Contacts of the helix formed by residues 105 - 120 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103F VAL* 3.5 2.6 - - - +
104F THR* 1.3 78.7 + - - +
106F PRO* 1.3 61.7 - - - +
107F HIS* 2.8 29.4 + - - +
108F ASN* 2.7 50.7 + - - +
109F LEU 3.0 9.0 + - - -
132F ALA* 3.8 1.8 - - - -
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Residues in contact with PRO 106 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104F THR 3.3 10.1 - - - +
105F ASP* 1.3 86.9 - - - +
107F HIS* 1.3 57.0 + - - +
109F LEU* 3.1 4.2 + - + +
110F GLY 2.8 26.7 + - - -
132F ALA* 3.5 17.7 - - + -
133F GLN* 4.3 7.0 - - + +
135F ASN* 3.6 38.4 - - - +
137F THR* 4.5 6.7 - - + -
138F ALA* 3.6 13.7 - - + +
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Residues in contact with HIS 107 (chain F).
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* 6.0 6.7 - + - -
105F ASP* 2.8 23.6 + - - +
106F PRO* 1.3 73.7 - - - +
108F ASN* 1.3 59.8 + - - +
110F GLY 3.3 0.2 + - - -
111F ALA* 2.9 29.7 + - + +
137F THR* 4.7 13.9 - - + +
141F VAL* 3.6 40.9 - - + +
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Residues in contact with ASN 108 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103F VAL* 3.5 16.0 - - + +
105F ASP* 2.7 37.8 + - - +
107F HIS* 1.3 77.8 + - - +
109F LEU* 1.3 56.4 + - - +
111F ALA* 3.2 5.6 + - - +
112F CYS* 2.8 40.0 + - - -
198F GLU* 5.0 4.6 + - - -
226F ASN* 4.2 19.9 + - - +
227F VAL* 4.8 19.0 - - + +
228F SER* 4.8 4.3 - - - -
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Residues in contact with LEU 109 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100F LEU* 4.1 20.4 - - + -
103F VAL* 3.6 10.6 - - + +
105F ASP 3.0 9.8 + - - +
106F PRO 3.4 7.4 - - - +
108F ASN* 1.3 78.1 - - - +
110F GLY* 1.3 61.6 + - - +
112F CYS* 3.5 3.2 + - - +
113F LEU* 3.2 25.3 + - + +
124F VAL* 5.2 0.4 - - + -
126F VAL* 4.7 5.8 - - + -
131F SER* 4.8 2.7 - - - +
132F ALA* 3.7 41.1 - - + +
133F GLN 3.9 15.5 - - - +
134F LEU* 4.0 13.7 - - + +
138F ALA* 4.7 0.9 - - + -
151F LEU* 4.0 30.5 - - + -
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Residues in contact with GLY 110 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106F PRO 2.8 14.2 + - - -
107F HIS 3.8 1.1 - - - -
109F LEU* 1.3 76.6 - - - +
111F ALA* 1.3 63.3 + - - +
113F LEU* 3.3 4.3 + - - -
114F ARG 3.1 18.4 + - - -
138F ALA* 3.5 27.1 - - - +
141F VAL* 3.9 7.2 - - - -
142F ALA* 3.3 18.0 - - - +
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Residues in contact with ALA 111 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226A ASN* 6.2 4.0 - - + -
229A VAL* 5.7 0.7 - - + +
107F HIS* 2.9 21.9 + - + +
108F ASN* 3.6 7.0 - - - +
110F GLY* 1.3 74.3 - - - +
112F CYS* 1.3 62.8 + - - +
114F ARG* 3.4 8.3 + - - +
115F SER* 3.3 20.8 + - - -
141F VAL* 3.4 17.6 - - + +
228F SER* 3.3 29.4 + - - +
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Residues in contact with CYS 112 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98F LEU* 4.2 5.4 - - + +
100F LEU* 3.7 32.5 - - + -
103F VAL* 5.1 2.2 - - - -
108F ASN* 2.8 26.0 + - - +
109F LEU 3.8 1.3 - - - +
111F ALA* 1.3 76.6 - - - +
113F LEU* 1.3 59.7 + - - +
115F SER* 3.3 7.0 + - - -
116F ALA* 2.9 28.5 + - - +
124F VAL* 6.4 0.2 - - - -
227F VAL* 4.1 9.4 - - - -
228F SER* 4.1 18.4 - - - +
231F THR* 3.8 30.1 - - + +
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Residues in contact with LEU 113 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100F LEU* 5.6 0.4 - - - +
109F LEU* 3.2 20.7 + - + +
110F GLY* 3.3 8.3 + - - +
112F CYS* 1.3 75.2 - - - +
114F ARG* 1.3 65.4 + - - +
116F ALA* 3.0 4.9 + - - +
117F ASP* 2.9 24.6 + - - +
124F VAL* 3.5 35.2 - - + -
134F LEU* 3.7 33.4 - - + -
142F ALA* 4.2 7.9 - - + -
145F ALA* 3.7 5.0 - - + +
146F ALA* 4.0 24.2 - - + +
149F VAL* 4.0 24.7 - - + +
151F LEU* 4.6 8.3 - - + -
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Residues in contact with ARG 114 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198A GLU* 3.0 32.5 + - - +
224A SER* 2.6 44.8 + - - +
225A LEU* 3.3 16.4 + - + -
226A ASN* 3.4 31.6 - - - +
9F HIS* 6.0 0.2 + - - -
110F GLY 3.1 9.3 + - - +
111F ALA* 3.4 11.9 - - - +
112F CYS 3.2 0.2 - - - -
113F LEU* 1.3 79.9 - - - +
115F SER* 1.3 62.2 + - - +
117F ASP* 3.4 5.7 + - - +
118F ALA* 3.1 21.0 + - - +
141F VAL* 3.7 16.6 + - - +
142F ALA* 3.7 12.1 - - - +
143F CYS* 3.6 22.8 - - + +
145F ALA* 3.8 12.5 - - + +
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Residues in contact with SER 115 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225A LEU* 4.0 15.6 - - - +
226A ASN 6.0 0.2 + - - -
229A VAL* 3.4 31.0 - - - +
111F ALA 3.3 8.5 + - - -
112F CYS* 3.3 11.1 + - - -
113F LEU 3.2 0.4 - - - -
114F ARG* 1.3 76.8 - - - +
116F ALA* 1.3 66.8 + - - +
118F ALA* 3.1 4.3 + - - +
119F ALA* 2.9 23.6 + - - +
228F SER* 4.5 2.4 + - - -
231F THR* 5.1 1.1 - - - -
232F GLY* 4.0 12.7 - - - -
235F LEU* 4.0 13.5 - - - +
236F PHE* 4.1 3.3 - - - -
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Residues in contact with ALA 116 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98F LEU* 3.8 16.8 - - + -
112F CYS 2.9 14.1 + - - +
113F LEU* 3.0 9.4 + - - +
115F SER* 1.3 76.1 - - - +
117F ASP* 1.3 57.4 + - - +
119F ALA 3.2 1.7 + - - -
120F GLY 3.0 8.7 + - - -
121F VAL* 2.9 52.1 + - + +
124F VAL* 3.9 13.7 - - + -
149F VAL* 4.6 3.4 - - + -
235F LEU* 3.8 5.5 - - - +
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Residues in contact with ASP 117 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219A ALA 3.1 21.0 - - - +
220A GLY* 5.5 0.5 - - - -
223A SER* 3.4 19.6 + - - -
224A SER 4.7 0.9 + - - -
17F ARG* 3.1 39.7 + - - -
113F LEU 2.9 4.6 + - - +
114F ARG* 3.5 6.8 - - - +
116F ALA* 1.3 73.3 - - - +
118F ALA* 1.3 65.2 + - - +
120F GLY* 3.4 7.4 + - - +
121F VAL 5.0 1.6 - - - +
145F ALA* 3.5 29.4 - - + +
148F SER* 4.1 6.6 - - - -
149F VAL* 3.5 16.3 - - + +
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Residues in contact with ALA 118 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217A PRO 4.1 1.2 - - - +
218A MSE 3.8 18.9 - - - -
219A ALA* 3.0 23.4 + - - +
223A SER* 3.7 12.3 - - - -
224A SER 4.1 3.4 - - - +
225A LEU* 3.3 34.1 - - + -
114F ARG 3.1 9.6 + - - +
115F SER 3.1 5.1 + - - +
117F ASP* 1.3 78.0 - - - +
119F ALA* 1.3 58.2 + - - +
236F PHE* 3.9 12.0 - - + -
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Residues in contact with ALA 119 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219A ALA* 4.0 4.9 - - - +
96F PHE* 3.4 20.5 - - + -
115F SER 2.9 16.0 + - - +
116F ALA 3.2 4.5 + - - +
118F ALA* 1.3 78.6 - - - +
120F GLY* 1.3 57.3 + - - +
121F VAL* 4.4 0.2 - - + -
235F LEU* 3.8 24.0 - - + -
236F PHE* 4.0 9.0 - - + -
239F VAL* 3.7 29.9 - - + +
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Residues in contact with GLY 120 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219A ALA* 3.7 16.8 - - - +
96F PHE* 3.9 8.6 - - - -
116F ALA 3.0 2.8 + - - -
117F ASP 3.4 9.2 + - - -
118F ALA 3.4 0.4 + - - -
119F ALA* 1.3 80.3 - - - +
121F VAL* 1.3 66.7 + - - +
122F HIS* 3.3 19.8 + - - -
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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