Contacts of the helix formed by residues 60 - 71 (chain A) in PDB entry 3ZO7
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 SER 60 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3A TYR* 3.4 7.8 + - - -
58A VAL* 3.5 9.9 + - - +
59A ASN* 1.3 82.6 - - - +
61A HIS* 1.3 64.7 + - - +
62A ASP* 3.5 11.0 + - - +
63A GLU* 3.1 28.6 + - - +
64A LEU* 3.2 16.8 + - - +
1B MET* 3.8 18.8 - - - -
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Residues in contact with HIS 61 (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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3A TYR* 2.8 35.2 + + - -
60A SER* 1.3 74.9 - - - +
62A ASP* 1.3 59.0 + - - +
64A LEU* 3.3 2.2 + - - -
65A HIS 2.9 24.6 + - - -
83A PRO* 5.7 0.2 - - + -
1B MET* 3.4 26.1 - - + +
2B LEU 2.9 30.6 + - - -
3B TYR* 3.4 36.3 - + - -
61B HIS* 3.8 5.2 - + - -
83B PRO* 3.6 19.0 - - + +
84B LEU 3.2 21.3 - - - +
85B SER* 3.3 11.5 + - - +
47C THR* 3.6 12.6 - - - +
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Residues in contact with ASP 62 (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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60A SER* 3.2 10.0 + - - +
61A HIS* 1.3 79.5 - - - +
63A GLU* 1.3 61.9 + - + +
65A HIS* 3.4 2.3 + - - +
66A GLU* 3.1 33.1 + - + +
85B SER* 3.0 15.1 - - - -
86B HIS* 2.7 43.4 + - - +
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Residues in contact with GLU 63 (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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39A GLN* 4.2 13.7 + - - +
58A VAL* 3.6 12.6 - - + +
59A ASN* 3.0 46.8 + - - +
60A SER* 3.1 23.4 + - - +
62A ASP* 1.3 73.8 - - + +
64A LEU* 1.3 64.9 + - - +
66A GLU* 3.5 5.4 + - - +
67A ILE* 3.2 29.0 + - + +
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Residues in contact with LEU 64 (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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3A TYR* 3.6 35.0 - - + -
5A VAL* 4.4 2.0 - - + -
56A PHE* 3.7 41.7 - - + -
58A VAL* 3.9 12.7 - - + +
60A SER 3.2 9.9 + - - +
61A HIS* 3.3 8.7 + - - +
63A GLU* 1.3 79.3 - - - +
65A HIS* 1.3 62.8 + - - +
67A ILE* 3.2 8.0 + - + +
68A LEU* 2.9 45.8 + - + +
81A VAL* 3.8 18.4 - - + -
47C THR* 4.1 8.3 - - + -
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Residues in contact with HIS 65 (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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61A HIS 2.9 16.8 + - - +
62A ASP* 3.9 4.3 - - - +
63A GLU 3.3 0.2 - - - -
64A LEU* 1.3 76.8 - - - +
66A GLU* 1.3 65.3 + - + +
68A LEU* 3.3 2.4 + - - +
69A TRP* 2.7 75.9 + + + +
85B SER* 3.8 14.1 - - - +
86B HIS 5.6 2.9 - - - -
88B PRO* 6.0 1.2 - - + +
45C ARG* 3.3 45.9 + - + +
47C THR* 4.0 8.7 - - + +
48C GLY* 3.3 21.9 + - - +
49C LYS 4.0 5.8 - - - -
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Residues in contact with GLU 66 (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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62A ASP* 3.1 24.5 + - + +
63A GLU* 3.8 6.3 - - - +
64A LEU 3.3 0.2 - - - -
65A HIS* 1.3 86.2 - - + +
67A ILE* 1.3 62.7 + - + +
69A TRP* 3.7 12.4 - - - +
70A SER* 3.2 24.1 + - - -
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Residues in contact with ILE 67 (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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30A ARG* 4.7 6.3 - - - +
34A LEU* 3.8 35.9 - - + -
39A GLN* 3.9 35.0 - - + +
56A PHE* 4.0 23.6 - - + -
58A VAL* 3.9 17.3 - - + -
63A GLU* 3.2 15.2 + - + +
64A LEU* 3.2 8.9 + - + +
65A HIS 3.2 0.4 - - - -
66A GLU* 1.3 76.2 - - + +
68A LEU* 1.3 68.4 + - + +
70A SER* 2.8 22.8 + - - -
71A LEU* 3.3 12.8 + - + +
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Residues in contact with LEU 68 (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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5A VAL* 4.3 5.6 - - + -
7A MET* 4.0 26.9 - - + -
56A PHE* 4.2 17.7 - - + -
64A LEU* 2.9 41.2 + - + +
65A HIS 3.8 2.7 - - - +
67A ILE* 1.3 77.0 - - + +
69A TRP* 1.3 63.1 + - - +
70A SER 3.1 1.0 + - - -
71A LEU* 3.2 24.0 + - + +
74A PHE* 3.0 18.3 - - + -
79A ILE* 4.4 15.0 - - + -
81A VAL* 4.0 16.2 - - + -
48C GLY* 3.6 32.3 - - - +
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Residues in contact with TRP 69 (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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65A HIS* 2.7 56.1 + + + +
66A GLU* 3.7 14.1 - - - +
67A ILE 3.2 0.2 - - - -
68A LEU* 1.3 73.8 - - - +
70A SER* 1.3 61.5 + - - +
71A LEU 3.7 0.7 + - - +
74A PHE* 3.6 51.8 - + - +
20C GLU* 5.7 0.2 - - - -
24C LYS* 4.0 27.9 - - + +
45C ARG* 4.1 18.2 - - - -
49C LYS 4.1 10.3 - - - -
50C TYR* 3.9 33.7 - + - -
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Residues in contact with SER 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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30A ARG* 3.3 29.8 + - - +
66A GLU 3.2 11.1 + - - -
67A ILE 2.8 17.6 + - - -
69A TRP* 1.3 80.2 - - - +
71A LEU* 1.3 66.7 + - - +
72A PRO* 3.3 6.4 - - - +
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Residues in contact with LEU 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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7A MET* 3.8 36.8 - - + -
30A ARG* 4.1 11.4 - - + -
34A LEU* 4.0 15.9 - - + -
40A TRP* 3.9 26.7 - - + -
56A PHE* 5.1 0.7 - - + -
67A ILE* 3.3 18.0 + - + +
68A LEU* 3.2 24.9 + - + +
69A TRP 4.3 0.5 - - - +
70A SER* 1.3 77.2 - - - +
72A PRO* 1.3 75.6 - - + +
73A PHE* 4.4 4.7 - - + +
74A PHE* 2.9 23.6 + - + +
75A PRO* 4.3 1.6 - - - +
77A LEU* 4.5 7.0 - - + -
79A ILE* 5.7 0.2 - - + -
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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