Contacts of the helix formed by residues 88 - 102 (chain A) in PDB entry 2ZQ3
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 ILE 88 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3A PHE* 3.8 29.8 - - + -
8A LEU* 3.9 11.2 - - + -
11A ALA* 3.7 31.2 - - + -
12A MET* 3.9 22.0 - - + -
15A HIS* 4.0 11.4 - - + +
40A THR* 4.6 5.2 - - + -
55A ILE* 4.3 22.2 - - + -
85A SER 5.2 0.7 - - - +
86A SER 4.6 0.4 - - - +
87A ASP* 1.3 74.5 + - - +
89A THR* 1.3 66.4 + - - +
90A ALA 3.4 1.6 - - - -
91A SER* 3.2 8.2 + - - -
92A VAL* 2.9 41.3 + - + +
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Residues in contact with THR 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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14A ARG* 5.7 0.2 - - - -
15A HIS* 3.2 33.3 + - + +
87A ASP* 2.4 33.1 + - - -
88A ILE* 1.3 72.4 - - - +
90A ALA* 1.3 64.8 + - - +
92A VAL* 3.1 4.1 + - - +
93A ASN* 2.9 40.9 + - - +
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Residues in contact with ALA 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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78A ILE* 4.6 7.9 - - + +
82A ALA* 3.4 38.4 - - + +
83A LEU* 3.9 6.5 - - + +
85A SER* 5.9 0.4 - - - -
87A ASP 4.7 2.5 + - - +
88A ILE 3.4 0.8 - - - -
89A THR* 1.3 78.3 - - - +
91A SER* 1.3 63.2 + - - +
93A ASN* 3.3 11.1 + - - +
94A CYS* 3.0 23.9 + - - +
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Residues in contact with SER 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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53A TYR 5.1 0.9 + - - -
55A ILE* 3.7 29.7 + - - +
56A LEU* 4.4 6.0 + - - +
58A ILE* 3.8 11.5 - - - +
83A LEU* 3.6 39.8 + - - +
88A ILE* 3.2 10.6 + - - -
90A ALA* 1.3 78.4 - - - +
92A VAL* 1.3 59.3 + - - +
94A CYS 3.4 0.2 + - - -
95A ALA* 2.8 30.5 + - - +
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Residues in contact with VAL 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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12A MET* 5.2 1.8 - - + -
15A HIS* 3.8 26.0 - - + +
17A LEU* 3.9 24.9 - - + -
56A LEU* 5.3 2.9 - - + -
88A ILE* 2.9 43.9 + - + +
89A THR* 3.5 8.1 - - - +
91A SER* 1.3 77.4 - - - +
93A ASN* 1.3 66.1 + - - +
95A ALA* 3.1 6.8 + - - +
96A LYS* 2.9 48.9 + - - +
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Residues in contact with ASN 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 THR* 2.9 37.9 + - - +
90A ALA* 3.7 9.8 - - - +
92A VAL* 1.3 78.4 - - - +
94A CYS* 1.3 60.7 + - - +
96A LYS* 3.5 19.4 + - - +
97A LYS* 3.4 32.5 + - - +
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Residues in contact with CYS 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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58A ILE* 3.8 39.0 - - + -
63A TRP* 3.9 3.6 - - - -
76A CYS* 2.0 52.3 - - + -
78A ILE* 4.1 11.7 - - + -
90A ALA 3.0 16.3 + - - +
93A ASN* 1.3 73.8 - - - +
95A ALA* 1.3 67.0 + - - +
97A LYS* 3.0 7.4 + - - +
98A ILE* 2.9 28.0 + - - +
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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 LEU* 5.2 2.7 - - + -
28A TRP* 4.1 10.5 - - + -
56A LEU* 3.7 24.9 - - + -
58A ILE* 4.3 1.7 - - + +
91A SER 2.8 19.0 + - - +
92A VAL* 3.5 7.0 - - - +
94A CYS* 1.3 76.4 - - - +
96A LYS* 1.3 62.5 + - - +
98A ILE* 3.2 4.0 + - - +
99A VAL* 3.0 27.1 + - - +
108A TRP* 3.7 23.1 - - + -
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Residues in contact with LYS 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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15A HIS 2.7 30.0 + - - -
16A GLY* 4.1 8.3 + - - -
17A LEU* 4.0 9.4 - - + -
20A TYR* 3.6 50.9 - - + +
92A VAL* 2.9 30.5 + - + +
93A ASN* 3.7 17.9 + - - +
94A CYS 3.2 0.2 - - - -
95A ALA* 1.3 75.9 - - - +
97A LYS* 1.3 58.4 + - + +
99A VAL* 3.4 2.9 - - - +
100A SER* 2.6 33.8 + - - -
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Residues in contact with LYS 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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63A TRP* 5.1 3.1 - - + -
75A LEU 4.6 5.8 + - - +
76A CYS* 3.4 44.9 + - - +
77A ASN* 5.3 2.6 - - - +
78A ILE* 5.6 1.0 - - - +
93A ASN* 3.4 22.4 - - - +
94A CYS* 3.0 7.7 + - - +
96A LYS* 1.3 80.2 - - + +
98A ILE* 1.3 60.5 + - - +
100A SER* 3.4 11.6 + - - -
101A ASP* 2.9 26.0 + - - +
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Residues in contact with ILE 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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58A ILE* 4.0 18.6 - - + -
63A TRP* 3.5 63.4 - - + +
94A CYS* 2.9 28.3 + - - +
95A ALA 3.6 6.5 - - - +
97A LYS* 1.3 78.6 - - - +
99A VAL* 1.3 62.4 + - - +
101A ASP* 4.3 1.6 - - - +
102A GLY* 3.3 22.2 + - - -
104A GLY 4.7 1.2 - - - +
107A ALA* 3.6 28.3 - - + +
108A TRP* 3.9 20.0 - - + -
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Residues in contact with VAL 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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20A TYR* 3.6 27.6 - - + -
21A ARG* 4.0 12.9 + - + +
23A TYR* 3.9 21.1 - - + -
28A TRP* 3.9 13.5 - - + -
95A ALA 3.0 19.5 + - - +
96A LYS 3.4 7.6 - - - +
98A ILE* 1.3 77.1 - - - +
100A SER* 1.3 63.9 + - - +
101A ASP 3.6 0.2 - - - -
102A GLY 4.1 4.8 + - - +
104A GLY* 3.5 44.1 + - - +
105A MET* 3.9 6.7 - - + +
108A TRP* 4.3 3.6 - - + -
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Residues in contact with SER 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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20A TYR* 3.2 22.2 + - - -
21A ARG* 3.3 43.3 + - - +
96A LYS 2.6 23.1 + - - -
97A LYS* 3.8 6.3 - - - -
98A ILE 3.2 0.6 - - - -
99A VAL* 1.3 79.3 - - - +
101A ASP* 1.3 59.5 + - - +
102A GLY 3.4 1.7 - - - +
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Residues in contact with ASP 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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63A TRP* 4.1 22.7 - - - -
75A LEU* 5.9 1.5 - - - +
97A LYS* 2.9 23.1 + - - +
98A ILE 4.5 1.6 - - - -
100A SER* 1.3 77.0 - - - +
102A GLY* 1.3 63.7 + - - +
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Residues in contact with GLY 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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63A TRP* 6.3 0.7 - - - -
98A ILE 3.3 18.1 + - - -
99A VAL 4.1 2.9 + - - +
100A SER 3.4 2.7 - - - +
101A ASP* 1.3 86.4 - - - +
103A ASN* 1.3 58.2 + - - -
104A GLY 3.2 9.8 + - - -
107A ALA* 6.2 1.3 - - - -
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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