Contacts of the helix formed by residues 113 - 125 (chain C) in PDB entry 4Z3K
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 113 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130A CYS* 4.2 1.6 - - - -
110C ASP 4.9 0.9 + - - +
111C LEU* 3.5 1.2 - - - +
112C SER* 1.3 76.3 + - - +
114C SER* 1.3 62.7 + - - +
115C THR* 3.0 22.9 + - - -
116C GLN* 3.2 32.4 + - - +
117C VAL* 3.1 22.9 + - - +
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Residues in contact with SER 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A GLU* 2.5 40.3 + - - -
73A LEU* 3.6 24.7 - - - -
74A GLN* 4.0 4.0 + - - +
126A THR* 3.7 11.4 - - - -
130A CYS* 3.7 11.9 - - - -
112C SER 3.4 5.0 + - - -
113C ASP* 1.3 75.0 + - - +
115C THR* 1.3 60.0 + - - +
117C VAL* 3.7 1.2 - - - +
118C ASN* 2.9 37.3 + - - -
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Residues in contact with THR 115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A GLU* 4.7 9.2 + - - +
113C ASP* 3.0 10.3 + - - -
114C SER* 1.3 84.1 + - - +
116C GLN* 1.3 56.5 + - - +
118C ASN* 3.4 5.8 + - - +
119C ASN* 3.0 48.7 + - - +
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Residues in contact with GLN 116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102C GLY* 5.9 0.2 - - - -
103C ASP* 4.4 14.1 - - - +
106C LYS* 3.5 29.1 + - - +
110C ASP 5.4 1.7 - - - +
111C LEU* 4.1 19.1 - - - +
113C ASP* 3.2 36.0 + - - +
115C THR* 1.3 76.2 - - - +
117C VAL* 1.3 63.2 + - - +
119C ASN* 3.2 10.8 + - - +
120C TYR* 3.1 22.8 + - + +
166C LEU* 4.2 13.6 - - + +
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Residues in contact with VAL 117 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A THR* 3.5 18.8 - - + +
129A LEU* 4.0 28.5 - - + -
130A CYS* 4.3 9.6 - - - -
111C LEU* 4.4 18.6 - - + +
113C ASP 3.1 17.7 + - - +
114C SER 3.8 4.0 - - - +
116C GLN* 1.3 75.7 - - + +
118C ASN* 1.3 62.8 + - - +
120C TYR* 3.2 17.0 + - - +
121C TRP* 3.2 39.0 + - + +
166C LEU* 4.3 11.2 - - + -
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Residues in contact with ASN 118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A GLU* 4.5 10.5 + - - -
118A ASN* 4.8 3.7 - - - +
121A TRP* 5.2 0.2 - - - +
122A ALA* 3.6 24.0 + - - +
126A THR* 2.5 33.2 + - - +
114C SER 2.9 25.2 + - - +
115C THR* 3.8 6.5 - - - +
117C VAL* 1.3 76.5 - - - +
119C ASN* 1.3 58.8 + - - +
121C TRP* 3.2 9.1 + - - +
122C ALA* 2.9 29.7 + - - +
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Residues in contact with ASN 119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68C GLY* 4.7 11.7 - - - +
115C THR* 3.0 37.6 + - - +
116C GLN* 3.2 8.3 + - - +
118C ASN* 1.3 74.4 - - - +
120C TYR* 1.3 67.6 + - - +
122C ALA* 3.2 7.6 + - - +
123C LEU* 3.1 23.0 + - - +
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Residues in contact with TYR 120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100C SER* 2.8 33.0 + - - -
101C LEU 3.9 1.3 - - - -
102C GLY* 3.6 23.3 - - - -
116C GLN* 3.1 12.4 + - + +
117C VAL 3.4 9.6 - - - +
118C ASN 3.2 0.2 - - - -
119C ASN* 1.3 78.7 - - - +
121C TRP* 1.3 78.5 + + - +
123C LEU* 4.9 1.6 - - - -
124C ASN* 3.0 62.7 + - + +
166C LEU* 3.3 45.3 - - + -
167C TYR* 3.2 23.8 + - - -
170C GLY* 4.7 3.2 - - - -
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Residues in contact with TRP 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A ASN* 5.2 0.2 - - - +
121A TRP* 3.7 36.3 - - + -
125A LEU* 3.7 32.6 - - + +
126A THR* 3.1 27.3 + - - -
129A LEU* 4.5 7.0 - - + -
173A ALA* 5.5 0.2 - - + -
177A LEU* 4.7 7.0 - - + -
117C VAL* 3.2 25.3 + - + +
118C ASN* 3.8 8.3 - - - +
120C TYR* 1.3 95.5 - + - +
122C ALA* 1.3 61.1 + - - +
125C LEU* 2.8 44.8 + - + +
126C THR* 3.0 9.2 + - - -
166C LEU* 3.7 33.7 - - + -
169C ALA* 4.0 18.6 - - + -
170C GLY* 4.1 12.1 - - - -
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Residues in contact with ALA 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A ASN* 3.6 30.2 + - - +
67C LEU 3.8 2.8 - - - +
68C GLY* 3.8 21.1 - - - +
73C LEU* 5.8 0.2 - - - +
118C ASN 2.9 17.4 + - - +
119C ASN* 3.2 9.4 + - - +
121C TRP* 1.3 77.1 - - - +
123C LEU* 1.3 57.1 + - - +
126C THR* 3.5 4.0 - - + +
127C SER* 3.1 30.0 + - - -
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Residues in contact with LEU 123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67C LEU* 4.1 11.0 - - + -
68C GLY* 3.9 19.4 - - - +
98C ALA* 5.2 6.2 - - + +
99C GLY* 4.6 7.9 - - - +
100C SER* 3.6 34.1 - - - +
119C ASN 3.1 14.7 + - - +
120C TYR* 3.8 2.7 - - - +
122C ALA* 1.3 77.3 - - - +
124C ASN* 1.3 70.1 + - - +
125C LEU 3.6 0.5 + - - -
127C SER* 2.6 26.1 + - - +
128C MET 4.3 0.3 + - - -
174C ARG* 5.1 1.2 + - - -
301C NAP 3.7 46.7 - - + +
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Residues in contact with ASN 124 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98C ALA 5.5 0.2 - - - -
99C GLY* 3.2 10.2 - - - -
100C SER* 3.0 49.0 + - - +
120C TYR* 3.0 55.2 + - + +
123C LEU* 1.3 85.3 - - - +
125C LEU* 1.3 63.3 + - + +
128C MET* 3.7 1.7 - - - +
167C TYR* 5.5 1.2 - - - -
170C GLY* 5.3 2.5 - - - -
171C LYS* 5.2 4.3 + - - -
174C ARG* 2.9 44.5 + - - +
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Residues in contact with LEU 125 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A TRP* 3.7 40.2 - - + +
125A LEU* 4.1 9.4 - - + -
121C TRP* 2.8 40.4 + - + +
124C ASN* 1.3 84.0 - - + +
126C THR* 1.3 59.9 + - - +
127C SER 3.4 1.3 - - - -
128C MET* 3.2 7.9 - - - +
129C LEU* 2.9 32.0 + - - +
170C GLY* 3.4 29.8 - - - +
173C ALA* 3.7 20.6 - - + -
174C ARG* 3.7 8.5 - - + +
177C LEU* 4.7 5.0 - - + +
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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