Contacts of the helix formed by residues 1306 - 1324 (chain U) in PDB entry 5MQF
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 ARG1306 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1305U ALA* 3.8 28.7 - - - +
1307U VAL* 3.8 26.7 - - - +
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Residues in contact with VAL1307 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1306U ARG* 3.8 29.4 - - - +
1308U SER* 3.8 27.4 - - - +
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Residues in contact with SER1308 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1307U VAL* 3.8 25.8 - - - +
1309U LEU* 3.8 28.3 - - - +
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Residues in contact with LEU1309 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1308U SER* 3.8 26.9 - - - +
1310U PHE* 3.8 28.5 - - - +
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Residues in contact with PHE1310 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1309U LEU* 3.8 26.7 - - - +
1311U GLN* 3.8 29.2 - - - +
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Residues in contact with GLN1311 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1310U PHE* 3.8 28.9 - - - +
1312U ASN* 3.8 26.2 - - - +
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Residues in contact with ASN1312 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1311U GLN* 3.8 28.9 - - - +
1313U CYS* 3.8 26.7 - - - +
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Residues in contact with CYS1313 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1312U ASN* 3.8 28.9 - - - +
1314U PHE* 3.8 28.9 - - - +
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Residues in contact with PHE1314 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1313U CYS* 3.8 29.4 - - - +
1315U GLU* 3.8 26.9 - - - +
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Residues in contact with GLU1315 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1314U PHE* 3.8 29.2 - - - +
1316U LEU* 3.8 26.2 - - - +
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Residues in contact with LEU1316 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1315U GLU* 3.8 26.9 - - - +
1317U THR* 3.8 28.9 - - - +
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Residues in contact with THR1317 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1316U LEU* 3.8 29.2 - - - +
1318U PRO* 3.8 27.6 - - - -
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Residues in contact with PRO1318 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1317U THR* 3.8 25.8 - - - -
1319U ALA* 3.8 28.5 - - - -
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Residues in contact with ALA1319 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1318U PRO* 3.8 27.6 - - - -
1320U PHE* 3.8 28.7 - - - +
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Residues in contact with PHE1320 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1319U ALA* 3.8 29.4 - - - +
1321U SER* 3.8 27.1 - - - +
1323U LEU* 4.6 16.8 - - - +
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Residues in contact with SER1321 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1320U PHE* 3.8 24.5 - - - +
1322U GLN* 3.8 29.4 - - - +
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Residues in contact with GLN1322 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1321U SER* 3.8 29.8 - - - +
1323U LEU* 3.8 26.2 - - - +
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Residues in contact with LEU1323 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1320U PHE* 4.6 14.8 - - - +
1322U GLN* 3.8 28.7 - - - +
1324U THR* 3.8 26.5 - - - +
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Residues in contact with THR1324 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1323U LEU* 3.8 25.8 - - - +
1325U ALA* 3.8 29.2 - - - +
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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