Contacts of the helix formed by residues 147 - 157 (chain A) in PDB entry 2GM4
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 147 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144A ARG* 4.8 8.8 - - - +
145A LYS 4.9 3.8 - - - +
146A ILE* 1.3 72.9 - - + +
148A ARG* 1.3 63.7 + - - +
149A ASP* 3.2 14.8 - - - +
150A ALA* 3.3 28.7 + - + +
151A VAL* 3.3 15.3 - - - +
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Residues in contact with ARG 148 (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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144A ARG* 3.3 56.5 - - + +
146A ILE 3.0 8.7 + - - +
147A ASP* 1.3 69.0 - - - +
149A ASP* 1.3 61.0 + - - +
150A ALA 3.2 0.7 - - - -
151A VAL* 3.4 11.8 + - - +
152A LEU* 3.1 34.7 + - + +
177A LYS* 5.1 7.1 - - - +
178A VAL* 4.0 42.5 + - + +
181A GLU* 3.2 30.8 + - - +
25Y A 4.0 24.2 + - - -
26Y T 5.0 12.6 + - - +
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Residues in contact with ASP 149 (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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144A ARG* 3.8 21.6 + - - -
147A ASP* 3.2 14.4 - - - +
148A ARG* 1.3 80.2 - - - +
150A ALA* 1.3 59.7 + - - +
152A LEU* 4.4 5.2 - - - +
153A ASN* 2.9 36.2 + - - +
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Residues in contact with ALA 150 (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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147A ASP* 3.3 24.6 + - + +
149A ASP* 1.3 81.1 - - - +
151A VAL* 1.3 59.4 + - - +
153A ASN* 4.2 4.8 + - - +
154A MET* 3.5 32.9 + - + +
168A MET* 3.7 20.5 - - - +
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Residues in contact with VAL 151 (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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146A ILE* 5.0 7.2 - - + +
147A ASP 3.3 17.7 - - - +
148A ARG* 3.4 10.7 + - + +
149A ASP 3.3 0.4 - - - -
150A ALA* 1.3 76.9 - - - +
152A LEU* 1.3 61.1 + - - +
153A ASN 3.3 0.2 - - - -
154A MET* 3.0 18.5 + - - +
155A TRP* 3.2 13.2 + - + +
164A ILE* 4.9 6.6 - - + +
168A MET* 3.7 25.1 - - + -
170A ILE* 5.3 7.0 - - + -
175A VAL* 4.3 36.1 - - + +
178A VAL* 4.5 16.4 - - + -
179A ILE* 5.1 6.1 - - + -
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Residues in contact with LEU 152 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148A ARG* 3.1 20.2 + - + +
149A ASP* 4.4 5.6 - - - +
151A VAL* 1.3 76.0 - - - +
153A ASN* 1.3 57.7 + - - +
155A TRP* 3.4 12.6 + - + +
156A GLN* 3.1 53.8 + - + +
178A VAL* 5.8 5.5 - - + +
179A ILE* 5.6 15.0 - - + -
182A SER* 4.1 21.5 - - - +
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Residues in contact with ASN 153 (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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149A ASP* 2.9 26.3 + - - +
150A ALA* 4.3 5.8 - - - +
151A VAL 3.3 0.2 - - - -
152A LEU* 1.3 78.1 - - - +
154A MET* 1.3 60.2 + - + +
155A TRP 3.2 1.8 + - - -
156A GLN* 4.4 8.7 - - - +
157A GLN* 3.5 27.7 + - - +
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Residues in contact with MET 154 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150A ALA* 3.5 19.5 + - + +
151A VAL 3.0 12.1 + - - +
153A ASN* 1.3 80.2 - - + +
155A TRP* 1.3 58.0 + - - +
157A GLN* 4.1 9.4 - - - +
159A LEU* 3.2 43.9 - - + +
164A ILE* 3.6 39.2 - - + +
167A THR* 4.2 22.9 - - + -
168A MET* 4.1 11.4 - - + -
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Residues in contact with TRP 155 (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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151A VAL 3.2 11.5 + - - +
152A LEU* 4.0 10.5 - - + +
153A ASN 3.2 0.2 - - - -
154A MET* 1.3 79.5 - - - +
156A GLN* 1.3 65.6 + - + +
157A GLN 3.0 4.7 - - - -
158A GLY* 2.8 25.9 + - - +
159A LEU 4.5 13.2 - - - +
161A ALA* 5.4 6.9 - - + +
164A ILE* 5.2 7.6 - - + -
179A ILE* 3.5 53.3 - - + +
6X G 5.0 13.8 + - - -
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Residues in contact with GLN 156 (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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152A LEU* 3.1 39.9 + - + +
153A ASN* 4.4 9.7 - - - +
155A TRP* 1.3 81.5 - - + +
157A GLN* 1.3 61.6 + - - +
158A GLY* 3.0 2.2 + - - -
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Residues in contact with GLN 157 (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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153A ASN 3.5 21.1 + - - +
154A MET* 4.1 11.8 - - + +
156A GLN* 1.3 79.8 - - - +
158A GLY* 1.3 57.9 + - - +
159A LEU* 4.0 24.7 - - + +
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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