Contacts of the helix formed by residues 139 - 147 (chain A) in PDB entry 3HM5
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 139 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137A VAL 4.0 0.8 + - - -
138A TYR* 1.3 77.4 - - - +
140A GLU* 1.3 65.5 + - - +
141A GLN* 3.6 7.8 + - - +
142A GLU* 2.9 40.2 + - - +
143A TYR* 3.0 22.0 + - - +
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Residues in contact with GLU 140 (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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139A SER* 1.3 73.8 - - - +
141A GLN* 1.3 63.0 + - - +
143A TYR* 3.3 4.2 + - - +
144A GLN* 3.0 22.9 + - - +
154A LYS* 4.5 20.0 - - - +
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Residues in contact with GLN 141 (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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139A SER* 3.2 8.3 + - - +
140A GLU* 1.3 76.5 - - - +
142A GLU* 1.3 66.1 + - + +
144A GLN* 3.2 6.2 + - + +
145A LEU* 3.0 51.6 + - + +
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Residues in contact with GLU 142 (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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138A TYR* 3.3 7.6 - - + -
139A SER* 2.9 37.6 + - - +
141A GLN* 1.3 77.6 - - + +
143A TYR* 1.3 61.8 + - - +
146A TYR* 3.1 47.0 + - + +
147A LEU* 3.7 2.8 + - - +
202A LEU* 3.8 12.9 - - + +
205A VAL* 4.4 3.0 - - + +
206A ARG* 2.9 53.9 + - - +
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Residues in contact with TYR 143 (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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138A TYR* 3.8 21.8 - + + -
139A SER 3.0 12.6 + - - +
140A GLU 3.6 7.6 - - - +
142A GLU* 1.3 76.6 - - - +
144A GLN* 1.3 63.6 + - - +
147A LEU* 3.0 43.1 + - + +
148A HIS* 3.5 38.3 + + - -
152A TRP 4.1 5.5 + - - -
153A THR 3.4 4.7 + - - -
154A LYS* 3.4 50.7 + - + -
157A THR* 3.2 26.7 + - + -
194A ARG* 2.9 31.1 + - - -
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Residues in contact with GLN 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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5A UNX 3.1 5.9 - - - -
140A GLU 3.0 16.6 + - - +
141A GLN* 3.2 8.2 + - - +
143A TYR* 1.3 76.9 - - - +
145A LEU* 1.3 62.4 + - + +
148A HIS* 3.0 33.5 - - - +
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Residues in contact with LEU 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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5A UNX 2.9 14.0 - - - -
141A GLN* 3.0 49.2 + - + +
144A GLN* 1.3 76.8 - - + +
146A TYR* 1.3 98.6 + - + +
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Residues in contact with TYR 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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5A UNX 3.2 6.7 - - - -
142A GLU* 3.1 32.5 + - + +
145A LEU* 1.3 112.1 - - + +
147A LEU* 1.3 66.8 + - + +
148A HIS 3.6 2.0 + - - +
197A HIS* 4.8 6.6 - - - -
201A LYS* 3.8 32.4 - - + +
202A LEU* 5.7 0.2 - - + -
205A VAL* 3.8 44.5 - - + +
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Residues in contact with LEU 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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138A TYR* 3.6 44.0 - - + -
142A GLU 3.7 9.6 - - - +
143A TYR* 3.0 33.7 + - + +
146A TYR* 1.3 85.0 - - + +
148A HIS* 1.3 63.9 + - - +
194A ARG* 2.8 34.5 + - - +
197A HIS* 5.4 3.4 - - + -
198A ILE* 3.9 30.1 - - + -
201A LYS* 3.8 26.9 - - + -
202A LEU* 4.2 12.3 - - + -
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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