Contacts of the helix formed by residues 105 - 120 (chain C) in PDB entry 1GZ0
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 105 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103C VAL* 3.6 1.9 - - - +
104C THR* 1.3 84.0 - - + +
106C PRO* 1.3 69.7 - - - +
107C HIS* 2.9 29.6 + - - +
108C ASN* 2.8 50.8 + - - +
109C LEU* 2.9 10.6 + - - +
132C ALA* 3.5 2.2 - - - -
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Residues in contact with PRO 106 (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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104C THR 3.6 6.5 - - - +
105C ASP* 1.3 90.8 - - - +
107C HIS* 1.3 61.2 + - - +
109C LEU* 3.7 4.0 - - + -
110C GLY 3.0 19.2 + - - -
132C ALA* 3.4 16.3 - - + -
133C GLN* 4.1 9.2 - - + +
135C ASN* 3.6 37.5 - - - +
137C THR* 4.6 6.1 - - + -
138C ALA* 3.5 16.4 - - + +
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Residues in contact with HIS 107 (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 ASP* 2.9 22.0 + - - +
106C PRO* 1.3 78.6 - - - +
108C ASN* 1.3 63.9 + - - +
111C ALA* 3.1 23.6 + - + +
137C THR* 4.9 12.7 - - + +
141C VAL* 3.7 39.9 - - + +
107H HIS* 5.3 15.4 + + - -
226H ASN* 5.4 8.1 - - - -
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Residues in contact with ASN 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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103C VAL* 3.6 17.4 - - + +
105C ASP* 2.8 34.6 + - - +
107C HIS* 1.3 76.9 + - - +
109C LEU* 1.3 65.9 + - - +
111C ALA* 3.3 0.3 + - - +
112C CYS* 2.9 28.8 + - - -
198C GLU* 4.9 3.0 + - - -
226C ASN* 3.4 24.5 + - - +
227C VAL* 3.6 22.7 - - + +
228C SER* 3.6 14.6 + - - +
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Residues in contact with LEU 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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100C LEU* 4.2 21.1 - - + -
103C VAL* 3.5 14.7 - - + +
105C ASP 2.9 10.9 + - - +
106C PRO* 3.6 10.3 - - + +
108C ASN* 1.3 78.8 - - - +
110C GLY* 1.3 63.9 + - - +
112C CYS* 3.1 9.7 + - - +
113C LEU* 3.2 20.1 + - + +
124C VAL* 5.4 0.2 - - + -
126C VAL* 4.9 5.8 - - + -
132C ALA* 4.1 17.5 - - + +
133C GLN 4.0 28.3 - - - +
134C LEU* 4.0 7.9 - - + +
138C ALA* 4.5 2.9 - - + -
151C LEU* 4.1 33.4 - - + -
153C ARG* 4.4 0.7 - - - +
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Residues in contact with GLY 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106C PRO 3.0 14.2 + - - -
107C HIS 4.0 1.1 - - - -
109C LEU* 1.3 76.1 - - - +
111C ALA* 1.3 61.8 + - - +
113C LEU* 3.1 8.1 + - - +
114C ARG 3.1 16.5 + - - -
138C ALA* 3.4 28.6 - - - +
141C VAL* 4.2 0.9 - - - -
142C ALA* 3.3 21.9 - - - -
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Residues in contact with ALA 111 (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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107C HIS* 3.1 20.2 + - + +
108C ASN* 3.7 0.7 - - - +
109C LEU 3.3 0.2 - - - -
110C GLY* 1.3 75.2 - - - +
112C CYS* 1.3 60.3 + - - +
114C ARG* 3.3 9.9 + - - +
115C SER* 3.1 25.4 + - - -
141C VAL* 3.7 16.6 - - + +
228C SER* 3.0 30.9 - - - +
226H ASN* 5.8 6.7 - - + +
229H VAL* 5.3 6.1 - - + +
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Residues in contact with CYS 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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98C LEU* 4.1 6.2 - - + +
100C LEU* 3.9 33.2 - - + -
103C VAL* 4.6 8.1 - - - -
108C ASN 2.9 21.9 + - - +
109C LEU 3.1 5.4 + - - +
111C ALA* 1.3 77.1 - - - +
113C LEU* 1.3 58.6 + - - +
115C SER* 3.5 6.2 + - - -
116C ALA* 3.0 28.2 + - - +
124C VAL* 5.5 0.2 - - - -
227C VAL* 4.5 2.2 - - - -
228C SER* 4.0 18.4 - - - +
231C THR* 3.6 28.1 - - + +
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Residues in contact with LEU 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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100C LEU* 6.4 0.2 - - + -
109C LEU* 3.2 20.4 + - + +
110C GLY* 3.1 10.9 + - - +
112C CYS* 1.3 75.1 - - - +
114C ARG* 1.3 61.1 + - - +
116C ALA* 3.7 2.6 - - - +
117C ASP* 2.9 24.6 + - - +
124C VAL* 3.6 31.9 - - + -
134C LEU* 4.5 22.2 - - + -
142C ALA* 4.3 5.2 - - + -
145C ALA* 3.3 17.8 - - + +
146C ALA* 4.2 27.8 - - + -
149C VAL* 4.0 23.1 - - + +
151C LEU* 4.7 14.1 - - + -
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Residues in contact with ARG 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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9C HIS* 5.5 2.8 + - - -
110C GLY 3.1 8.9 + - - +
111C ALA* 3.4 11.2 - - - +
113C LEU* 1.3 79.7 - - - +
115C SER* 1.3 61.9 + - - +
117C ASP* 3.3 4.0 + - - +
118C ALA* 3.1 22.2 + - - +
141C VAL* 3.5 23.1 + - - +
142C ALA* 3.8 13.7 - - - +
143C CYS* 3.8 26.4 - - - +
145C ALA* 3.7 10.0 - - - +
198H GLU* 2.9 40.6 + - - -
222H VAL* 4.2 15.5 - - + +
224H SER* 3.5 26.1 + - - -
225H LEU* 3.6 7.8 - - + +
226H ASN* 3.6 32.0 - - - +
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Residues in contact with SER 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 ALA 3.1 13.6 + - - -
112C CYS* 3.8 8.0 - - - -
113C LEU 3.3 0.2 - - - -
114C ARG* 1.3 76.7 - - - +
116C ALA* 1.3 59.9 + - - +
118C ALA* 3.1 2.5 + - - +
119C ALA* 2.7 31.5 + - - +
228C SER 4.4 3.1 + - - -
231C THR* 4.8 1.3 - - - -
232C GLY* 4.2 22.6 - - - -
235C LEU* 4.4 7.6 - - - -
236C PHE* 4.1 3.5 - - - -
225H LEU* 4.2 14.8 - - - +
229H VAL* 3.9 24.0 - - - +
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Residues in contact with ALA 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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98C LEU* 4.0 17.9 - - + -
112C CYS 3.0 19.4 + - - +
113C LEU 3.7 4.3 - - - +
115C SER* 1.3 76.8 - - - +
117C ASP* 1.3 62.7 + - - +
119C ALA 3.3 0.5 + - - -
120C GLY 2.9 4.9 + - - -
121C VAL* 2.8 48.0 + - + +
124C VAL* 4.0 13.0 - - + -
149C VAL* 4.5 4.7 - - + -
235C LEU* 4.1 8.5 - - - +
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Residues in contact with ASP 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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17C ARG* 5.0 5.9 + - - -
113C LEU 2.9 17.9 + - - +
114C ARG 3.5 4.5 - - - +
115C SER 3.2 0.2 - - - -
116C ALA* 1.3 77.2 - - - +
118C ALA* 1.3 61.0 + - - +
120C GLY* 3.0 14.8 + - - -
121C VAL 4.9 1.3 - - - +
145C ALA* 3.7 7.9 - - + -
148C SER* 2.8 30.2 + - - -
149C VAL* 3.5 16.6 - - + +
220H GLY* 3.9 13.3 + - - -
221H SER* 3.6 11.1 + - - -
222H VAL* 2.9 39.9 + - + +
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Residues in contact with ALA 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 ARG 3.1 5.9 + - - +
115C SER 3.1 6.0 + - - +
117C ASP* 1.3 81.8 + - - +
119C ALA* 1.3 56.0 + - - +
236C PHE* 3.9 9.6 - - + -
239C VAL* 5.3 0.9 - - - +
217H PRO 4.1 1.2 - - - +
218H MSE 3.8 24.7 - - + -
219H ALA* 2.9 32.2 + - - +
220H GLY 4.7 1.1 - - - +
222H VAL* 4.4 3.8 - - + -
225H LEU* 3.3 34.5 - - + -
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Residues in contact with ALA 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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96C PHE* 3.5 17.7 - - + -
115C SER 2.7 19.0 + - - +
116C ALA 3.8 4.0 - - - +
118C ALA* 1.3 73.4 - - - +
120C GLY* 1.3 59.8 + - - +
121C VAL* 3.5 1.1 - - + -
235C LEU* 3.7 29.2 - - + -
236C PHE* 4.1 5.8 - - + -
239C VAL* 3.6 32.7 - - + +
219H ALA* 3.9 5.3 - - - +
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Residues in contact with GLY 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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17C ARG* 5.7 5.0 + - - -
96C PHE* 3.9 9.6 - - - -
116C ALA 2.9 3.4 + - - -
117C ASP 3.0 13.4 + - - -
118C ALA 3.2 0.8 - - - -
119C ALA* 1.3 80.9 - - - +
121C VAL* 1.3 66.6 + - - +
122C HIS* 3.5 15.2 + - - -
219H ALA* 3.8 13.9 - - - -
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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