Contacts of the helix formed by residues 67 - 81 (chain F) in PDB entry 1NZB
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 67 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52F TRP* 5.3 0.2 - - - -
62F LYS* 4.6 22.6 + - + +
65F PRO 3.5 3.7 + - - +
66F ALA* 1.3 71.3 - - - +
68F PRO* 1.3 81.6 - - + +
69F GLU* 4.4 11.6 - - + +
70F ASP* 2.9 37.4 + - - +
71F VAL* 3.2 9.9 + - - +
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Residues in contact with PRO 68 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66F ALA 3.7 7.8 - - - +
67F GLU* 1.3 94.8 - - + +
69F GLU* 1.3 66.3 + - + +
71F VAL* 3.1 4.6 + - + +
72F ARG* 3.0 21.2 + - - +
107F PRO* 5.0 6.1 - - + +
110F SER* 3.8 33.0 - - - +
112F ALA* 4.7 7.6 - - + -
113F VAL* 3.4 21.6 - - + +
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Residues in contact with GLU 69 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25E LYS* 4.7 9.9 + - - +
29E ASP* 3.9 10.4 - - - +
32E ARG* 3.2 30.0 + - - -
61F ARG* 5.9 0.2 - - - -
67F GLU* 3.2 8.1 + - + +
68F PRO* 1.3 82.7 - - + +
70F ASP* 1.3 64.7 + - - +
72F ARG* 3.5 11.6 + - - +
73F ASP* 3.1 34.4 + - - +
112F ALA* 4.0 14.9 - - + +
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Residues in contact with ASP 70 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52F TRP* 3.9 17.9 - - + -
55F TRP* 4.3 3.0 + - - +
61F ARG* 2.5 55.9 + - + +
62F LYS* 4.5 6.3 + - - +
67F GLU* 2.9 28.0 + - + +
69F GLU* 1.3 84.0 - - - +
71F VAL* 1.3 55.8 + - - +
72F ARG 3.1 0.2 - - - -
73F ASP* 3.1 7.8 + - - +
74F TYR* 2.7 35.2 + - - +
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Residues in contact with VAL 71 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52F TRP* 4.0 15.0 - - + -
66F ALA* 3.6 31.0 - - + -
67F GLU 3.2 7.1 + - - +
68F PRO 3.1 6.8 + - - +
70F ASP* 1.3 76.8 - - - +
72F ARG* 1.3 58.1 + - - +
74F TYR* 3.2 4.2 + - + +
75F LEU* 2.8 35.8 + - + +
92F LEU* 4.2 11.2 - - + -
95F LEU* 5.2 10.1 - - + -
107F PRO* 3.9 19.5 - - + -
113F VAL* 3.7 28.9 - - + -
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Residues in contact with ARG 72 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32E ARG* 2.9 57.3 - - - +
33E ASP* 2.9 25.1 + - - -
68F PRO 3.0 12.0 + - - +
69F GLU* 3.7 14.0 + - - +
71F VAL* 1.3 76.4 - - - +
73F ASP* 1.3 71.6 + - - +
75F LEU* 3.3 2.9 + - - +
76F LEU* 3.1 46.7 + - - +
112F ALA* 3.6 17.0 - - + -
113F VAL* 4.2 6.2 - - - +
116F VAL* 3.3 33.7 - - + +
119F ARG* 4.0 4.9 - - - +
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Residues in contact with ASP 73 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55F TRP* 3.7 22.3 - - + -
61F ARG* 3.9 19.7 + - - +
69F GLU* 3.1 22.6 + - - +
70F ASP 3.1 9.5 + - - +
72F ARG* 1.3 83.9 + - - +
74F TYR* 1.3 59.4 + - - +
76F LEU* 3.2 11.8 + - - +
77F TYR* 3.0 27.0 + - - +
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Residues in contact with TYR 74 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48F VAL 4.2 1.0 + - - -
51F SER* 2.5 40.3 + - - -
52F TRP* 3.2 49.5 + + + -
55F TRP* 3.8 29.5 - + + +
70F ASP 2.7 11.9 + - - +
71F VAL* 3.5 6.1 - - + +
73F ASP* 1.3 72.0 - - - +
75F LEU* 1.3 73.4 + - + +
77F TYR* 3.4 18.6 + + - +
78F LEU* 3.2 32.3 + - + +
91F HIS* 3.3 35.1 + - + -
95F LEU* 4.7 10.3 - - + -
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Residues in contact with LEU 75 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71F VAL* 2.8 26.6 + - + +
72F ARG* 3.8 6.3 - - - +
73F ASP 3.2 0.2 - - - -
74F TYR* 1.3 89.1 - - + +
76F LEU* 1.3 63.0 + - - +
78F LEU* 3.3 13.3 + - + +
79F GLN 3.1 16.8 + - - -
88F ILE* 3.8 19.3 - - + +
92F LEU* 3.9 50.5 - - + +
113F VAL* 4.4 7.2 - - + -
116F VAL* 4.5 12.3 - - + -
117F MET* 4.1 12.6 - - + -
120F ILE* 3.4 22.2 - - + +
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Residues in contact with LEU 76 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72F ARG* 3.1 48.2 + - - +
73F ASP* 3.6 12.3 - - - +
75F LEU* 1.3 74.5 - - - +
77F TYR* 1.3 66.6 + - - +
79F GLN* 3.2 28.6 + - - +
80F ALA* 3.0 22.0 + - - +
116F VAL* 3.9 8.7 - - + -
119F ARG* 4.3 20.6 - - - +
120F ILE* 4.1 12.3 - - + -
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Residues in contact with TYR 77 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51F SER* 5.8 2.5 - - - -
55F TRP* 3.1 57.4 - + + -
73F ASP 3.0 7.8 + - - +
74F TYR* 3.6 22.4 - + - +
75F LEU 3.3 0.2 - - - -
76F LEU* 1.3 77.3 - - - +
78F LEU* 1.3 64.3 + - + +
80F ALA* 3.0 11.9 + - + +
81F ARG* 2.9 60.6 + - + +
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Residues in contact with LEU 78 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51F SER* 5.2 2.0 - - - +
74F TYR* 3.2 40.1 + - + +
75F LEU* 3.5 10.3 - - + +
76F LEU 3.2 0.4 - - - -
77F TYR* 1.3 84.4 - - + +
79F GLN* 1.3 64.0 + - - +
81F ARG* 3.1 29.1 + - - +
82F GLY 3.5 3.5 + - - -
83F LEU* 3.3 32.3 + - + +
88F ILE* 3.9 28.0 - - + -
91F HIS* 3.5 44.4 - - + +
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Residues in contact with GLN 79 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75F LEU 3.1 10.0 + - - +
76F LEU* 3.2 29.6 + - - +
78F LEU* 1.3 76.8 - - - +
80F ALA* 1.3 59.8 + - - +
82F GLY* 2.9 22.5 + - - -
83F LEU 4.1 2.2 + - - +
88F ILE* 3.9 10.2 - - - +
119F ARG* 5.2 0.9 + - - -
120F ILE* 3.3 29.7 - - + +
123F GLU* 3.1 27.3 + - - +
124F ASN* 2.5 36.3 + - - +
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Residues in contact with ALA 80 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76F LEU 3.0 11.7 + - - +
77F TYR* 3.2 15.7 - - + +
79F GLN* 1.3 73.7 - - - +
81F ARG* 1.3 56.3 + - - +
82F GLY* 2.9 10.7 + - - -
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Residues in contact with ARG 81 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51F SER* 6.0 0.4 + - - -
77F TYR* 2.9 57.4 + - + +
78F LEU* 3.1 19.9 + - - +
80F ALA* 1.3 74.4 - - - +
82F GLY* 1.3 61.0 + - - +
83F LEU* 3.6 22.0 + - + +
111G T 4.4 0.4 + - - -
112G A 2.6 40.0 + - - -
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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