Contacts of the helix formed by residues 90 - 103 (chain A) in PDB entry 1ZIO
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 VAL 90 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89A THR* 1.3 74.1 - - - +
91A ALA* 1.3 57.6 + - - +
93A ALA* 3.3 2.6 + - - +
94A GLU* 3.0 43.0 + - + +
178A GLN* 4.4 3.8 + - - +
181A PRO* 4.3 26.0 - - + +
182A LEU* 3.9 19.3 - - + -
185A PHE* 4.4 17.7 - - + -
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Residues in contact with ALA 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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61A ASP* 4.4 16.2 - - + +
65A ILE* 4.0 5.5 - - + +
89A THR* 3.1 7.5 + - - +
90A VAL* 1.3 79.4 - - - +
92A GLN* 1.3 64.8 + - - +
94A GLU* 3.8 10.6 - - - +
95A ALA* 3.0 24.1 + - - +
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Residues in contact with GLN 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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59A VAL 4.5 0.6 + - - -
61A ASP* 2.7 30.0 + - - +
64A THR* 4.0 9.1 - - - -
65A ILE* 4.1 16.6 - - + -
86A PHE* 3.5 26.2 - - + -
87A PRO* 3.6 8.5 - - + -
88A ARG 2.9 22.1 + - - -
89A THR* 3.1 18.7 + - - +
91A ALA* 1.3 78.2 - - - +
93A ALA* 1.3 58.1 + - - +
95A ALA* 3.4 2.4 + - - +
96A LEU* 2.9 28.2 + - - +
218A AP5 3.0 40.6 + - - -
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Residues in contact with ALA 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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87A PRO* 3.5 12.1 - - + +
89A THR 3.1 5.6 + - - +
90A VAL 3.6 6.1 - - - +
91A ALA 3.1 0.2 - - - -
92A GLN* 1.3 76.1 - - - +
94A GLU* 1.3 64.1 + - - +
96A LEU* 3.5 3.3 + - - +
97A GLU* 3.2 25.8 + - - +
182A LEU* 3.5 30.5 - - + -
185A PHE* 3.8 13.5 - - + -
186A TYR* 3.5 21.0 + - - +
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Residues in contact with GLU 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 VAL* 3.0 27.6 + - - +
91A ALA* 3.4 9.8 + - - +
93A ALA* 1.3 75.0 - - - +
95A ALA* 1.3 63.0 + - - +
97A GLU* 3.4 15.5 + - - +
98A THR* 3.5 18.7 + - - +
185A PHE* 4.1 24.3 - - + -
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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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65A ILE* 3.3 46.2 - - + -
91A ALA 3.0 9.7 + - - +
92A GLN 3.6 3.8 - - - +
94A GLU* 1.3 77.5 - - - +
96A LEU* 1.3 55.7 + - - +
98A THR* 2.8 23.3 + - - -
99A MET* 3.0 21.2 + - + +
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Residues in contact with LEU 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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4A VAL* 4.2 1.3 - - + -
72A LEU* 4.0 14.4 - - + -
83A LEU* 3.8 29.4 - - + -
86A PHE* 4.0 12.3 - - + -
87A PRO* 3.6 28.3 - - + -
92A GLN 2.9 18.1 + - - +
93A ALA 3.7 6.1 - - - +
94A GLU 3.3 0.2 - - - -
95A ALA* 1.3 74.1 - - - +
97A GLU* 1.3 67.4 + - - +
99A MET* 3.5 9.1 - - - +
100A LEU* 2.9 48.1 + - + +
107A LEU* 3.9 24.9 - - + -
186A TYR* 4.1 3.4 - - - +
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Residues in contact with GLU 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 ALA 3.2 13.1 + - - +
94A GLU* 3.4 11.6 + - - +
96A LEU* 1.3 78.6 - - - +
98A THR* 1.3 60.8 + - + +
100A LEU* 3.5 7.6 + - - +
101A ALA* 3.1 27.8 + - - +
105A ARG 5.0 0.3 - - - +
106A LYS* 5.2 4.5 - - - +
107A LEU* 4.0 16.5 + - - +
185A PHE* 4.8 3.6 - - + -
186A TYR* 4.7 3.0 + - - -
189A LYS* 4.0 30.0 + - - +
191A TYR* 3.4 34.2 + - - -
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Residues in contact with THR 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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94A GLU 3.5 12.5 + - - +
95A ALA* 2.8 23.8 + - - -
97A GLU* 1.3 75.1 - - + +
99A MET* 1.3 64.3 + - - +
101A ALA* 3.3 8.2 + - - +
102A ASP* 3.1 31.3 + - - +
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Residues in contact with MET 99 (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 ILE* 3.7 33.7 - - + +
68A VAL* 3.9 17.0 - - + -
69A ARG* 3.6 46.7 - - + +
72A LEU* 4.0 17.3 - - + -
86A PHE* 4.8 3.8 - - + -
95A ALA* 3.1 22.9 - - + +
96A LEU* 3.5 11.2 - - + +
98A THR* 1.3 82.6 + - - +
100A LEU* 1.3 61.3 + - - +
102A ASP* 3.5 20.2 + - - +
103A ILE* 3.7 12.3 + - - +
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Residues in contact with LEU 100 (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 LEU* 4.0 18.6 - - + -
81A PHE* 3.6 29.8 - - + -
96A LEU* 2.9 32.9 + - + +
97A GLU* 3.8 7.9 - - - +
99A MET* 1.3 74.6 - - - +
101A ALA* 1.3 67.2 + - - +
103A ILE* 2.9 22.0 + - + +
104A GLY 3.2 0.2 + - - -
105A ARG* 3.0 39.2 + - + +
106A LYS* 4.5 2.5 - - - -
107A LEU* 3.6 46.0 - - + +
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Residues in contact with ALA 101 (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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97A GLU 3.1 18.5 + - - +
98A THR* 3.3 9.6 + - - +
100A LEU* 1.3 76.4 - - - +
102A ASP* 1.3 64.0 + - - +
104A GLY* 3.1 13.7 + - - +
105A ARG 3.6 9.1 + - - +
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Residues in contact with ASP 102 (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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98A THR* 3.1 22.4 + - - +
99A MET* 3.6 13.4 - - - +
100A LEU 3.1 0.4 - - - -
101A ALA* 1.3 78.4 - - - +
103A ILE* 1.3 64.2 + - + +
104A GLY 3.4 0.7 - - - -
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Residues in contact with ILE 103 (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 LEU* 3.6 34.5 - - + +
73A SER* 5.0 12.6 - - - -
77A CYS* 5.9 1.6 - - + -
78A GLN* 5.9 4.0 - - - +
81A PHE* 5.4 2.5 - - + -
99A MET* 3.9 13.0 - - + +
100A LEU* 2.9 23.8 + - + +
102A ASP* 1.3 82.9 - - + +
104A GLY* 1.3 61.1 + - - +
105A ARG* 3.8 29.9 - - - +
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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