Contacts of the helix formed by residues 144 - 160 (chain I) in PDB entry 1G3I
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 SER 144 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8I ARG* 5.1 0.4 - - - +
142I GLU 4.0 1.0 + - - -
143I LEU* 1.3 81.9 - - - +
145I ALA* 1.3 67.4 + - - +
146I HIS* 3.4 15.1 + - - +
147I GLU* 3.2 32.2 + - - +
148I ILE* 3.0 21.8 + - - +
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Residues in contact with ALA 145 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6I VAL* 4.2 25.0 - - + +
8I ARG* 3.9 41.0 + - + +
11I GLN* 4.2 15.0 - - + +
13I VAL* 4.6 3.8 - - + -
143I LEU 3.6 1.6 + - - -
144I SER* 1.3 72.9 + - - +
146I HIS* 1.3 66.3 + - - +
148I ILE* 3.1 14.9 + - - +
149I VAL* 3.2 15.8 + - - +
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Residues in contact with HIS 146 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13I VAL* 3.9 14.8 - - + +
144I SER* 3.4 9.3 + - - +
145I ALA* 1.3 78.7 - - - +
147I GLU* 1.3 71.3 + - + +
149I VAL* 3.1 7.4 + - - +
150I GLU* 3.1 35.3 + - + +
169I ILE* 4.4 28.9 + - + +
171I GLU* 3.6 38.8 - - + +
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Residues in contact with GLU 147 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143I LEU* 3.8 20.2 - - + +
144I SER* 3.2 35.4 + - - +
145I ALA 3.2 0.8 - - - -
146I HIS* 1.3 82.7 + - + +
148I ILE* 1.3 66.6 + - - +
150I GLU* 3.1 7.8 + - - +
151I LYS* 3.0 50.4 + - - +
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Residues in contact with ILE 148 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6I VAL* 4.0 13.9 - - + -
8I ARG* 3.9 13.7 - - - +
134I ALA* 3.5 35.4 - - + -
137I LEU* 3.4 38.6 - - + +
138I VAL* 3.2 28.3 - - + -
143I LEU* 4.0 11.4 - - + +
144I SER 3.0 15.3 + - - +
145I ALA 3.1 6.3 + - - +
147I GLU* 1.3 74.5 - - - +
149I VAL* 1.3 65.5 + - - +
151I LYS* 3.4 1.3 + - - +
152I SER* 2.8 30.8 + - - +
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Residues in contact with VAL 149 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4I VAL* 4.1 13.2 - - + +
5I SER* 4.5 0.2 - - - -
6I VAL* 3.9 29.6 - - + +
13I VAL* 3.9 19.7 - - + +
15I GLY* 3.9 20.9 - - - +
145I ALA 3.2 12.3 + - - +
146I HIS 3.1 8.7 + - - +
148I ILE* 1.3 78.1 - - - +
150I GLU* 1.3 65.9 + - - +
152I SER* 3.6 1.7 - - - -
153I LEU* 2.8 47.7 + - + +
169I ILE* 3.9 10.8 - - + -
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Residues in contact with GLU 150 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146I HIS* 3.1 20.2 + - + +
147I GLU* 3.3 13.2 - - - +
149I VAL* 1.3 81.8 - - - +
151I LYS* 1.3 75.3 + - + +
153I LEU* 3.3 5.7 + - - +
154I ARG* 3.2 44.4 + - - +
167I PHE* 3.5 17.7 - - - -
169I ILE* 4.1 20.6 - - + +
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Residues in contact with LYS 151 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137I LEU* 4.0 17.0 - - + -
143I LEU* 4.7 10.2 - - + +
147I GLU* 3.0 48.6 + - + +
148I ILE 3.9 2.2 - - - +
150I GLU* 1.3 87.9 + - + +
152I SER* 1.3 62.7 + - - +
154I ARG* 3.2 9.6 + - - +
155I ILE* 3.0 28.9 + - + +
139O GLU* 6.1 1.1 - - - +
140O ASN* 3.7 33.4 + - - +
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Residues in contact with SER 152 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4I VAL* 4.6 4.5 - - - -
130I ALA* 3.3 27.3 - - - -
133I ALA* 3.3 13.4 - - - +
134I ALA* 3.0 31.2 + - - +
137I LEU* 4.1 1.9 - - - +
148I ILE* 2.8 25.5 + - - +
149I VAL* 3.6 2.5 - - - -
151I LYS* 1.3 69.3 - - - +
153I LEU* 1.3 68.7 + - - +
155I ILE* 3.1 3.5 + - - +
156I ALA* 2.9 23.4 + - - +
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Residues in contact with LEU 153 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2I THR* 3.7 23.3 - - + +
4I VAL* 3.6 17.0 - - + -
15I GLY 3.6 19.7 - - - +
16I GLY* 3.8 18.6 - - - +
17I ASP* 4.6 0.9 - - + +
130I ALA* 4.7 0.9 - - - -
149I VAL* 2.8 34.9 + - + +
150I GLU 3.5 1.6 - - - +
152I SER* 1.3 73.5 - - - +
154I ARG* 1.3 65.2 + - - +
156I ALA* 3.2 5.7 + - - +
157I GLY* 2.8 20.3 + - - -
163I THR* 5.0 2.9 - - - +
167I PHE* 3.4 45.0 - - + -
169I ILE* 4.1 9.9 - - + -
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Residues in contact with ARG 154 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150I GLU* 3.2 35.6 + - - +
151I LYS* 3.2 11.9 + - - +
152I SER 3.1 0.2 - - - -
153I LEU* 1.3 78.9 - - - +
155I ILE* 1.3 67.3 + - + +
157I GLY* 2.7 15.9 + - - +
158I ASP* 2.9 28.9 + - - +
165I THR* 3.8 32.1 + - + +
167I PHE* 3.2 17.2 - - + -
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Residues in contact with ILE 155 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129I TYR 5.3 0.4 - - - +
133I ALA* 3.5 25.1 - - + -
137I LEU* 5.2 4.0 - - + -
151I LYS* 3.0 19.6 + - + +
152I SER* 3.5 7.0 - - - +
154I ARG* 1.3 74.9 - - + +
156I ALA* 1.3 61.5 + - - +
158I ASP* 3.5 9.4 + - - +
159I ILE* 3.1 30.0 + - + +
132O SER* 3.7 35.7 - - - +
135O ARG* 4.5 13.8 + - + +
136O ALA* 3.6 30.7 - - + +
139O GLU* 5.0 10.1 - - - +
140O ASN* 5.6 1.3 - - - +
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Residues in contact with ALA 156 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2I THR* 3.9 9.0 - - + +
126I GLY 3.3 26.7 - - - +
129I TYR* 3.8 12.3 - - + -
130I ALA* 3.5 19.3 - - + +
152I SER 2.9 7.7 + - - +
153I LEU 3.4 8.3 - - - +
154I ARG 2.7 4.0 + - - -
155I ILE* 1.3 71.6 - - - +
157I GLY* 1.3 54.1 + - - +
158I ASP 3.0 2.0 - - - -
159I ILE* 2.8 5.2 + - - +
160I CYS* 2.7 37.6 + - - +
163I THR* 4.8 0.4 - - - -
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Residues in contact with GLY 157 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153I LEU 2.8 10.2 + - - -
154I ARG* 2.7 13.1 + - - -
156I ALA* 1.3 72.2 - - - +
158I ASP* 1.3 58.2 + - - +
160I CYS 3.0 18.6 - - - +
163I THR* 3.0 36.2 - - - +
164I ASN* 4.1 7.1 - - - -
165I THR* 5.2 4.2 - - - +
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Residues in contact with ASP 158 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154I ARG* 2.9 28.1 + - - +
155I ILE* 3.6 13.0 - - - +
156I ALA 3.0 0.2 - - - -
157I GLY* 1.3 79.0 - - - +
159I ILE* 1.3 60.0 + - - +
165I THR* 4.2 14.6 - - - +
26N VAL* 3.5 24.8 - - - +
135O ARG* 4.4 15.0 + - - +
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Residues in contact with ILE 159 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129I TYR* 3.7 24.9 - - + -
155I ILE* 3.1 17.7 - - + +
156I ALA 2.8 5.4 + - - +
158I ASP* 1.3 81.7 - - - +
160I CYS* 1.3 59.5 + - - +
25N THR* 3.1 16.5 - - + -
26N VAL* 3.0 33.4 + - - +
128O ASN* 3.8 29.6 - - + +
131O LEU* 4.2 14.4 - - + -
132O SER* 3.0 32.1 - - - +
135O ARG* 3.8 19.3 - - - +
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Residues in contact with CYS 160 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125I SER* 3.8 15.7 - - - -
126I GLY* 4.2 16.4 - - - -
129I TYR* 4.6 7.6 - - + -
156I ALA 2.7 13.5 + - - +
157I GLY 3.0 17.3 - - - +
159I ILE* 1.3 77.5 - - - +
161I VAL* 1.3 58.2 + - - +
162I PHE* 3.1 31.6 - - - -
163I THR* 3.1 34.9 - - - +
24N ASN* 4.1 5.2 - - - -
26N VAL* 4.8 2.3 - - - +
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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