Contacts of the helix formed by residues 67 - 81 (chain L) 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 THR 67 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38L ILE* 6.0 0.5 - - - +
56L SER* 3.8 18.8 + - - +
60L LYS* 3.3 32.5 - - - +
61L SER* 5.0 0.2 - - - +
63L ASN* 2.4 38.7 + - + +
64L LYS* 3.6 9.1 + - - -
66L ASP* 1.3 72.2 - - - +
68L ALA* 1.3 56.6 + - - +
69L ALA 3.2 2.0 - - - -
70L ALA* 2.6 53.6 + - + +
71L VAL* 3.0 8.3 - - - +
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Residues in contact with ALA 68 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33L ARG* 2.5 30.5 + - - +
38L ILE* 6.4 0.7 - - - -
64L LYS 5.2 2.1 + - - -
65L THR 4.6 7.2 - - - +
66L ASP* 2.3 32.0 + - - +
67L THR* 1.3 68.9 - - - +
69L ALA* 1.3 59.8 + - - +
71L VAL* 3.1 7.0 - - - +
72L GLY 3.5 0.9 + - - -
99L ARG* 3.9 11.2 - - - +
102L ALA* 3.0 24.7 - - + -
103L LEU 3.5 2.1 + - - -
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Residues in contact with ALA 69 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66L ASP 3.9 2.0 + - - +
67L THR 3.2 0.8 - - - -
68L ALA* 1.3 77.6 - - + +
70L ALA* 1.3 59.0 + - - +
72L GLY 2.8 0.3 + - - -
73L LYS* 2.5 43.3 + - + +
102L ALA* 3.9 3.7 - - + +
106L ALA* 3.5 21.5 - - + -
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Residues in contact with ALA 70 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56L SER* 4.4 2.0 - - - +
67L THR* 2.6 48.1 + - + +
69L ALA* 1.3 72.3 - - - +
71L VAL* 1.3 48.5 + - - +
73L LYS* 3.5 5.1 - - - +
74L ALA* 2.5 40.6 + - - +
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Residues in contact with VAL 71 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33L ARG* 3.6 6.1 - - - +
38L ILE* 3.8 14.6 - - + -
40L ALA* 3.4 19.5 - - + -
54L ALA 2.8 19.9 - - - +
55L SER 2.5 22.4 - - - +
56L SER* 2.9 14.6 + - - +
67L THR* 3.0 17.7 - - - +
68L ALA* 3.1 13.7 - - - +
70L ALA* 1.3 72.2 - - - +
72L GLY* 1.3 57.2 + - - +
74L ALA* 3.7 4.0 - - - -
75L LEU* 2.7 31.9 + - - +
103L LEU* 3.4 11.9 - - + -
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Residues in contact with GLY 72 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68L ALA 3.5 3.2 + - - -
69L ALA 2.8 8.0 + - - -
71L VAL* 1.3 78.8 - - - +
73L LYS* 1.3 54.6 + - - +
75L LEU* 3.1 2.6 + - - +
76L ALA 2.8 31.4 + - - -
103L LEU* 3.2 38.1 - - - -
106L ALA* 3.6 1.6 - - - -
107L ALA* 3.2 14.1 - - - +
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Residues in contact with LYS 73 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69L ALA* 2.5 25.0 + - + +
70L ALA* 3.7 4.7 - - - +
72L GLY* 1.3 68.5 - - - -
74L ALA* 1.3 62.8 + - - +
76L ALA* 4.8 0.2 - - - +
77L ALA* 3.3 23.7 + - - +
106L ALA* 3.7 17.6 - - + +
110L GLY* 5.0 10.0 - - - -
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Residues in contact with ALA 74 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54L ALA* 3.3 16.7 - - + +
55L SER 5.1 0.7 - - - +
70L ALA 2.5 26.5 + - - +
71L VAL* 3.7 6.1 - - - +
73L LYS* 1.3 73.5 - - - +
75L LEU* 1.3 57.2 + - - +
77L ALA* 3.9 3.0 - - - +
78L ALA* 2.9 27.2 + - - +
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Residues in contact with LEU 75 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29L LEU* 3.4 28.5 - - + -
40L ALA* 3.0 30.5 - - + +
42L ILE* 5.2 6.3 - - + -
52L ALA* 4.8 1.8 - - + -
53L ALA* 3.2 14.6 - - - +
54L ALA* 2.8 39.9 - - + +
71L VAL 2.7 19.5 + - - +
72L GLY 3.1 4.4 + - - +
74L ALA* 1.3 71.5 - - - +
76L ALA* 1.3 59.2 + - - +
77L ALA 3.1 2.0 - - - -
78L ALA* 2.4 34.7 + - + +
79L ALA* 3.2 4.4 + - + +
103L LEU* 3.4 11.4 - - + -
107L ALA* 4.7 2.5 - - + -
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Residues in contact with ALA 76 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72L GLY 2.8 10.3 + - - +
73L LYS 4.8 0.2 - - - +
75L LEU* 1.3 74.9 - - - +
77L ALA* 1.3 62.5 + - - +
79L ALA* 3.6 12.6 + - - +
80L ALA* 3.8 6.1 + - - +
107L ALA* 3.2 31.3 - - + +
110L GLY* 3.2 8.1 - - - -
111L GLY* 3.1 36.9 - - - +
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Residues in contact with ALA 77 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73L LYS 3.3 19.6 + - - +
74L ALA* 3.9 3.1 - - - +
75L LEU 3.1 0.6 - - - -
76L ALA* 1.3 78.6 - - - +
78L ALA* 1.3 58.1 + - - +
80L ALA* 2.7 33.0 - - - +
81L GLU* 4.1 2.3 + - - +
110L GLY 3.6 12.2 + - - +
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Residues in contact with ALA 78 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52L ALA* 4.3 15.4 - - + +
53L ALA 4.8 3.6 - - - +
54L ALA* 4.1 8.7 - - + -
74L ALA 2.9 16.8 + - - +
75L LEU* 2.4 34.2 + - + +
77L ALA* 1.3 69.4 - - - +
79L ALA* 1.3 61.2 + - - +
80L ALA 2.9 1.6 + - - -
81L GLU* 3.3 17.1 + - - +
82L LYS* 4.2 4.5 - - - +
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Residues in contact with ALA 79 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42L ILE* 5.9 4.9 - - + -
52L ALA* 3.9 18.7 - - + +
75L LEU* 3.2 5.4 + - + +
76L ALA* 3.6 8.0 + - - +
77L ALA 3.5 0.4 - - - -
78L ALA* 1.3 77.7 - - - +
80L ALA* 1.3 49.9 + - - +
81L GLU 3.2 0.4 - - - -
82L LYS* 2.7 13.4 + - - +
83L GLY* 2.4 33.5 + - - -
84L ILE* 4.0 32.3 - - + +
87L VAL* 6.2 0.9 - - + -
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Residues in contact with ALA 80 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76L ALA 3.8 4.0 + - - +
77L ALA* 2.7 26.2 + - - +
78L ALA 2.9 0.2 + - - -
79L ALA* 1.3 71.9 - - - +
81L GLU* 1.3 56.6 + - + +
82L LYS 2.8 14.9 + - - -
83L GLY* 3.2 13.3 + - - +
84L ILE 5.4 0.2 - - - +
111L GLY 6.2 0.2 - - - +
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Residues in contact with GLU 81 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77L ALA 5.2 1.6 - - - +
78L ALA* 3.3 9.8 + - - +
79L ALA 3.2 0.8 - - - -
80L ALA* 1.3 78.6 - - + +
82L LYS* 1.3 76.2 + - + +
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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