Contacts of the helix formed by residues 143 - 150 (chain A) in PDB entry 5E63
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 143 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135A LYS* 4.9 2.1 - - - +
141A GLY 3.6 2.0 + - - -
142A LEU* 1.3 77.3 - - - +
144A GLU* 1.3 61.7 + - - +
145A GLU* 3.2 22.5 + - - +
146A LEU* 3.2 26.5 + - - +
147A GLN* 2.9 29.1 + - - +
17C G 5.3 0.4 - - - -
18C A 3.5 25.0 + - - -
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Residues in contact with GLU 144 (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 LEU 5.9 0.2 - - - -
143A SER* 1.3 75.9 - - - +
145A GLU* 1.3 58.3 + - - +
147A GLN* 3.4 9.3 + - - +
148A ALA* 3.0 29.5 + - - +
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Residues in contact with GLU 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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27A VAL 5.4 1.6 - - - +
28A ARG* 5.7 0.9 - - - -
29A LYS* 4.0 27.2 + - + +
37A TRP* 4.4 23.2 - - + -
143A SER* 3.2 9.9 + - - +
144A GLU* 1.3 80.2 - - - +
146A LEU* 1.3 59.3 + - - +
148A ALA* 3.4 6.0 + - - +
149A ALA* 2.9 28.4 + - + +
19C G 5.3 4.5 + - - -
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Residues in contact with LEU 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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27A VAL* 3.4 36.6 - - + +
37A TRP* 3.6 21.8 - - + -
132A VAL* 4.8 3.4 - - + -
135A LYS* 3.5 35.4 - - + -
142A LEU* 4.1 15.2 - - + +
143A SER* 3.2 26.2 + - - +
145A GLU* 1.3 79.7 - - + +
147A GLN* 1.3 60.3 + - - +
149A ALA 4.4 0.2 - - - +
150A PHE* 2.8 57.2 + - + +
18C A 5.5 1.6 - - - +
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Residues in contact with GLN 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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136A ALA* 5.9 0.6 - - - +
142A LEU* 3.5 38.5 + - + +
143A SER 2.9 24.5 + - - +
144A GLU* 3.5 9.0 - - - +
146A LEU* 1.3 74.4 - - - +
148A ALA* 1.3 57.6 + - - +
150A PHE 3.7 2.6 - - - +
151A PRO* 3.1 34.0 - - - +
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Residues in contact with ALA 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 GLU 3.0 16.4 + - - +
145A GLU* 3.8 6.7 - - - +
147A GLN* 1.3 76.1 - - - +
149A ALA* 1.3 62.8 + - - +
150A PHE 3.5 0.3 + - - -
151A PRO* 3.6 15.5 - - - +
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Residues in contact with ALA 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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37A TRP* 3.5 33.2 - - + -
145A GLU* 2.9 22.1 + - + +
148A ALA* 1.3 73.4 - - - +
150A PHE* 1.3 75.7 + - + +
151A PRO* 3.6 5.4 - - - +
152A GLN* 4.9 1.9 + - - -
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Residues in contact with PHE 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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27A VAL* 4.9 0.4 - - + -
37A TRP* 4.0 18.8 - + - -
125A GLN* 4.6 7.9 - - - -
128A LEU* 3.9 27.1 - - + -
129A GLU* 4.4 14.4 - - + -
132A VAL* 3.7 47.6 - - + -
142A LEU* 4.6 4.4 - - + +
146A LEU* 2.8 37.6 + - + +
147A GLN* 3.3 8.0 - - - +
149A ALA* 1.3 92.9 - - + +
151A PRO* 1.4 58.0 - - - +
152A GLN* 3.1 36.4 + - - +
153A CYS* 3.3 12.2 + - + +
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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