Contacts of the helix formed by residues 87 - 98 (chain A) in PDB entry 1ZD4
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 87 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68A GLU* 6.2 0.2 - - - -
85A ASN 3.7 5.7 + - - -
86A PHE* 1.3 76.7 - - - +
88A ILE* 1.3 60.4 + - - +
89A LYS* 3.6 7.6 + - - +
90A GLU* 3.2 32.5 + - - +
91A ILE* 2.9 36.4 + - - +
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Residues in contact with ILE 88 (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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37A LEU* 5.3 2.0 - - + -
63A TRP* 4.6 1.3 - - + -
64A ILE* 3.9 26.2 - - + +
67A MET* 3.9 33.4 - - + -
68A GLU* 3.7 27.9 + - + +
71A CYS* 4.2 9.2 - - - -
86A PHE* 3.7 33.5 + - + -
87A SER* 1.3 67.4 + - - +
89A LYS* 1.3 67.1 + - - +
91A ILE* 3.1 7.3 + - + +
92A PHE* 3.0 51.7 + - + -
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Residues in contact with LYS 89 (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 SER* 5.5 3.6 - - - -
64A ILE* 3.6 37.2 - - + +
87A SER* 3.3 7.3 + - - +
88A ILE* 1.3 79.5 - - - +
90A GLU* 1.3 53.2 + - - +
92A PHE* 3.9 2.8 - - - +
93A ASP* 2.6 59.3 + - - +
130A ARG* 3.9 17.4 - - - +
131A ALA* 4.2 6.8 - - - +
132A GLU* 2.8 33.7 + - - -
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Residues in contact with GLU 90 (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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87A SER* 3.2 30.8 + - - +
89A LYS* 1.3 78.5 - - - +
91A ILE* 1.3 62.1 + - + +
93A ASP* 3.7 10.4 + - - +
94A LYS* 3.3 43.9 + - - +
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Residues in contact with ILE 91 (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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22A VAL* 3.7 20.9 - - + +
23A LEU* 6.2 1.6 - - + -
26A THR* 3.4 37.2 - - + +
30A LEU* 5.4 0.2 - - + -
37A LEU* 5.2 1.8 - - + -
86A PHE* 3.3 38.6 - - + -
87A SER 2.9 19.7 + - - +
88A ILE* 3.1 10.7 + - + +
90A GLU* 1.3 77.7 - - + +
92A PHE* 1.3 68.2 + - + +
94A LYS* 3.7 5.5 + - - +
95A ALA* 3.1 24.6 + - - +
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Residues in contact with PHE 92 (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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19A VAL* 4.3 22.7 - - + -
22A VAL* 5.1 7.0 - - + -
23A LEU* 4.5 12.8 - - + -
41A PHE* 4.0 19.7 - + - -
60A LEU* 5.7 7.6 - - + -
63A TRP* 3.5 34.3 - + - -
64A ILE* 6.1 4.0 - - + -
67A MET* 4.2 8.7 - - + -
88A ILE* 3.0 50.7 + - + +
89A LYS* 4.1 3.1 - - - +
91A ILE* 1.3 85.0 - - + +
93A ASP* 1.3 56.9 + - - +
95A ALA* 3.9 5.8 - - + -
96A ILE* 2.7 51.7 + - + +
126A TRP* 5.6 5.8 - + - -
130A ARG* 5.1 4.5 - - - -
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Residues in contact with ASP 93 (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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89A LYS* 2.6 49.4 + - - +
90A GLU* 3.7 12.2 + - - +
92A PHE* 1.3 77.6 - - - +
94A LYS* 1.3 61.7 + - + +
96A ILE* 3.9 1.0 - - - +
97A SER* 2.9 28.9 + - - -
130A ARG* 2.6 36.5 + - - +
132A GLU* 2.7 21.9 - - + +
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Residues in contact with LYS 94 (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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90A GLU* 3.3 43.4 + - - +
91A ILE* 4.0 5.2 - - - +
92A PHE 3.3 0.2 - - - -
93A ASP* 1.3 75.2 - - + +
95A ALA* 1.3 59.1 + - - +
97A SER* 3.2 7.2 + - - -
98A ALA* 2.9 35.1 + - + +
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Residues in contact with ALA 95 (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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17A PRO* 4.8 3.1 - - - +
19A VAL* 4.3 16.8 - - + +
22A VAL* 3.7 34.8 - - + -
25A ARG* 4.9 6.0 + - - +
91A ILE 3.1 17.1 + - - +
92A PHE* 3.3 7.6 + - - +
94A LYS* 1.3 81.4 - - - +
96A ILE* 1.3 61.9 + - - +
98A ALA* 3.4 12.1 + - - +
99A ARG* 3.4 12.3 + - - +
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Residues in contact with ILE 96 (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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19A VAL* 4.2 24.5 - - + -
60A LEU* 4.6 1.6 - - + -
92A PHE* 2.7 32.7 + - + +
93A ASP 3.9 2.5 - - - +
95A ALA* 1.3 70.1 - - - +
97A SER* 1.3 59.1 + - - +
98A ALA 3.0 4.7 - - - -
99A ARG* 3.0 42.6 + - - +
126A TRP* 3.6 26.5 - - + -
128A ASP* 4.1 1.8 - - - +
130A ARG* 3.8 43.7 - - - +
135A GLY 5.8 0.4 - - - -
136A LEU* 4.3 15.5 - - + +
139A LEU* 5.7 1.5 - - + +
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Residues in contact with SER 97 (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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93A ASP 2.9 18.5 + - - -
94A LYS* 3.2 11.3 + - - -
96A ILE* 1.3 79.5 - - - +
98A ALA* 1.3 49.0 + - - +
99A ARG 3.2 3.7 + - - +
100A LYS* 2.7 31.5 + - - +
135A GLY* 6.6 0.7 - - - -
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Residues in contact with ALA 98 (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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17A PRO* 3.0 26.2 - - + +
94A LYS 2.9 21.1 + - - +
95A ALA* 3.5 9.0 - - - +
96A ILE 3.0 0.4 - - - -
97A SER* 1.3 77.6 - - - +
99A ARG* 1.3 60.4 + - - +
100A LYS* 3.6 12.5 + - - +
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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