6 9.9 - - - +
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Residues in contact with LEU 81 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202K SER 3.7 2.9 - - - +
204K ALA* 3.8 14.6 - - + +
209K ASP* 3.4 31.9 - - - +
77Q MET* 3.4 42.1 + - + +
79Q PRO 3.3 0.8 - - - -
80Q TYR* 1.3 83.4 - - + +
82Q ILE* 1.4 63.5 + - - +
83Q ASN 3.3 0.5 + - - -
84Q TYR* 3.2 31.5 + - + +
85Q TYR* 3.1 63.8 + - + +
299Q PRO* 4.5 1.3 - - + -
302Q VAL* 6.0 0.4 - - + -
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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