Contacts of the helix formed by residues 69 - 79 (chain A) in PDB entry 3FZ7
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 69 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67A TRP* 3.9 23.4 - - + -
68A ASP* 1.3 74.7 - - - +
70A GLU* 1.3 65.6 + - - +
71A ASN* 2.8 34.1 + - - +
72A VAL* 3.1 28.4 + - + +
73A HIS* 3.1 17.9 + - - -
329A TYR* 3.2 26.1 + - - -
330A GLU* 4.8 0.9 - - - +
333A ARG* 4.3 10.0 + - - -
427A ARG* 5.1 2.6 + - - +
44B GLN* 5.6 2.2 - - - -
39F ASP* 4.5 4.3 - - - +
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Residues in contact with GLU 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A ASP 4.2 0.4 - - - -
69A ASP* 1.3 74.1 + - - +
71A ASN* 1.3 61.9 + - - +
73A HIS* 3.2 12.8 + - + +
74A LYS* 2.9 54.2 + - + +
74C LYS* 5.0 14.5 + - - -
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Residues in contact with ASN 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A ASP* 2.8 11.5 + - - +
70A GLU* 1.3 75.9 - - - +
72A VAL* 1.3 57.9 + - - +
74A LYS* 3.2 15.8 + - - +
75A LEU* 2.9 36.5 + - - +
329A TYR* 2.8 38.8 + - + +
39F ASP* 3.6 15.8 + - - +
40F ASP* 2.9 28.6 + - - +
43F PHE* 3.8 25.5 - - + -
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Residues in contact with VAL 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A ASP* 3.1 22.2 + - + +
71A ASN* 1.3 74.1 - - - +
73A HIS* 1.3 56.1 + - + +
75A LEU* 3.1 7.6 + - - +
76A MET* 2.7 34.9 + - + +
281A PRO* 4.1 13.7 - - + -
326A ALA* 4.1 21.5 - - + -
329A TYR* 3.6 20.0 - - + -
330A GLU* 3.4 25.4 - - - +
427A ARG* 6.1 0.4 - - - +
80F ILE* 4.1 19.5 - - + -
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Residues in contact with HIS 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A ASP* 2.8 34.2 + - + +
69A ASP 3.1 33.2 + - - -
70A GLU* 3.2 13.7 + - + +
72A VAL* 1.3 76.8 - - + +
74A LYS* 1.3 56.5 + - + +
76A MET* 3.5 2.7 + - - +
77A ASP* 3.0 29.8 + - - +
77F ASP* 2.6 39.4 + - - +
80F ILE* 3.6 34.7 - - + +
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Residues in contact with LYS 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A GLU* 2.9 47.6 + - + +
71A ASN* 3.7 14.8 + - - +
73A HIS* 1.3 74.2 - - + +
75A LEU* 1.3 65.0 + - - +
77A ASP* 3.3 6.0 + - - +
78A LEU* 3.0 31.7 + - + +
70E GLU* 4.5 17.2 + - - -
43F PHE* 3.7 35.3 - - + -
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Residues in contact with LEU 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A ASN 2.9 19.7 + - - +
72A VAL* 3.6 4.7 - - - +
74A LYS* 1.3 77.1 - - - +
76A MET* 1.4 63.4 + - - +
77A ASP 3.4 0.2 + - - -
78A LEU* 3.6 12.7 + - + +
79A SER* 2.8 29.8 + - - -
322A GLY* 4.9 2.1 - - - -
325A ILE* 4.2 20.9 - - + +
326A ALA* 4.4 8.3 - - + +
329A TYR* 3.5 42.4 - - + -
43F PHE* 3.5 24.5 - - + -
46F ILE* 4.1 24.7 - - + -
47F ASN 4.6 3.6 - - - +
50F LEU* 4.4 4.5 - - + -
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Residues in contact with MET 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A VAL* 2.7 24.4 + - + +
73A HIS* 4.0 3.6 - - - +
75A LEU* 1.4 70.5 - - - +
77A ASP* 1.3 63.6 + - - +
79A SER* 3.0 13.7 + - - -
80A ILE* 3.3 12.5 + - - +
281A PRO* 3.9 18.8 - - + -
282A LEU 5.3 0.2 - - - +
320A PRO* 5.9 2.7 - - + -
322A GLY* 3.3 32.8 - - - +
323A GLN* 3.6 31.6 - - + +
326A ALA* 4.6 1.6 - - + -
76F MET* 6.2 4.3 - - + -
77F ASP* 6.1 0.2 - - - +
80F ILE* 4.0 31.2 - - + -
320F PRO* 5.9 2.5 - - + -
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Residues in contact with ASP 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A HIS 3.0 18.4 + - - +
74A LYS* 3.7 7.0 - - - +
75A LEU 3.2 0.2 - - - -
76A MET* 1.3 78.4 - - - +
78A LEU* 1.3 64.2 + - - +
79A SER 3.2 0.7 + - - -
80A ILE* 3.4 22.9 - - - +
73F HIS* 2.6 51.3 + - - +
76F MET* 6.1 0.2 - - - +
77F ASP* 5.0 9.3 - - + +
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Residues in contact with LEU 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A LYS* 3.0 27.2 + - + +
75A LEU* 3.9 20.9 - - + +
76A MET 3.4 0.2 - - - -
77A ASP* 1.3 77.0 - - - +
79A SER* 1.3 60.9 + - - +
80A ILE* 3.4 3.5 + - - +
81A ASN* 5.0 0.7 + - - +
82A LYS* 3.7 15.8 + - - +
43F PHE* 4.5 6.5 - - + -
47F ASN* 3.3 27.8 - - - +
50F LEU* 4.8 12.3 - - + -
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Residues in contact with SER 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A LEU 2.8 21.7 + - - -
76A MET 3.0 4.3 + - - -
78A LEU* 1.3 78.4 - - - +
80A ILE* 1.3 65.7 + - - +
81A ASN 2.9 5.1 + - - -
82A LYS* 2.9 35.9 + - - +
320A PRO* 4.2 7.0 - - - +
321A ALA 4.3 0.2 + - - -
322A GLY* 3.5 27.2 - - - -
325A ILE* 3.6 18.3 - - - +
50F LEU* 4.4 3.1 - - - +
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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