Contacts of the helix formed by residues 146 - 154 (chain B) in PDB entry 2GER
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 GLY 146 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118B ILE* 5.0 7.0 - - - -
135B TYR* 5.1 11.6 - - - -
141B ALA 3.9 3.4 + - - -
142B GLN* 5.4 1.8 - - - -
143B VAL 2.8 8.0 + - - -
145B ASP* 1.3 81.1 - - - +
147B ARG* 1.3 55.7 + - - +
148B LEU 2.9 4.3 - - - -
149B MET* 2.9 28.9 + - - +
150B GLU* 3.6 4.2 + - - +
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Residues in contact with ARG 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B TYR* 6.0 0.4 - - - -
143B VAL 3.7 4.7 + - - +
144B GLU* 3.8 28.5 - - - +
146B GLY* 1.3 73.6 - - - +
148B LEU* 1.3 57.1 + - - +
149B MET 3.3 0.2 - - - -
150B GLU* 2.4 48.6 + - - +
151B GLN* 2.8 42.2 + - - +
154B SER* 6.2 0.4 - - - -
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Residues in contact with LEU 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B MET* 5.9 8.3 - - + -
91B ILE* 5.7 4.3 - - + -
116B ARG* 6.2 1.1 - - - +
144B GLU* 3.8 25.0 - - + +
145B ASP* 4.3 17.3 - - - +
147B ARG* 1.3 79.1 - - - +
149B MET* 1.3 64.9 + - + +
151B GLN* 3.6 26.8 + - - +
152B LEU* 3.5 18.2 + - - +
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Residues in contact with MET 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B VAL* 5.3 3.8 - - + -
67B PHE* 4.8 6.3 - - + -
91B ILE* 4.5 10.5 - - + -
93B VAL* 3.0 41.5 - - + -
118B ILE* 3.1 47.6 - - + -
135B TYR* 4.9 13.2 - - + -
145B ASP 4.3 8.5 - - - +
146B GLY* 2.9 11.5 + - - +
148B LEU* 1.3 76.5 - - + +
150B GLU* 1.3 66.1 + - - +
151B GLN 3.0 2.8 + - - -
152B LEU* 3.1 6.6 + - - +
153B LEU* 3.1 41.4 + - + +
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Residues in contact with GLU 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B TYR* 2.5 43.4 + - + +
146B GLY 3.6 3.0 + - - -
147B ARG* 2.4 58.9 + - - +
148B LEU 3.4 0.6 - - - -
149B MET* 1.3 79.0 - - - +
151B GLN* 1.3 57.0 + - - +
154B SER* 2.8 50.9 + - - +
159B CYS* 4.0 16.8 - - + -
160B THR* 4.3 4.6 + - - -
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Residues in contact with GLN 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144B GLU* 5.0 4.0 + - - -
147B ARG* 2.8 47.1 + - - +
148B LEU* 3.6 28.4 - - - +
149B MET 3.0 0.4 - - - -
150B GLU* 1.3 80.9 - - - +
152B LEU* 1.3 64.1 + - - +
153B LEU 3.1 1.4 + - - -
154B SER* 3.6 5.1 + - - -
155B SER* 3.6 15.4 + - - -
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Residues in contact with LEU 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B MET* 5.4 11.4 - - + -
3B VAL* 5.4 4.5 - - + -
19B PHE* 3.2 45.1 - - + -
23B GLY 6.0 0.4 - - - +
24B VAL* 6.2 2.9 - - + -
25B LEU* 4.4 18.6 - - + -
65B VAL* 5.6 2.5 - - + -
67B PHE* 4.4 25.8 - - + -
148B LEU 3.5 8.5 + - - +
149B MET* 3.1 9.3 + - - +
151B GLN* 1.3 78.3 - - - +
153B LEU* 1.3 68.6 + - + +
155B SER* 3.1 13.9 + - - -
156B VAL* 4.2 0.7 - - - +
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Residues in contact with LEU 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B LEU* 4.5 11.9 - - + -
19B PHE* 4.4 13.2 - - + -
67B PHE* 5.3 11.4 - - + -
93B VAL* 6.0 0.9 - - + -
120B CYS* 5.3 11.0 - - + -
133B THR* 4.7 14.1 - - + +
134B VAL 6.1 0.4 - - - +
135B TYR* 5.2 9.0 - - + -
149B MET* 3.1 35.0 + - + +
152B LEU* 1.3 98.7 - - + +
154B SER* 1.3 52.8 + - - +
155B SER 2.5 17.9 + - - -
156B VAL* 2.8 17.9 + - + +
157B GLY* 3.5 8.5 + - - -
158B PHE 4.4 0.7 + - - -
159B CYS* 3.6 21.8 - - - -
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Residues in contact with SER 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B ARG* 5.4 4.7 + - - -
147B ARG* 6.2 0.2 - - - -
150B GLU* 2.8 41.7 + - - +
151B GLN* 4.2 2.0 - - - -
153B LEU* 1.3 69.6 - - - +
155B SER* 1.3 56.8 + - - +
157B GLY 4.5 6.6 - - - +
158B PHE* 4.5 6.7 - - - +
159B CYS* 3.9 26.1 + - - +
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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