Contacts of the helix formed by residues 72 - 82 (chain K) in PDB entry 2ZJQ
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 ASP 72 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26K THR* 5.0 6.0 + - + +
30K ARG* 3.0 25.0 + - - +
70K ILE* 3.2 7.2 - - - +
71K HIS* 1.3 75.3 - - - +
73K LYS* 1.3 69.6 + - - +
74K ASP* 3.0 25.2 + - - +
75K VAL* 3.0 29.3 + - + +
76K VAL* 3.1 10.1 + - - +
1306X U 4.9 3.6 + - - -
1307X U 5.8 0.8 - - - +
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Residues in contact with LYS 73 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71K HIS 3.8 3.8 + - - +
72K ASP* 1.3 72.4 + - - +
74K ASP* 1.3 63.8 + - - +
76K VAL* 2.6 31.7 - - - +
77K ARG* 3.2 24.5 + - - +
1468X A 5.6 13.0 - - - +
1469X U 4.7 18.8 + - - +
2680X U 3.0 31.6 + - - +
2681X A 3.2 33.5 + - - +
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Residues in contact with ASP 74 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72K ASP* 3.0 16.8 + - - +
73K LYS* 1.3 74.0 - - - +
75K VAL* 1.3 67.9 + - + +
77K ARG* 2.3 54.8 + - - +
78K LYS* 2.9 11.3 + - - +
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Residues in contact with VAL 75 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26K THR* 3.5 36.3 - - + +
29K LEU* 4.0 27.6 - - + +
30K ARG* 3.7 24.0 - - + +
70K ILE* 3.9 11.4 - - + -
72K ASP* 3.0 28.7 + - + +
74K ASP* 1.3 74.6 - - + +
76K VAL* 1.3 64.1 + - - +
78K LYS* 3.0 11.5 + - + +
79K VAL* 2.9 22.5 + - - +
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Residues in contact with VAL 76 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63K ARG* 4.4 11.9 - - + +
66K VAL* 4.0 26.0 - - + -
67K ALA* 4.4 12.3 - - + +
70K ILE* 3.5 19.4 - - + +
72K ASP 3.1 4.1 + - - +
73K LYS* 2.6 35.7 - - - +
74K ASP 2.9 1.4 + - - -
75K VAL* 1.3 77.2 - - - +
77K ARG* 1.3 55.3 + - + +
79K VAL* 2.6 25.8 - - - +
80K MET* 2.6 33.4 + - + +
1469X U 5.6 4.7 - - - +
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Residues in contact with ARG 77 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63K ARG* 4.1 16.8 - - - +
73K LYS* 3.2 22.8 + - - +
74K ASP* 2.3 58.3 + - - +
76K VAL* 1.3 75.6 - - + +
78K LYS* 1.3 58.1 + - - +
80K MET* 4.0 6.3 - - - -
81K ASP* 2.6 47.5 + - - +
1468X A 4.1 26.6 + - - +
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Residues in contact with LYS 78 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29K LEU 2.9 30.3 + - - +
30K ARG* 3.4 25.6 + - + +
31K GLU* 4.1 4.2 - - - +
32K GLY* 4.7 4.4 - - - +
74K ASP 2.9 10.3 + - - +
75K VAL* 3.3 13.0 - - - +
77K ARG* 1.3 75.7 - - - +
79K VAL* 1.3 60.5 + - - +
82K GLU* 2.7 61.9 + - + +
83K VAL* 3.1 17.0 + - + -
115K LEU* 5.4 4.1 - - - +
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Residues in contact with VAL 79 (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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29K LEU* 3.8 31.6 + - + -
51K LEU* 5.3 1.6 - - + +
52K ILE* 4.9 10.5 - - + -
55K ALA* 3.8 18.6 - - + -
66K VAL* 4.4 12.8 - - + -
70K ILE* 5.0 1.3 - - + -
75K VAL 2.9 11.4 + - - +
76K VAL* 2.6 42.2 - - + +
78K LYS* 1.3 76.3 - - - +
80K MET* 1.3 61.1 + - + +
83K VAL* 2.9 20.4 - - + +
84K ALA* 2.8 37.1 + - + +
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Residues in contact with MET 80 (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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55K ALA* 3.7 38.2 - - + +
58K GLY* 4.9 13.9 - - - +
63K ARG* 3.1 71.6 - - - +
66K VAL* 3.8 13.9 - - + -
76K VAL* 2.6 32.6 + - + +
77K ARG 3.6 2.7 - - - +
79K VAL* 1.3 76.2 - - + +
81K ASP* 1.3 61.4 + - - +
84K ALA* 4.0 4.3 - - - +
85K PRO* 3.9 10.7 - - - +
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Residues in contact with ASP 81 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63K ARG* 3.3 26.0 + - - -
77K ARG* 2.6 33.4 + - - +
80K MET* 1.3 78.7 - - - +
82K GLU* 1.3 62.5 + - + +
85K PRO* 2.8 23.4 - - - +
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Residues in contact with GLU 82 (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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77K ARG 3.8 0.2 + - - -
78K LYS* 2.7 45.8 + - + +
81K ASP* 1.3 76.2 - - + +
83K VAL* 1.3 61.0 + - + +
85K PRO* 3.2 7.8 - - - +
86K LYS* 3.2 40.6 + - - +
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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