Contacts of the helix formed by residues 1317 - 1323 (chain A) in PDB entry 4UHX
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 ASP1317 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1001A TYR* 5.8 0.7 - - + -
1002A TRP* 3.6 26.6 - - + -
1175A CYS 4.5 0.7 - - - +
1294A ARG* 3.8 10.5 + - - +
1312A ARG* 2.8 30.6 + - - -
1315A CYS 3.5 4.2 - - - +
1316A GLU* 1.3 77.2 - - - +
1318A LYS* 1.3 64.1 + - - +
1319A PHE* 3.0 14.2 + - - +
1320A THR* 2.9 44.0 + - - +
1321A LYS* 3.3 25.6 + - - +
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Residues in contact with LYS1318 (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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487A GLU* 3.1 36.0 + - - +
490A LEU* 5.4 3.9 - - - +
491A ASP* 4.1 16.0 + - - +
524A PHE* 5.1 7.9 - - - -
549A TYR* 5.3 5.4 + - - -
1002A TRP* 5.8 4.5 - - + -
1317A ASP* 1.3 76.9 - - + +
1319A PHE* 1.3 98.6 + - + +
1321A LYS* 4.1 7.4 - - - +
1322A MET* 3.0 32.4 + - - +
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Residues in contact with PHE1319 (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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490A LEU* 5.6 2.2 - - + -
494A CYS* 4.3 17.5 - - - -
517A THR* 4.3 3.4 - - + -
520A ILE* 3.5 34.6 - - + +
521A SER* 4.2 7.0 - - - +
524A PHE* 3.4 48.7 - + + -
1002A TRP* 4.1 12.6 - + - -
1176A LEU* 4.1 6.7 - - + -
1312A ARG* 4.0 15.0 - - - +
1317A ASP* 3.0 20.7 + - - +
1318A LYS* 1.3 108.7 - - + +
1320A THR* 1.3 63.6 + - - +
1322A MET* 3.4 3.9 + - - -
1323A ILE* 3.4 28.2 + - - +
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Residues in contact with THR1320 (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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517A THR* 4.3 5.4 - - + -
1312A ARG* 3.7 21.8 - - - +
1313A MET* 4.2 26.7 - - + +
1315A CYS 3.9 0.7 - - - +
1316A GLU* 3.3 25.8 - - - +
1317A ASP* 2.9 34.0 + - - +
1319A PHE* 1.3 73.7 - - - +
1321A LYS* 1.3 69.1 + - - +
1323A ILE* 3.3 14.9 - - - +
1325A ARG* 3.1 29.7 + - - +
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Residues in contact with LYS1321 (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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1296A LEU* 5.4 13.4 - - - +
1316A GLU* 5.3 8.2 - - + -
1317A ASP* 3.3 30.1 + - - +
1318A LYS* 4.3 6.3 - - - +
1320A THR* 1.3 86.4 + - - +
1322A MET* 1.3 60.1 + - - +
1323A ILE 3.7 3.5 + - - +
1325A ARG* 5.2 2.6 + - - +
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Residues in contact with MET1322 (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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491A ASP* 3.2 33.0 - - + +
494A CYS* 3.5 26.7 - - + -
495A ARG* 3.3 39.7 - - + +
498A LEU* 3.9 14.3 - - + +
520A ILE* 4.1 12.1 - - + -
1318A LYS* 3.0 23.9 + - - +
1319A PHE* 3.7 9.9 - - - +
1320A THR 3.2 0.6 - - - -
1321A LYS* 1.3 76.8 - - - +
1323A ILE* 1.3 68.5 + - - +
1324A PRO* 3.7 0.9 - - - +
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Residues in contact with ILE1323 (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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498A LEU* 4.4 4.3 - - + -
513A GLU* 3.6 36.3 - - + +
516A ARG* 3.6 26.0 - - + +
517A THR* 3.7 19.3 - - - +
520A ILE* 4.2 5.8 - - + -
1313A MET* 5.4 1.8 - - - -
1319A PHE 3.5 13.9 - - - +
1320A THR 3.3 16.8 - - - +
1321A LYS 3.5 4.4 - - - +
1322A MET* 1.3 81.1 - - - +
1324A PRO* 1.4 83.0 - - + +
1325A ARG* 3.7 29.8 + - + +
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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