Contacts of the helix formed by residues 144 - 154 (chain A) in PDB entry 4M83
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 VAL 144 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137A TRP* 3.7 25.8 - - + -
140A TYR* 2.7 41.5 + - + +
142A GLU 3.4 0.8 - - - -
143A GLU* 1.3 81.9 - - + +
145A ALA* 1.3 66.5 + - - +
146A GLU 3.3 1.6 - - - -
147A PRO* 3.3 8.1 - - - +
148A MET* 3.2 25.8 + - - +
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Residues in contact with ALA 145 (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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140A TYR* 2.9 27.9 + - + +
141A GLU* 3.6 36.1 - - - +
144A VAL* 1.3 76.3 - - - +
146A GLU* 1.3 62.4 + - - +
148A MET* 3.4 12.7 - - + +
149A TRP* 3.1 34.1 + - + +
179A ASP* 5.6 3.6 - - - +
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Residues in contact with GLU 146 (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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141A GLU* 2.9 21.1 + - + +
142A GLU* 4.1 9.3 - - - +
145A ALA* 1.3 76.3 - - - +
147A PRO* 1.4 65.9 - - + +
149A TRP* 3.1 3.9 + - - +
150A ARG* 2.8 78.8 + - - +
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Residues in contact with PRO 147 (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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142A GLU 3.8 9.6 - - - +
143A GLU 3.8 13.7 - - - +
144A VAL* 3.3 18.8 - - - +
146A GLU* 1.4 104.6 - - + +
148A MET* 1.3 60.2 + - - +
150A ARG* 4.0 25.2 + - + +
151A GLU 5.0 1.6 + - - -
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Residues in contact with MET 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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77A LEU* 3.6 32.0 - - + +
81A VAL* 6.3 0.9 - - + -
140A TYR* 4.7 13.7 - - - +
144A VAL* 3.2 27.8 + - - +
145A ALA* 3.4 10.1 - - + +
146A GLU 3.1 0.4 - - - -
147A PRO* 1.3 81.9 - - - +
149A TRP* 1.3 86.3 + - + +
152A PRO* 3.5 15.2 - - - +
1400A ERY 5.9 4.3 - - - +
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Residues in contact with TRP 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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77A LEU* 3.7 26.5 - - + -
78A LEU* 3.5 43.5 - - + -
81A VAL* 3.8 20.4 - - + +
145A ALA* 3.1 29.0 + - + +
146A GLU* 4.1 2.7 - - - +
148A MET* 1.3 101.7 - - + +
150A ARG* 1.3 64.7 + - - +
151A GLU 3.4 1.6 - - - -
152A PRO* 3.7 2.2 - - + -
153A ARG* 2.9 58.4 + - + +
158A GLY* 5.1 0.4 - - - -
161A TYR* 3.7 12.1 - + - -
162A TYR* 3.2 41.7 + + - -
179A ASP* 4.5 10.0 + - - +
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Residues in contact with ARG 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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146A GLU* 2.8 51.7 + - - +
147A PRO* 4.1 23.2 - - - +
148A MET 3.5 2.0 - - - -
149A TRP* 1.3 78.6 - - - +
151A GLU* 1.3 66.3 + - + +
153A ARG* 4.3 1.5 - - - +
154A GLN* 3.1 24.9 + - - +
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Residues in contact with GLU 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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147A PRO 5.0 1.6 + - - -
148A MET 4.8 0.2 + - - -
150A ARG* 1.3 88.0 - - + +
152A PRO* 1.3 65.6 - - + +
154A GLN* 3.6 13.2 - - + +
155A THR* 3.3 19.2 - - - +
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Residues in contact with PRO 152 (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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77A LEU* 4.0 14.6 - - + -
78A LEU* 3.7 20.6 - - + -
148A MET 3.5 19.5 - - - +
149A TRP* 3.5 15.9 - - + +
151A GLU* 1.3 92.5 - - + +
153A ARG* 1.3 59.4 + - - +
154A GLN 2.9 1.6 - - - -
155A THR* 2.3 39.1 + - + +
158A GLY* 3.2 8.0 - - - -
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Residues in contact with ARG 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 TRP* 2.9 39.9 + - + +
150A ARG* 4.3 1.3 - - - +
152A PRO* 1.3 73.8 - - - +
154A GLN* 1.3 49.4 + - - +
158A GLY* 3.9 10.8 - - - +
159A ARG* 2.8 41.0 + - + +
162A TYR* 3.2 49.5 - - + +
177A HIS* 3.1 41.9 + - - -
179A ASP* 4.1 5.3 + - - -
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Residues in contact with GLN 154 (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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150A ARG 3.1 18.9 + - - +
151A GLU* 3.6 13.0 - - + +
153A ARG* 1.3 76.5 - - - +
155A THR* 1.3 66.0 + - + +
156A GLU 3.9 0.5 + - - -
159A ARG* 3.1 32.8 + - - +
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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