Contacts of the helix formed by residues 105 - 120 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103A VAL* 3.6 1.5 - - - +
104A THR* 1.3 80.1 + - - +
106A PRO* 1.4 64.1 - - - +
107A HIS* 2.8 23.3 + - - +
108A ASN* 2.7 58.5 + - - +
109A LEU 3.2 7.8 + - - -
132A ALA* 3.6 2.8 - - - +
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Residues in contact with PRO 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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104A THR 3.3 9.6 - - - +
105A ASP* 1.4 87.9 - - - +
107A HIS* 1.3 59.6 + - - +
109A LEU* 3.5 3.0 + - + +
110A GLY 3.2 17.0 + - - -
132A ALA* 3.4 17.6 - - + -
133A GLN 4.1 7.6 - - - +
135A ASN* 3.4 38.6 - - - +
137A THR* 4.8 6.1 - - + -
138A ALA* 3.4 15.7 - - - +
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Residues in contact with HIS 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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105A ASP* 2.8 23.0 + - - +
106A PRO* 1.3 74.0 - - - +
108A ASN* 1.3 73.0 + - - +
110A GLY 3.3 1.4 + - - -
111A ALA* 3.1 23.7 + - + +
137A THR* 4.7 11.6 - - + +
141A VAL* 3.5 41.3 - - + +
107F HIS* 6.0 5.8 - + - -
226F ASN* 6.0 3.8 - - - -
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Residues in contact with ASN 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 VAL* 3.9 12.9 - - + +
104A THR 6.0 0.2 - - - +
105A ASP* 2.7 39.9 + - - +
107A HIS* 1.3 79.4 + - - +
109A LEU* 1.3 58.6 + - - +
111A ALA* 3.2 4.7 + - - +
112A CYS* 2.9 34.9 + - - -
198A GLU* 5.6 1.6 + - - -
226A ASN* 4.3 10.3 + - - +
227A VAL* 3.6 32.4 - - + +
228A SER* 4.8 4.3 - - - -
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Residues in contact with LEU 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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100A LEU* 4.2 17.5 - - + -
103A VAL* 3.7 15.3 - - + +
105A ASP 3.2 7.9 + - - +
106A PRO 3.7 8.7 - - - +
107A HIS 3.3 0.2 - - - -
108A ASN* 1.3 76.4 - - - +
110A GLY* 1.3 63.3 + - - +
112A CYS* 3.6 2.9 + - + +
113A LEU* 3.0 30.5 + - + +
124A VAL* 5.1 0.7 - - + -
126A VAL* 5.5 5.6 - - + -
131A SER* 5.3 1.8 - - - +
132A ALA* 3.6 32.8 - - + +
133A GLN 4.1 14.6 - - - +
134A LEU* 4.2 4.3 - - + +
138A ALA* 4.7 2.5 - - + -
151A LEU* 3.9 41.5 - - + -
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Residues in contact with GLY 110 (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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106A PRO 3.2 9.7 + - - -
107A HIS 3.3 2.9 + - - -
108A ASN 3.2 0.2 - - - -
109A LEU* 1.3 80.8 - - - +
111A ALA* 1.3 56.6 + - - +
113A LEU* 3.1 6.4 + - - +
114A ARG 2.9 24.4 + - - -
138A ALA* 3.5 27.5 - - - +
141A VAL* 3.9 7.4 - - - -
142A ALA* 3.4 14.3 - - - -
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Residues in contact with ALA 111 (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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107A HIS* 3.1 21.4 + - + +
108A ASN* 3.2 5.6 + - - +
110A GLY* 1.3 74.2 - - - +
112A CYS* 1.3 63.8 + - - +
114A ARG* 3.2 8.9 + - - +
115A SER* 3.1 27.3 + - - -
141A VAL* 3.5 12.2 - - + +
228A SER* 3.3 31.2 - - - +
226F ASN* 6.2 2.9 - - + +
229F VAL* 5.3 4.6 - - + +
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Residues in contact with CYS 112 (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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98A LEU* 4.2 7.1 - - + +
100A LEU* 3.7 33.9 - - + -
103A VAL* 5.0 2.2 - - - -
108A ASN 2.9 22.0 + - - +
109A LEU 3.9 1.8 - - - +
111A ALA* 1.3 77.1 - - - +
113A LEU* 1.3 57.4 + - - +
115A SER* 3.5 3.6 + - - -
116A ALA* 2.9 29.7 + - - +
124A VAL* 5.7 0.7 - - - -
227A VAL* 4.7 8.3 - - - -
228A SER* 4.1 15.7 - - - +
231A THR* 3.5 36.1 - - + +
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Residues in contact with LEU 113 (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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109A LEU* 3.0 25.3 + - + +
110A GLY* 3.3 8.7 - - - +
112A CYS* 1.3 75.3 - - - +
114A ARG* 1.3 66.7 + - - +
116A ALA* 3.2 3.4 + - - +
117A ASP* 3.0 19.8 + - - +
124A VAL* 3.6 31.6 - - + +
134A LEU* 3.8 29.8 - - + -
142A ALA* 4.2 6.1 - - + -
145A ALA* 3.3 17.7 - - + +
146A ALA* 4.4 14.4 - - - -
149A VAL* 4.1 23.7 - - + +
151A LEU* 4.5 14.8 - - + -
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Residues in contact with ARG 114 (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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9A HIS* 6.3 0.4 - - - -
110A GLY 2.9 12.3 + - - +
111A ALA* 3.2 11.2 + - - +
113A LEU* 1.3 77.0 - - - +
115A SER* 1.3 58.1 + - - +
117A ASP* 3.4 4.7 - - - +
118A ALA* 3.0 25.7 + - - +
141A VAL* 3.8 16.5 + - - +
142A ALA 3.5 14.1 - - - +
143A CYS* 3.6 32.1 - - + +
145A ALA* 3.6 11.2 - - + +
198F GLU* 2.9 29.9 + - - +
224F SER* 2.8 40.6 + - - +
225F LEU* 3.6 13.0 + - + +
226F ASN* 3.6 33.2 - - - +
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Residues in contact with SER 115 (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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111A ALA 3.1 15.9 + - - -
112A CYS* 3.8 5.8 - - - -
114A ARG* 1.3 74.8 - - - +
116A ALA* 1.3 60.0 + - - +
117A ASP 3.2 0.2 - - - -
118A ALA* 3.4 9.2 + - - +
119A ALA* 2.9 29.3 + - - +
228A SER 4.3 2.3 + - - -
231A THR* 4.9 1.3 - - - -
232A GLY* 4.5 19.1 - - - -
235A LEU* 4.1 6.6 - - - +
236A PHE* 4.0 5.2 - - - -
225F LEU* 4.2 9.0 - - - +
229F VAL* 3.6 27.1 - - - +
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Residues in contact with ALA 116 (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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98A LEU* 3.9 17.7 - - + -
112A CYS 2.9 18.7 + - - +
113A LEU* 3.7 4.7 - - - +
115A SER* 1.3 73.0 - - - +
117A ASP* 1.3 65.3 + - - +
119A ALA 3.1 1.7 + - - -
120A GLY 2.9 4.5 + - - -
121A VAL* 2.8 46.7 + - + +
124A VAL* 4.0 14.8 - - + -
149A VAL* 4.5 3.1 - - + -
235A LEU* 4.0 11.0 - - - +
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Residues in contact with ASP 117 (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 ARG* 5.5 0.9 - - - +
113A LEU 3.0 12.8 + - - +
114A ARG 3.4 9.5 - - - +
116A ALA* 1.3 76.8 - - - +
118A ALA* 1.3 56.5 + - - +
120A GLY* 2.8 25.0 + - - -
121A VAL 4.9 0.9 - - - +
145A ALA* 3.9 12.5 - - + +
148A SER* 3.3 29.6 - - - -
149A VAL* 3.6 17.9 - - + +
219F ALA 3.8 5.0 - - - +
222F VAL* 3.8 11.1 - - - +
223F SER* 3.0 40.5 + - - -
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Residues in contact with ALA 118 (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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114A ARG 3.0 6.6 + - - +
115A SER 3.5 7.0 - - - +
117A ASP* 1.3 80.8 + - - +
119A ALA* 1.3 57.8 + - - +
236A PHE* 3.9 12.8 - - + -
239A VAL* 5.5 0.2 - - - +
217F PRO 4.2 1.2 - - - +
218F MSE 3.9 8.6 - - - -
219F ALA* 3.0 24.4 + - - +
223F SER* 3.2 22.8 + - - -
224F SER 4.5 0.4 - - - +
225F LEU* 3.2 35.2 - - + -
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Residues in contact with ALA 119 (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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96A PHE* 3.6 13.6 - - + -
115A SER 2.9 17.3 + - - +
116A ALA 3.6 4.5 - - - +
117A ASP 3.0 0.4 - - - -
118A ALA* 1.3 77.1 - - - +
120A GLY* 1.3 60.2 + - - +
121A VAL* 4.5 1.1 - - + +
235A LEU* 3.8 27.4 - - + -
236A PHE* 4.0 7.0 - - + -
239A VAL* 3.6 33.6 - - + +
219F ALA* 4.1 4.4 - - - +
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Residues in contact with GLY 120 (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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96A PHE* 3.8 10.0 - - - -
117A ASP 2.8 15.3 + - - -
118A ALA 3.3 0.6 + - - -
119A ALA* 1.3 79.6 - - - +
121A VAL* 1.3 66.6 + - - +
122A HIS* 3.4 16.1 + - - -
219F ALA* 3.7 15.0 - - - -
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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