Contacts of the helix formed by residues 144 - 160 (chain L) 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 L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8L ARG* 5.1 0.4 - - - +
142L GLU 3.9 0.8 + - - -
143L LEU* 1.3 80.0 - - - +
145L ALA* 1.3 68.4 + - - +
146L HIS* 3.4 14.7 + - - +
147L GLU* 3.1 33.0 + - - +
148L ILE* 2.9 22.3 + - - +
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Residues in contact with ALA 145 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6L VAL* 4.3 22.3 - - + +
7L ARG* 4.6 0.9 - - - -
8L ARG* 4.0 41.4 + - + +
11L GLN* 4.2 14.8 - - + -
13L VAL* 4.6 5.2 - - + -
143L LEU 3.6 2.2 + - - -
144L SER* 1.3 75.9 + - - +
146L HIS* 1.3 66.5 + - - +
148L ILE* 3.0 12.8 + - - +
149L VAL* 3.2 14.4 + - - +
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Residues in contact with HIS 146 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13L VAL* 3.8 14.8 - - + +
144L SER* 3.3 8.8 + - - +
145L ALA* 1.3 78.2 - - - +
147L GLU* 1.3 71.2 + - + +
149L VAL* 3.2 6.2 + - - +
150L GLU* 3.1 29.0 + - + -
169L ILE* 4.0 37.6 + - + +
171L GLU* 3.7 37.9 - - + +
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Residues in contact with GLU 147 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143L LEU* 4.1 23.2 - - + +
144L SER* 3.1 35.6 + - - +
146L HIS* 1.3 82.2 - - - +
148L ILE* 1.3 66.7 + - - +
150L GLU* 3.0 8.7 + - - +
151L LYS* 2.9 38.5 + - - +
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Residues in contact with ILE 148 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6L VAL* 4.1 14.4 - - + -
8L ARG* 3.9 14.4 - - - +
134L ALA* 3.7 34.8 - - + -
137L LEU* 3.7 35.7 - - + +
138L VAL* 3.3 27.4 - - + -
143L LEU* 3.9 14.8 - - + +
144L SER 2.9 20.1 + - - +
145L ALA* 3.0 7.4 + - - +
147L GLU* 1.3 74.3 - - - +
149L VAL* 1.3 64.0 + - - +
151L LYS* 3.3 1.5 + - - +
152L SER* 2.9 30.0 + - - +
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Residues in contact with VAL 149 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4L VAL* 4.0 15.4 - - + +
6L VAL* 4.0 24.5 - - + +
13L VAL* 3.9 26.9 - - + +
15L GLY* 3.8 31.0 - - - +
145L ALA 3.2 11.4 + - - +
146L HIS 3.2 7.5 + - - +
148L ILE* 1.3 76.5 - - - +
150L GLU* 1.3 65.2 + - - +
152L SER* 3.8 1.4 - - - -
153L LEU* 2.9 34.9 + - + +
169L ILE* 3.9 13.7 - - + -
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Residues in contact with GLU 150 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146L HIS* 3.1 18.4 + - + +
147L GLU* 3.0 14.5 + - - +
149L VAL* 1.3 81.1 - - - +
151L LYS* 1.3 69.5 + - + +
153L LEU* 3.5 2.6 + - - -
154L ARG* 3.3 45.6 + - - +
167L PHE* 3.6 20.2 - - + -
169L ILE* 4.1 20.6 - - + -
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Residues in contact with LYS 151 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137L LEU* 3.8 20.6 - - + -
143L LEU* 4.3 22.0 - - + -
147L GLU* 2.9 32.3 + - - +
150L GLU* 1.3 79.0 + - + +
152L SER* 1.3 56.8 + - - +
154L ARG* 3.5 7.9 + - - +
155L ILE* 3.1 34.5 + - + +
140R ASN* 3.0 40.7 + - - +
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Residues in contact with SER 152 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4L VAL* 4.7 4.5 - - - -
130L ALA* 3.4 28.7 - - - -
133L ALA* 3.4 13.5 - - - +
134L ALA* 3.0 29.9 + - - +
137L LEU* 4.1 2.8 - - - +
148L ILE* 2.9 18.9 + - - +
149L VAL 3.8 2.7 - - - -
151L LYS* 1.3 73.4 - - - +
153L LEU* 1.3 68.7 + - - +
155L ILE* 3.4 1.4 + - - +
156L ALA* 3.0 24.8 + - - +
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Residues in contact with LEU 153 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2L THR* 3.8 24.9 - - + +
4L VAL* 3.6 16.6 - - + -
15L GLY* 3.5 22.2 - - - +
16L GLY* 3.7 20.4 - - - +
17L ASP* 4.6 1.3 - - + +
130L ALA* 4.9 0.7 - - - -
149L VAL* 2.9 29.0 + - + +
152L SER* 1.3 77.1 - - - +
154L ARG* 1.3 53.0 + - - +
156L ALA* 3.1 4.8 + - - +
157L GLY* 2.7 33.3 + - - -
163L THR* 5.1 2.3 - - - +
167L PHE* 3.4 47.0 - - + -
169L ILE* 4.2 5.8 - - + -
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Residues in contact with ARG 154 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150L GLU* 3.3 37.4 + - - +
151L LYS* 3.5 10.5 - - - +
152L SER 3.1 0.6 - - - -
153L LEU* 1.3 78.1 - - - +
155L ILE* 1.3 68.3 + - + +
157L GLY* 2.7 15.5 + - - +
158L ASP* 2.8 28.2 + - - +
165L THR* 3.8 33.9 + - + +
167L PHE* 3.3 15.3 - - + -
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Residues in contact with ILE 155 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129L TYR 5.5 0.4 - - - +
133L ALA* 3.7 14.8 - - + -
137L LEU* 5.4 3.1 - - + -
151L LYS* 3.1 19.0 + - + +
152L SER 3.7 5.4 - - - +
154L ARG* 1.3 78.1 - - + +
156L ALA* 1.3 61.1 + - - +
158L ASP* 3.3 10.8 + - - +
159L ILE* 3.1 30.0 + - + +
132R SER* 3.7 36.1 - - - +
135R ARG* 4.5 15.0 + - + +
136R ALA* 3.6 40.6 - - + +
139R GLU* 5.0 10.1 - - - +
140R ASN* 5.7 1.6 - - - +
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Residues in contact with ALA 156 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2L THR* 4.0 12.6 - - + +
126L GLY* 3.6 24.7 - - - +
129L TYR* 3.8 12.3 - - + -
130L ALA* 3.6 12.8 - - - +
152L SER 3.0 12.2 + - - +
153L LEU 3.3 8.3 - - - +
154L ARG 2.7 3.8 + - - -
155L ILE* 1.3 70.7 - - - +
157L GLY* 1.3 57.1 + - - +
158L ASP 2.9 1.6 - - - -
159L ILE* 2.6 24.3 + - - +
160L CYS* 2.7 17.1 + - - +
163L THR* 4.9 0.4 - - - -
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Residues in contact with GLY 157 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153L LEU 2.7 11.0 + - - -
154L ARG* 2.7 12.0 + - - -
156L ALA* 1.3 73.2 - - - +
158L ASP* 1.3 58.5 + - - +
160L CYS 3.0 20.1 - - - +
163L THR* 3.1 36.8 - - - +
164L ASN* 4.1 6.9 - - - -
165L THR* 5.2 4.3 - - - -
26Q VAL* 5.7 0.2 - - - +
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Residues in contact with ASP 158 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154L ARG* 2.8 28.7 + - - +
155L ILE* 3.4 13.4 + - - +
157L GLY* 1.3 78.2 - - - +
159L ILE* 1.3 60.4 + - - +
165L THR* 4.1 14.7 - - - +
26Q VAL* 3.5 25.7 - - - +
135R ARG* 4.5 13.2 + - - +
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Residues in contact with ILE 159 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129L TYR* 3.7 25.4 - - + -
155L ILE* 3.1 17.9 - - + +
156L ALA 2.6 13.4 + - - +
158L ASP* 1.3 77.2 - - - +
160L CYS* 1.3 58.2 + - - +
25Q THR* 3.0 36.7 - - + +
26Q VAL* 3.1 12.8 + - - +
128R ASN* 4.0 14.8 - - + +
131R LEU* 4.1 17.7 - - + -
132R SER* 2.9 31.4 - - - +
135R ARG* 3.7 21.3 - - - +
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Residues in contact with CYS 160 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125L SER* 3.7 17.7 - - - -
126L GLY* 4.2 14.6 - - - -
129L TYR* 4.5 7.6 - - + -
156L ALA 2.7 13.9 + - - +
157L GLY 3.0 16.5 - - - +
158L ASP 4.9 0.2 - - - -
159L ILE* 1.3 80.4 - - - +
161L VAL* 1.3 62.5 + - - +
162L PHE* 3.0 30.3 - - - -
163L THR* 3.2 31.1 - - - +
24Q ASN* 4.0 5.6 - - - -
26Q VAL* 4.8 2.7 - - - +
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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