Contacts of the helix formed by residues 105 - 120 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103G VAL* 3.7 2.6 - - - +
104G THR* 1.3 79.3 - - + +
106G PRO* 1.3 91.2 - - - +
107G HIS* 3.0 24.3 + - - +
108G ASN* 3.2 31.2 + - - +
109G LEU* 3.2 9.2 + - - +
132G ALA* 3.3 5.0 - - - +
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Residues in contact with PRO 106 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104G THR 3.6 7.0 - - - +
105G ASP* 1.3 91.3 - - - +
107G HIS* 1.3 62.0 + - - +
109G LEU* 3.1 4.6 + - + +
110G GLY 3.0 18.5 + - - -
132G ALA* 3.3 16.1 - - + -
133G GLN* 4.2 10.3 - - + +
135G ASN* 3.4 39.9 - - - +
137G THR* 4.6 6.1 - - + -
138G ALA* 3.5 13.0 - - + +
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Residues in contact with HIS 107 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B HIS* 5.6 10.1 + + - -
105G ASP* 3.0 18.5 + - - +
106G PRO* 1.3 77.8 - - - +
108G ASN* 1.3 71.2 + - - +
110G GLY* 3.2 2.9 + - - -
111G ALA* 3.0 23.8 + - + +
137G THR* 4.5 18.2 - - + +
138G ALA* 5.1 0.4 - - - +
141G VAL* 3.7 37.0 - - + +
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Residues in contact with ASN 108 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103G VAL* 3.6 22.6 - - + +
105G ASP* 3.2 23.0 + - - +
107G HIS* 1.3 85.0 + - - +
109G LEU* 1.3 62.0 + - - +
111G ALA* 3.4 5.1 + - - +
112G CYS* 3.0 30.6 + - - -
198G GLU* 5.0 8.9 + - - +
226G ASN* 4.1 22.2 + - - +
227G VAL* 4.8 16.9 - - + +
228G SER* 4.4 6.3 - - - -
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Residues in contact with LEU 109 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100G LEU* 4.0 19.3 - - + -
103G VAL* 4.0 10.4 - - + +
105G ASP 3.2 11.1 + - - +
106G PRO 3.1 10.2 + - - +
108G ASN* 1.3 76.5 - - - +
110G GLY* 1.3 64.1 + - - +
112G CYS* 3.4 3.8 + - - +
113G LEU* 3.2 28.8 + - + +
126G VAL* 5.0 5.4 - - + -
132G ALA* 2.9 33.2 - - + +
133G GLN 4.0 11.7 - - - +
134G LEU* 4.3 7.0 - - + -
138G ALA* 4.8 3.1 - - + -
151G LEU* 3.7 40.8 - - + -
153G ARG* 5.0 0.2 - - - +
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Residues in contact with GLY 110 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106G PRO 3.0 12.5 + - - -
107G HIS 3.2 3.3 + - - -
109G LEU* 1.3 78.0 - - - +
111G ALA* 1.3 60.4 + - - +
113G LEU* 3.3 6.5 + - - +
114G ARG 3.2 17.5 + - - -
138G ALA* 3.4 27.6 - - - -
141G VAL* 4.3 0.9 - - - -
142G ALA* 3.2 21.6 - - - -
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Residues in contact with ALA 111 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226B ASN* 6.3 3.4 - - + -
229B VAL* 5.4 2.5 - - + +
107G HIS* 3.0 21.0 + - + +
108G ASN* 3.9 4.3 - - - +
109G LEU 3.4 0.2 - - - -
110G GLY* 1.3 75.3 - - - +
112G CYS* 1.3 61.1 + - - +
114G ARG* 3.4 9.2 + - - +
115G SER* 3.3 23.7 + - - -
141G VAL* 3.4 18.2 - - + +
228G SER* 3.0 28.8 + - - +
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Residues in contact with CYS 112 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98G LEU* 4.2 5.6 - - + +
100G LEU* 3.9 28.9 - - + -
103G VAL* 5.1 2.0 - - - -
108G ASN 3.0 24.4 + - - +
109G LEU 3.8 4.3 - - - +
111G ALA* 1.3 73.8 - - - +
113G LEU* 1.3 54.5 + - - +
115G SER* 3.0 8.1 + - - -
116G ALA* 2.6 36.3 + - - +
227G VAL* 4.3 10.5 - - - -
228G SER* 4.1 13.2 - - - +
231G THR* 3.6 35.4 - - + -
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Residues in contact with LEU 113 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100G LEU* 5.8 0.2 - - - +
109G LEU* 3.2 28.5 + - + +
110G GLY* 3.4 10.8 - - - +
112G CYS* 1.3 77.8 - - - +
114G ARG* 1.3 56.1 + - - +
116G ALA* 3.0 4.9 + - - +
117G ASP* 2.7 37.2 + - - +
124G VAL* 4.0 28.3 - - + -
134G LEU* 4.7 14.1 - - + -
142G ALA* 4.2 8.3 - - + -
145G ALA* 3.7 12.0 - - + +
146G ALA* 4.2 23.6 - - + -
149G VAL* 4.1 27.2 - - + +
151G LEU* 4.4 12.8 - - + -
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Residues in contact with ARG 114 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B GLU* 2.5 39.2 + - - +
224B SER* 2.7 41.5 + - - +
225B LEU* 3.5 7.8 + - + -
226B ASN* 3.7 30.6 - - - +
110G GLY 3.2 9.2 + - - +
111G ALA* 3.5 13.0 - - - +
112G CYS 3.2 0.2 - - - -
113G LEU* 1.3 79.6 - - - +
115G SER* 1.3 57.9 + - - +
117G ASP* 3.8 3.0 - - - +
118G ALA* 3.1 26.0 + - - +
141G VAL* 3.6 20.2 + - - +
142G ALA 3.8 9.2 - - - +
143G CYS* 3.7 24.3 - - + +
145G ALA* 3.6 11.1 - - - +
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Residues in contact with SER 115 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225B LEU* 4.5 7.3 - - - +
229B VAL* 3.6 27.8 - - - +
111G ALA 3.3 9.9 + - - -
112G CYS* 3.0 10.8 + - - -
114G ARG* 1.3 75.4 - - - +
116G ALA* 1.3 66.7 + - - +
117G ASP 3.2 0.4 - - - -
118G ALA* 3.3 6.3 + - - +
119G ALA* 3.0 26.7 + - - +
228G SER 4.5 2.5 + - - -
231G THR* 5.1 0.4 - - - -
232G GLY* 4.2 12.6 - - - -
235G LEU* 3.9 15.6 - - - +
236G PHE* 4.3 3.4 - - - -
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Residues in contact with ALA 116 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98G LEU* 3.9 8.5 - - + -
112G CYS 2.6 17.6 + - - +
113G LEU* 3.2 10.5 - - - +
115G SER* 1.3 74.6 - - - +
117G ASP* 1.3 62.6 + - - +
120G GLY 3.3 2.6 + - - -
121G VAL* 3.0 45.6 + - + +
124G VAL* 3.8 28.7 - - + -
149G VAL* 4.3 4.7 - - + -
235G LEU* 3.8 4.9 - - - +
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Residues in contact with ASP 117 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219B ALA* 3.7 8.9 - - - +
222B VAL* 4.7 7.2 - - - +
223B SER* 2.3 37.6 + - - -
113G LEU 2.7 17.3 + - - +
114G ARG 3.8 4.6 - - - +
116G ALA* 1.3 72.0 - - - +
118G ALA* 1.3 64.1 + - - +
120G GLY* 2.9 15.9 + - - -
121G VAL 4.9 0.9 - - - +
145G ALA* 4.3 10.3 - - + -
148G SER* 2.6 30.2 + - - +
149G VAL* 3.3 22.5 - - + +
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Residues in contact with ALA 118 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218B MSE 3.5 19.9 - - + +
219B ALA 2.8 26.2 + - - -
223B SER* 3.7 13.2 - - - -
224B SER 3.9 5.6 - - - +
225B LEU* 3.4 33.4 - - + -
114G ARG 3.1 12.1 + - - +
115G SER 3.3 2.9 + - - +
117G ASP* 1.3 79.2 + - - +
119G ALA* 1.3 56.6 + - - +
236G PHE* 3.9 7.1 - - + -
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Residues in contact with ALA 119 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219B ALA* 3.9 4.2 - - - +
96G PHE* 3.3 14.4 - - + -
115G SER 3.0 16.6 + - - +
116G ALA 3.9 3.6 - - - +
117G ASP 3.0 0.4 + - - -
118G ALA* 1.3 75.5 - - - +
120G GLY* 1.3 58.4 + - - +
121G VAL* 4.5 0.2 - - + -
235G LEU* 4.0 18.2 - - + -
236G PHE* 3.6 16.2 - - + -
239G VAL* 3.3 35.9 - - + +
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Residues in contact with GLY 120 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219B ALA* 3.4 19.4 - - - +
96G PHE* 3.4 13.4 - - - -
117G ASP 2.9 9.4 + - - -
119G ALA* 1.3 80.9 - - - +
121G VAL* 1.3 66.7 + - - +
122G HIS* 3.4 16.6 + - - -
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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