Contacts of the helix formed by residues 50 - 68 (chain F) in PDB entry 5ZX2
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 ASN 50 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346D ARG* 3.5 15.2 - - - +
391D VAL* 5.5 1.3 - - - +
392D THR* 4.2 29.4 + - - +
45F LEU* 3.9 3.7 - - - +
48F THR* 2.8 23.2 + - - +
49F ARG* 1.3 80.4 - - - +
51F PRO* 1.3 84.5 - - - +
52F ALA* 3.8 7.9 + - - +
53F ASP* 2.8 33.0 + - + +
54F ALA* 3.0 10.0 + - - +
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Residues in contact with PRO 51 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389D ARG* 3.9 30.7 - - + +
41F TYR* 3.7 18.6 + - - +
45F LEU* 4.1 6.7 - - + -
50F ASN* 1.3 93.4 - - - +
52F ALA* 1.3 58.5 + - + +
54F ALA* 3.3 2.1 + - - +
55F GLU* 2.9 39.6 + - - +
32G G 3.5 25.4 - - + +
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Residues in contact with ALA 52 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346D ARG* 3.5 31.0 - - - +
350D ARG* 3.4 20.2 + - - +
391D VAL* 4.8 13.9 - - + -
50F ASN* 3.4 6.8 + - - +
51F PRO* 1.3 81.9 - - + +
53F ASP* 1.3 59.7 + - - +
55F GLU* 3.1 4.8 + - - -
56F ASP* 2.9 32.9 + - - +
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Residues in contact with ASP 53 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346D ARG* 2.7 23.9 + - - -
48F THR* 3.7 24.4 - - + +
50F ASN* 2.8 26.6 + - - +
51F PRO 3.4 0.4 - - - -
52F ALA* 1.3 76.3 - - - +
54F ALA* 1.3 56.5 + - - +
56F ASP* 3.9 8.2 - - - +
57F LEU* 2.9 30.1 + - - +
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Residues in contact with ALA 54 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41F TYR* 3.6 19.0 - - + -
44F ALA* 3.7 7.8 - - + +
45F LEU* 3.8 23.8 - - + +
48F THR* 3.4 14.7 + - - +
50F ASN 3.0 20.5 + - - +
51F PRO 3.5 5.2 - - - +
52F ALA 3.2 0.2 - - - -
53F ASP* 1.3 74.4 - - - +
55F GLU* 1.3 59.8 + - - +
57F LEU* 3.4 1.2 + - - +
58F LEU* 2.9 31.4 + - - +
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Residues in contact with GLU 55 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350D ARG* 2.9 24.3 + - - +
372D ARG* 4.0 16.3 + - - +
373D MET* 3.8 28.5 - - - +
376D GLU* 3.9 14.3 - - - +
41F TYR* 3.9 22.1 + - + -
51F PRO* 2.9 24.3 + - - +
52F ALA* 3.1 6.6 + - - +
54F ALA* 1.3 76.1 - - - +
56F ASP* 1.3 62.8 + - - +
58F LEU* 3.3 4.0 + - - +
59F GLN* 2.9 27.9 + - - +
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Residues in contact with ASP 56 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346D ARG* 3.8 21.7 + - - +
349D ASN* 5.7 3.4 - - - +
350D ARG* 2.8 28.7 + - - +
353D ARG* 3.2 32.4 + - - +
373D MET* 3.4 1.2 - - - +
52F ALA 2.9 20.2 + - - +
53F ASP* 4.0 9.5 - - - +
55F GLU* 1.3 75.4 - - - +
57F LEU* 1.3 62.4 + - - +
59F GLN* 3.3 1.9 + - - +
60F GLU* 3.0 29.1 + - - +
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Residues in contact with LEU 57 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44F ALA* 3.7 25.6 - - + +
47F MET* 4.4 3.4 - - - -
48F THR* 4.1 14.8 - - + -
53F ASP 2.9 19.8 + - - +
54F ALA 3.7 2.7 - - - +
56F ASP* 1.3 77.0 - - - +
58F LEU* 1.3 63.1 + - - +
60F GLU* 3.3 3.3 + - - +
61F THR* 2.9 27.0 + - - +
86F LEU* 3.7 21.5 - - + +
89F THR* 4.0 13.9 - - + -
90F TYR* 3.7 45.8 - - + +
93F SER* 6.2 1.3 - - - -
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Residues in contact with LEU 58 (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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369D ASN* 6.1 2.2 - - - +
37F LEU* 4.3 31.2 - - + +
40F LEU* 3.6 30.7 - - + -
41F TYR* 3.7 32.5 - - + +
44F ALA* 4.8 4.0 - - + -
54F ALA 2.9 17.8 + - - +
55F GLU* 3.8 4.3 - - - +
57F LEU* 1.3 76.4 - - - +
59F GLN* 1.3 64.2 + - + +
61F THR* 3.3 2.8 - - - -
62F MET* 2.9 36.8 + - + +
86F LEU* 4.0 15.0 - - + +
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Residues in contact with GLN 59 (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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353D ARG* 3.5 12.6 - - - +
357D LEU* 3.6 19.9 - - - +
366D ILE* 3.7 25.6 + - - +
369D ASN* 3.4 25.8 + - - +
370D GLU* 2.6 32.4 + - - +
373D MET* 3.6 20.3 - - + +
55F GLU 2.9 20.6 + - - +
56F ASP 3.7 2.9 - - - +
58F LEU* 1.3 81.0 - - + +
60F GLU* 1.3 61.0 + - - +
62F MET* 3.1 6.8 + - - +
63F VAL* 2.9 30.0 + - - +
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Residues in contact with GLU 60 (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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353D ARG* 3.0 30.3 + - - +
356D ARG* 2.6 35.2 + - - -
56F ASP 3.0 16.2 + - - +
57F LEU* 3.9 4.3 - - - +
59F GLN* 1.3 75.0 - - - +
61F THR* 1.3 62.6 + - - +
63F VAL* 3.1 14.8 + - - +
64F LYS* 3.0 31.1 + - - +
89F THR* 4.2 17.5 - - + -
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Residues in contact with THR 61 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40F LEU* 5.6 0.9 - - + -
57F LEU* 2.9 16.8 + - - +
58F LEU* 3.3 10.1 - - + -
60F GLU* 1.3 76.9 - - - +
62F MET* 1.3 75.3 + - + +
64F LYS* 3.1 5.4 + - - +
65F ALA* 2.9 26.4 + - + +
82F LEU* 4.0 9.9 - - + +
85F ILE* 4.0 13.8 - - + +
86F LEU* 3.1 49.3 - - + +
89F THR* 4.0 7.9 + - - +
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Residues in contact with MET 62 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357D LEU* 5.5 1.6 - - - -
366D ILE* 4.1 31.2 - - + -
29F PHE* 4.5 20.8 - - + -
33F ALA* 5.6 3.1 - - - +
34F ILE* 6.0 1.8 - - - -
37F LEU* 3.6 27.1 - - + -
40F LEU* 3.8 26.5 - - + -
58F LEU* 2.9 20.5 + - + +
59F GLN* 3.1 9.8 + - - +
61F THR* 1.3 94.3 - - + +
63F VAL* 1.3 65.1 + - - +
65F ALA* 3.9 2.0 - - + +
66F TYR* 2.9 28.6 + - - +
82F LEU* 4.3 16.6 - - + -
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Residues in contact with VAL 63 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353D ARG* 4.2 13.2 - - + +
356D ARG* 4.5 21.8 - - + +
357D LEU* 3.6 32.1 - - + -
360D LEU* 4.4 18.3 - - + +
59F GLN 2.9 19.6 + - - +
60F GLU* 3.1 20.4 + - - +
62F MET* 1.3 76.0 - - - +
64F LYS* 1.3 66.2 + - + +
66F TYR* 4.3 1.6 - - - +
67F ALA* 3.0 28.9 + - + +
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Residues in contact with LYS 64 (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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60F GLU* 3.0 19.3 + - - +
61F THR 3.1 6.3 + - - +
63F VAL* 1.3 78.6 - - + +
65F ALA* 1.3 57.7 + - - +
67F ALA* 3.8 4.1 - - - +
68F GLY* 2.9 27.2 + - - -
85F ILE* 3.7 15.9 + - + -
88F ASN* 4.6 1.6 - - - +
89F THR* 2.9 43.4 + - - +
92F ASN* 3.2 28.1 - - - +
25G G 5.5 1.2 + - - -
26G T 3.8 26.6 + - - +
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Residues in contact with ALA 65 (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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29F PHE* 4.3 10.1 - - + -
61F THR* 2.9 16.4 + - + +
62F MET* 3.9 9.0 - - + +
63F VAL 3.3 0.2 - - - -
64F LYS* 1.3 76.3 - - - +
66F TYR* 1.3 58.4 + - - +
68F GLY 3.1 2.3 + - - -
69F PHE* 2.8 34.8 + - - +
81F TRP* 3.8 14.3 - - + -
82F LEU* 3.7 30.7 - - + -
85F ILE* 4.2 6.5 - - + +
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Residues in contact with TYR 66 (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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357D LEU* 6.4 0.9 - - + -
360D LEU* 3.2 33.9 + - + -
361D GLY 3.0 19.9 + - - -
362D ALA* 4.5 7.9 - - + -
363D PRO* 3.7 27.6 - - + -
25F LEU 5.8 0.4 - - - -
26F THR* 3.3 35.6 - - + +
29F PHE* 3.8 32.6 - + + -
62F MET 2.9 19.3 + - - +
63F VAL* 4.3 2.0 - - - +
65F ALA* 1.3 74.6 - - - +
67F ALA* 1.3 69.4 + - - +
68F GLY 3.2 0.2 + - - -
69F PHE* 3.4 13.3 + - + +
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Residues in contact with ALA 67 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360D LEU* 3.8 22.0 - - + +
63F VAL* 3.0 22.0 + - + +
64F LYS* 3.9 4.7 - - - +
66F TYR* 1.3 80.0 - - - +
68F GLY* 1.3 57.4 + - - +
69F PHE 3.8 0.5 + - - -
70F ARG* 5.2 0.9 + - - +
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Residues in contact with GLY 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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64F LYS 2.9 16.0 + - - -
65F ALA 3.3 3.4 - - - -
67F ALA* 1.3 77.9 - - - +
69F PHE* 1.3 58.9 + - - +
70F ARG* 3.2 4.6 + - - -
71F SER* 2.7 30.0 + - - -
81F TRP* 3.8 8.9 - - - -
26G T 5.3 4.7 - - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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