Contacts of the helix formed by residues 64 - 79 (chain A) in PDB entry 1Z6T
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 64 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A MET* 3.9 13.0 - - - +
34A PHE* 3.9 9.7 - - - -
63A LYS* 1.3 82.2 - - - +
65A ASN* 1.3 64.2 + - - +
66A ASP* 3.3 29.6 + - - +
67A SER* 2.9 34.6 + - - -
68A TYR 3.6 4.7 + - - -
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Residues in contact with ASN 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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1A MET* 3.4 11.2 - - - +
2A ASP* 3.0 45.2 + - - +
64A ASP* 1.3 75.1 - - - +
66A ASP* 1.3 65.9 + - - +
68A TYR* 3.4 17.7 - - - +
69A VAL* 3.4 14.1 + - - +
92A PRO* 3.4 20.1 - - + +
93A VAL 3.8 19.5 - - - +
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Residues in contact with ASP 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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34A PHE* 3.2 36.3 - - + -
64A ASP* 3.2 14.8 - - - +
65A ASN* 1.3 80.2 - - - +
67A SER* 1.3 54.3 + - - +
69A VAL* 3.4 7.5 + - - +
70A SER* 2.8 35.0 + - - -
94A VAL* 3.7 34.7 - - + +
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Residues in contact with SER 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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29A MET* 3.6 8.9 - - - +
34A PHE* 3.2 34.5 + - - +
60A ILE* 4.7 5.2 - - - -
63A LYS* 3.8 23.8 - - - +
64A ASP* 2.9 27.0 + - - -
65A ASN 3.3 0.2 - - - -
66A ASP* 1.3 75.4 - - - +
68A TYR* 1.3 55.0 + - - +
70A SER* 3.2 2.1 + - - -
71A PHE* 2.7 38.3 + - - +
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Residues in contact with TYR 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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1A MET* 3.8 28.9 - - + -
5A ALA* 3.4 22.9 - - + -
8A CYS* 3.2 24.8 - - - +
9A LEU* 4.0 20.6 - - + -
60A ILE* 4.6 6.9 - - + +
64A ASP 3.6 2.6 + - - -
65A ASN* 3.4 13.4 + - - +
67A SER* 1.3 78.7 - - - +
69A VAL* 1.3 52.1 + - - +
71A PHE* 3.3 8.7 + + - +
72A TYR* 2.6 35.9 + - + +
87A LEU* 3.0 46.1 + - + +
90A GLY* 3.8 5.5 - - - -
91A ILE* 3.9 10.3 - - + -
92A PRO* 3.3 28.0 - - + -
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Residues in contact with VAL 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 ASN 3.4 13.9 + - - +
66A ASP 3.4 5.7 + - - +
67A SER 3.3 0.4 - - - -
68A TYR* 1.3 72.6 - - + +
70A SER* 1.3 56.7 + - - +
72A TYR* 3.2 12.5 + - + +
73A ASN* 2.7 55.5 + - - +
91A ILE* 4.9 8.3 - - + -
92A PRO* 3.6 29.4 - - + +
94A VAL* 3.6 34.5 - - + +
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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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28A HIS* 5.5 0.5 - - - +
29A MET* 3.6 17.8 - - - +
32A ASP* 2.8 35.0 + - - +
34A PHE* 3.6 21.1 - - - -
66A ASP 2.8 21.7 + - - -
67A SER* 3.4 5.6 - - - -
69A VAL* 1.3 72.7 - - - +
71A PHE* 1.3 55.7 + - - +
73A ASN* 3.2 7.8 + - - +
74A ALA* 2.8 28.6 + - - +
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Residues in contact with PHE 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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9A LEU* 4.6 7.0 - - + -
16A LEU* 4.3 14.1 - - + -
20A ILE* 4.1 25.4 - - + -
25A ILE* 3.8 19.7 - - + -
29A MET* 3.7 23.5 - - + +
56A LEU* 4.3 3.1 - - + -
57A ILE* 4.4 11.4 - - + -
60A ILE* 3.5 34.8 - - + -
67A SER 2.7 20.9 + - - +
68A TYR* 3.5 6.1 - + - +
70A SER* 1.3 69.9 - - - +
72A TYR* 1.3 65.3 + - - +
74A ALA* 3.2 3.3 + - - +
75A LEU* 2.9 43.5 + - + +
87A LEU* 3.9 27.4 - - + -
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Residues in contact with TYR 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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68A TYR* 2.6 19.4 + - + +
69A VAL* 3.3 17.7 - - + +
71A PHE* 1.3 73.0 - - - +
73A ASN* 1.3 70.5 + - - +
75A LEU* 3.3 13.5 + - - +
76A LEU* 3.2 42.3 + - + +
84A ALA* 3.1 39.6 - - + +
85A ALA* 5.6 0.3 - - - -
87A LEU* 4.1 15.3 - - + -
88A HIS* 3.5 22.4 + - - +
91A ILE* 3.5 35.7 - - + -
108A SER* 3.5 24.9 + - - -
112A THR* 5.8 0.2 - - - +
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Residues in contact with ASN 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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32A ASP* 5.2 5.4 + - - +
69A VAL* 2.7 40.0 + - - +
70A SER* 3.6 8.4 - - - +
72A TYR* 1.3 76.6 - - - +
74A ALA* 1.3 61.5 + - - +
76A LEU* 3.4 6.1 + - - +
77A HIS* 2.9 32.4 + - - +
108A SER* 3.6 16.3 + - - -
111A ARG* 3.4 40.3 + - - +
274D MET* 5.7 2.8 - - - +
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Residues in contact with ALA 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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25A ILE* 3.7 37.7 - - + +
28A HIS* 3.8 25.7 - - + +
29A MET* 4.4 1.3 - - + -
70A SER 2.8 17.1 + - - +
71A PHE* 3.2 9.6 + - - +
73A ASN* 1.3 72.0 - - - +
75A LEU* 1.3 57.0 + - - +
77A HIS* 3.3 0.6 + - - -
78A GLU* 2.8 37.4 + - - +
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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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16A LEU* 4.1 15.0 - - + -
20A ILE* 3.9 15.0 - - + -
25A ILE* 3.6 25.8 - - + -
71A PHE* 2.9 29.2 + - + +
72A TYR* 3.3 9.6 + - - +
74A ALA* 1.3 74.8 - - - +
76A LEU* 1.3 54.8 + - - +
78A GLU 3.7 0.3 - - - -
79A GLY 3.0 7.1 + - - -
80A TYR* 2.6 60.0 + - + +
83A LEU 4.6 0.2 - - - -
84A ALA* 4.1 16.4 - - + +
87A LEU* 3.9 28.9 - - + -
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Residues in contact with LEU 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 TYR* 3.2 38.2 + - + +
73A ASN* 3.8 8.3 - - - +
74A ALA 3.3 0.2 - - - -
75A LEU* 1.3 69.9 - - - +
77A HIS* 1.3 65.5 + - - +
78A GLU 3.1 2.0 - - - -
79A GLY* 3.1 14.3 + - - +
80A TYR 4.7 1.3 - - - +
81A LYS* 4.4 12.6 - - + +
84A ALA* 3.4 24.9 - - + -
108A SER* 3.5 45.3 - - - +
111A ARG* 3.9 15.3 - - + +
112A THR* 3.3 24.6 - - + -
115A CYS* 3.7 13.7 - - - +
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Residues in contact with HIS 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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28A HIS* 3.1 44.3 + + + +
73A ASN 2.9 19.6 + - - +
74A ALA* 3.4 5.4 - - - +
76A LEU* 1.3 75.0 - - - +
78A GLU* 1.3 53.8 + - - +
111A ARG* 4.2 29.0 + - + +
115A CYS* 4.2 3.7 - - - +
121A GLN* 2.7 49.7 + - + +
122A ARG* 5.3 8.5 + - + +
428A ARG* 4.9 0.2 + - - -
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Residues in contact with GLU 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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24A TYR* 3.4 14.1 - - - +
25A ILE* 4.2 13.9 - - + +
28A HIS* 2.3 38.6 + - + +
74A ALA 2.8 20.1 + - - +
77A HIS* 1.3 84.0 - - - +
79A GLY* 1.3 51.9 + - - +
80A TYR* 3.6 18.8 - - + -
115A CYS* 4.0 3.4 - - - -
121A GLN* 3.9 2.0 - - - +
428A ARG* 3.0 52.8 + - + +
429A ASN 3.5 0.3 - - - -
430A GLY* 2.4 32.5 + - - +
433A PHE* 5.5 0.7 - - - -
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Residues in contact with GLY 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 3.0 2.6 + - - -
76A LEU 3.1 7.1 + - - -
78A GLU* 1.3 79.6 - - - +
80A TYR* 1.3 58.4 + - - +
81A LYS* 3.2 13.6 + - - +
115A CYS* 3.1 25.5 - - - -
429A ASN* 3.9 8.0 + - - -
430A GLY* 3.4 16.5 + - - -
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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