Contacts of the helix formed by residues 107 - 122 (chain C) in PDB entry 3ZXR
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 107 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26C CYS 4.7 3.3 + - - +
61C PHE* 4.7 1.8 - - - -
93C PHE 4.9 1.1 - - - +
94C PHE* 3.3 15.7 - - - +
95C VAL* 2.7 52.5 + - + +
104C TYR* 3.3 19.2 + - + +
106C ARG* 1.3 76.7 - - - +
108C PRO* 1.4 65.0 - - - +
109C ARG* 2.9 20.0 + - - +
110C ASN* 2.9 33.7 + - + +
111C ILE* 3.1 14.6 + - - +
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Residues in contact with PRO 108 (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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26C CYS* 3.5 19.5 - - + +
27C ASP 3.3 16.6 - - - +
28C LEU* 4.2 9.0 - - + -
61C PHE* 4.5 0.7 - - + -
106C ARG 3.3 10.5 - - - +
107C ASP* 1.4 88.2 - - - +
109C ARG* 1.3 59.7 + - - +
111C ILE* 3.2 11.7 + - + +
112C ALA 3.3 6.2 + - - -
375C ASN* 3.3 38.8 - - - +
377C TYR* 3.2 24.9 - - + +
378C LEU* 4.0 14.4 - - + -
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Residues in contact with ARG 109 (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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25C PHE* 5.2 0.2 - - - +
26C CYS* 4.5 13.7 - - + +
32C MET* 5.1 1.3 - - - -
74C ASP* 2.8 28.1 + - - +
77C THR* 3.7 5.3 - - - +
92C ASN* 4.0 15.7 - - - +
93C PHE 3.2 30.0 + - - +
94C PHE* 3.4 43.4 - - + -
107C ASP* 2.9 14.0 + - - +
108C PRO* 1.3 73.4 - - - +
110C ASN* 1.3 64.3 + - - +
112C ALA* 3.5 2.8 + - - +
113C ARG* 3.1 21.3 + - - +
236C LEU* 4.1 9.1 - - + +
240C ASP* 2.9 37.3 + - - -
377C TYR* 3.6 34.9 - - + -
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Residues in contact with ASN 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95C VAL 5.5 0.2 - - - +
103C PRO* 3.4 24.8 + - + +
104C TYR 3.0 24.7 + - - +
105C SER* 4.6 1.4 - - - +
107C ASP* 2.9 23.2 + - + +
109C ARG* 1.3 77.4 - - - +
111C ILE* 1.3 58.9 + - - +
113C ARG* 3.1 35.0 + - - +
114C LYS* 2.8 57.9 + - - +
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Residues in contact with ILE 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105C SER 3.5 18.4 - - - +
106C ARG 5.4 0.7 - - - -
107C ASP 3.1 14.2 + - - +
108C PRO* 3.2 6.9 + - + +
110C ASN* 1.3 77.0 - - - +
112C ALA* 1.3 52.1 + - - +
114C LYS* 3.2 16.7 + - - +
115C ALA* 2.8 33.1 + - - +
377C TYR 5.2 0.2 - - - +
378C LEU* 3.7 23.8 - - + -
381C SER* 3.8 21.1 - - - +
442C VAL* 3.5 23.8 - - + +
443C PHE* 3.9 20.4 - - + -
447C LEU* 3.5 22.9 - - + -
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Residues in contact with ALA 112 (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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108C PRO 3.3 8.8 + - - +
109C ARG 3.8 3.6 - - - +
110C ASN 3.3 0.2 - - - -
111C ILE* 1.3 75.2 - - - +
113C ARG* 1.3 65.8 + - - +
115C ALA* 3.3 3.5 + - - +
116C GLU* 3.1 27.5 + - - +
235C LEU* 3.7 21.1 - - + +
236C LEU* 3.7 26.5 - - + -
377C TYR* 4.1 13.0 - - + -
381C SER* 3.4 13.4 + - - +
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Residues in contact with ARG 113 (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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94C PHE* 3.2 65.6 - - + +
95C VAL 5.3 0.4 + - - -
96C HIS* 3.9 8.1 + - - -
103C PRO* 3.7 23.5 - - - +
107C ASP* 5.1 0.2 + - - -
109C ARG 3.1 11.4 + - - +
110C ASN* 3.1 32.5 + - - +
112C ALA* 1.3 73.4 - - - +
114C LYS* 1.3 63.3 + - + +
116C GLU* 3.1 18.1 + - - +
117C ASN* 3.2 25.9 + - - +
236C LEU* 4.6 12.7 - - + +
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Residues in contact with LYS 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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105C SER* 4.6 6.1 + - - +
110C ASN* 2.8 42.9 + - - +
111C ILE* 3.5 21.5 - - - +
113C ARG* 1.3 77.3 - - + +
115C ALA* 1.3 57.6 + - - +
117C ASN* 3.2 10.0 + - - +
118C TYR* 2.9 30.5 + - - +
440C GLY 5.7 1.3 - - - +
441C GLY 3.0 20.2 + - - +
442C VAL* 2.8 37.4 + - + +
444C THR* 4.0 14.1 - - - +
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Residues in contact with ALA 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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111C ILE 2.8 16.7 + - - +
112C ALA 3.5 9.0 - - - +
113C ARG 3.3 0.2 - - - -
114C LYS* 1.3 73.6 - - - +
116C GLU* 1.3 63.0 + - - +
118C TYR* 3.4 2.6 + - - +
119C LEU* 3.1 23.4 + - - +
235C LEU* 4.2 13.7 - - + -
381C SER* 3.6 25.6 - - - +
384C LEU* 3.8 11.8 - - + +
385C MET* 5.1 2.9 - - - +
442C VAL* 3.9 17.1 - - + +
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Residues in contact with GLU 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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112C ALA 3.1 15.7 + - - +
113C ARG* 3.1 9.3 + - - +
115C ALA* 1.3 74.7 - - - +
117C ASN* 1.3 65.1 + - - +
119C LEU* 3.5 11.3 + - + +
120C ILE* 3.3 28.3 + - + +
126C ASP 5.0 1.0 - - - +
128C ALA* 6.0 2.6 + - + +
234C SER* 3.7 13.3 + - - -
235C LEU* 3.2 27.8 + - + -
236C LEU* 3.1 42.5 + - - +
237C HIS 4.8 0.2 + - - -
384C LEU* 5.2 2.0 - - + -
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Residues in contact with ASN 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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113C ARG* 3.2 23.4 + - - +
114C LYS* 3.2 10.8 + - - +
116C GLU* 1.3 77.8 - - - +
118C TYR* 1.3 64.6 + - - +
120C ILE* 3.1 18.8 + - - +
121C SER* 2.9 23.0 + - - -
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Residues in contact with TYR 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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114C LYS 2.9 15.8 + - - +
115C ALA 3.7 2.7 - - - +
117C ASN* 1.3 74.2 - - - +
119C LEU* 1.3 66.7 + - - +
121C SER* 2.8 29.8 + - - -
122C THR* 3.0 27.4 + - + +
385C MET* 3.7 28.5 - - + -
388C LEU* 3.9 20.0 - - + -
392C LYS* 3.3 21.4 + - - +
439C GLU* 3.5 26.1 + - + +
440C GLY* 3.8 33.7 - - - +
442C VAL* 3.6 15.0 - - + -
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Residues in contact with LEU 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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115C ALA 3.1 14.0 + - - +
116C GLU* 3.5 12.6 - - + +
117C ASN 3.2 0.2 - - - -
118C TYR* 1.3 75.8 - - - +
120C ILE* 1.3 62.8 + - - +
122C THR* 2.7 23.1 + - - +
123C GLY 3.8 0.2 + - - -
125C ALA* 3.2 36.4 - - + +
126C ASP 4.0 3.4 - - - +
127C THR* 3.6 15.9 - - - +
128C ALA* 3.5 40.4 - - + +
281C LEU* 4.2 5.4 - - + -
384C LEU* 4.2 9.9 - - + -
388C LEU* 3.8 36.1 - - + -
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Residues in contact with ILE 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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116C GLU* 3.3 16.6 + - + +
117C ASN* 3.1 21.3 + - - +
119C LEU* 1.3 75.5 - - - +
121C SER* 1.3 63.5 + - - +
123C GLY* 3.2 15.2 + - - -
125C ALA 3.8 7.1 - - - +
126C ASP* 3.7 33.7 - - + +
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Residues in contact with SER 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117C ASN 2.9 13.2 + - - -
118C TYR* 2.8 31.4 + - - -
120C ILE* 1.3 79.3 - - - +
122C THR* 1.3 59.1 + - - +
123C GLY 3.3 0.6 + - - -
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Residues in contact with THR 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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118C TYR* 3.0 39.2 + - + +
119C LEU* 2.7 20.6 + - - +
121C SER* 1.3 76.7 - - - +
123C GLY* 1.3 57.6 + - - +
124C ILE* 3.1 36.9 + - + +
388C LEU* 4.6 3.5 - - + +
392C LYS* 3.3 31.7 + - - +
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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