Contacts of the helix formed by residues 139 - 142 (chain A) in PDB entry 5JNQ
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 PRO 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 LEU* 3.8 6.0 - - - +
138A ILE* 1.4 92.3 - - + +
140A PHE* 1.3 78.0 + - + +
141A THR* 3.1 4.2 + - - -
142A GLY 4.6 2.1 + - - -
143A GLY 5.0 1.2 + - - -
252A LEU* 3.7 33.9 - - + +
253A PHE* 3.7 28.0 - - + -
256A VAL* 5.0 7.6 - - + -
318A ALA* 6.4 0.2 - - - -
321A GLY 2.6 24.1 - - - +
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Residues in contact with PHE 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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138A ILE* 3.9 2.6 - - - +
139A PRO* 1.3 87.7 - - + +
141A THR* 1.4 62.4 + - - +
256A VAL* 6.1 4.5 - - + -
317A VAL* 3.2 39.7 - - + -
318A ALA* 5.0 2.5 - - - -
320A LEU* 3.8 13.7 - - + -
321A GLY* 3.6 26.2 - - - -
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Residues in contact with THR 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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137A LEU* 4.7 0.3 - - - +
138A ILE* 2.7 51.7 + - + +
139A PRO 3.1 2.6 + - - -
140A PHE* 1.4 78.3 - - - +
142A GLY* 1.3 59.0 + - - +
143A GLY 4.7 0.2 + - - -
147A GLY* 3.4 7.1 + - - -
148A SER* 3.2 37.9 + - - +
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Residues in contact with GLY 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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139A PRO 4.6 0.4 + - - -
140A PHE 4.0 0.2 - - - -
141A THR* 1.3 79.8 + - - +
143A GLY* 1.3 63.8 + - - +
145A ASP* 4.4 2.4 + - - +
146A GLY* 3.2 22.8 + - - -
147A GLY* 3.2 8.0 + - - -
321A GLY 6.2 0.2 - - - -
323A GLY 3.1 24.5 - - - +
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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