Contacts of the helix formed by residues 97 - 109 (chain A) in PDB entry 4O0Z
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 ASN 97 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A VAL 4.9 1.9 + - - +
23A TYR* 3.5 51.0 - - + +
95A VAL 3.6 1.4 + - - -
96A PHE* 1.3 77.9 - - + +
98A GLU* 1.3 60.0 + - - +
99A LYS* 3.7 7.3 + - - +
100A GLY* 3.0 29.6 + - - -
101A TRP* 3.3 26.1 + - + +
143A TRP* 3.7 26.6 - - + +
147A TRP* 5.8 3.8 - - + -
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Residues in contact with GLU 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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80A ILE* 3.8 19.9 - - + +
81A GLN* 5.0 4.3 - - - +
84A LYS* 2.9 41.1 + - + +
96A PHE* 3.2 25.1 + - + +
97A ASN* 1.3 74.0 - - - +
99A LYS* 1.3 59.3 + - + +
101A TRP* 3.5 1.9 + - - +
102A ASN* 2.9 50.9 + - - +
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Residues in contact with LYS 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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97A ASN* 3.2 6.0 + - - +
98A GLU* 1.3 76.7 - - + +
100A GLY* 1.3 67.4 + - - +
102A ASN* 3.2 8.9 + - - +
103A TYR* 2.9 23.8 + - - +
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Residues in contact with GLY 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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97A ASN* 3.0 28.4 + - - -
99A LYS* 1.3 77.1 - - - +
101A TRP* 1.3 61.2 + - - +
103A TYR* 3.3 15.9 + - - +
104A ILE* 3.3 16.8 + - - +
140A GLU 5.8 0.4 - - - -
141A CYS* 5.3 0.7 - - - -
143A TRP* 3.7 17.2 - - - -
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Residues in contact with TRP 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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11A ILE* 4.1 12.3 - - + -
12A LEU* 3.6 34.1 - - + -
75A VAL* 3.6 32.1 - - + +
80A ILE* 3.7 21.4 - - + +
96A PHE* 3.6 21.2 - + + -
97A ASN* 3.3 26.6 + - + +
98A GLU 4.1 2.2 - - - +
99A LYS 3.3 0.8 - - - -
100A GLY* 1.3 72.4 - - - +
102A ASN* 1.3 64.9 + - - +
104A ILE* 3.4 15.9 + - + +
105A LEU* 3.1 16.5 + - - +
112A LEU* 4.1 13.2 - - + -
143A TRP* 3.4 23.0 - + - -
144A LEU* 4.0 15.9 - - + -
147A TRP* 3.4 51.5 - + - -
148A ILE* 6.0 0.4 - - + -
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Residues in contact with ASN 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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77A LYS* 5.7 2.4 - - - +
80A ILE* 3.3 22.8 - - - +
98A GLU* 2.9 47.2 + - - +
99A LYS* 3.2 8.7 + - - +
101A TRP* 1.3 77.0 - - - +
103A TYR* 1.3 56.7 + - - +
105A LEU* 3.0 11.5 + - - +
106A GLU* 2.8 45.9 + - - +
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Residues in contact with TYR 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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99A LYS 2.9 12.1 + - - +
100A GLY* 3.4 11.9 - - - +
102A ASN* 1.3 76.5 - - - +
104A ILE* 1.3 57.3 + - - +
106A GLU* 4.5 5.8 - - + +
107A LYS* 2.7 75.4 + - + +
108A TYR* 4.3 4.7 - + - -
138A ASP* 2.6 36.3 + - - -
140A GLU* 3.6 35.2 - - + +
141A CYS* 4.0 14.8 - - - -
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Residues in contact with ILE 104 (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 VAL* 3.8 21.8 - - + -
100A GLY 3.3 7.3 + - - +
101A TRP* 3.6 18.4 - - + +
102A ASN 3.3 0.6 - - - -
103A TYR* 1.3 76.4 - - - +
105A LEU* 1.3 63.1 + - - +
108A TYR* 3.1 25.4 + - - +
110A GLY 3.2 11.0 + - - -
111A HIS 3.3 25.8 - - - +
112A LEU* 4.6 1.8 - - + -
113A PRO* 4.0 5.4 - - + -
141A CYS* 3.8 18.2 - - - -
143A TRP* 3.8 25.8 - - + -
144A LEU* 3.7 30.1 - - + -
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Residues in contact with LEU 105 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73A LYS* 4.2 15.5 - - - +
75A VAL* 3.4 33.0 - - + +
76A THR* 4.1 4.5 - - - -
77A LYS* 3.9 34.5 - - + +
80A ILE* 4.2 10.3 - - + -
101A TRP 3.1 12.2 + - - +
102A ASN* 3.0 17.1 + - - +
104A ILE* 1.3 78.0 - - - +
106A GLU* 1.3 63.1 + - + +
109A ASP* 3.1 27.6 + - - +
110A GLY* 3.7 8.1 - - - +
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Residues in contact with GLU 106 (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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102A ASN* 2.8 33.7 + - + +
103A TYR* 4.2 5.2 - - + +
105A LEU* 1.3 82.8 - - + +
107A LYS* 1.3 63.8 + - - +
108A TYR 3.6 0.2 + - - -
109A ASP* 4.3 2.1 + - - -
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Residues in contact with LYS 107 (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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103A TYR* 2.7 58.9 + - + +
106A GLU* 1.3 74.9 - - - +
108A TYR* 1.3 92.4 + - + +
109A ASP 3.7 0.2 - - - -
138A ASP* 4.7 0.8 + - - -
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Residues in contact with TYR 108 (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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103A TYR* 4.3 4.5 - + - -
104A ILE* 3.1 15.7 + - - +
107A LYS* 1.3 106.1 - - + +
109A ASP* 1.3 72.0 + - - +
110A GLY 3.2 0.7 - - - -
111A HIS* 3.1 38.3 + - + +
113A PRO* 4.1 29.4 - - + -
137A THR* 5.1 2.8 + - - -
138A ASP* 2.5 39.8 + - + +
464A ASN* 5.4 12.3 - - + -
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Residues in contact with ASP 109 (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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73A LYS* 3.2 43.9 + - - +
105A LEU* 3.1 16.4 + - - +
106A GLU 4.3 1.8 + - - -
107A LYS 3.7 1.2 - - - -
108A TYR* 1.3 78.9 - - - +
110A GLY* 1.3 55.8 + - - +
111A HIS* 3.1 23.1 + - + +
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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