Contacts of the helix formed by residues 339 - 344 (chain X) in PDB entry 1UL1
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 ARG 339 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A SER 5.1 1.6 - - - +
44A HIS* 3.1 15.5 - - + +
45A VAL* 4.3 0.7 - - - +
335X SER* 6.3 0.2 - - - -
337X GLN 3.3 5.3 + - - +
338X GLY* 1.3 74.2 - - - -
340X LEU* 1.3 55.6 + - - +
341X ASP* 2.5 38.4 + - + +
342X ASP* 3.0 25.8 + - - +
343X PHE* 3.5 7.7 - - - -
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Residues in contact with LEU 340 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A MET* 4.4 5.2 - - - -
44A HIS 2.7 11.7 + - - +
45A VAL 3.1 40.8 - - - +
46A SER* 3.2 9.0 - - - +
47A LEU* 3.2 30.7 - - + +
126A LEU* 3.6 17.9 - - + +
234A PRO* 4.8 7.4 - - + -
250A TYR* 3.5 28.3 - - + +
252A ALA* 4.1 7.6 - - + +
339X ARG* 1.3 69.9 - - - +
341X ASP* 1.3 55.7 + - - +
342X ASP 3.3 0.4 - - - -
343X PHE* 3.9 8.5 - - - -
344X PHE* 3.0 46.0 + - + +
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Residues in contact with ASP 341 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A MET* 3.5 14.8 - - - +
44A HIS* 2.6 47.0 + - - +
124A GLU* 3.5 10.2 - - - +
126A LEU* 5.0 2.9 - - - -
339X ARG* 2.5 20.1 + - + +
340X LEU* 1.3 75.2 - - - +
342X ASP* 1.3 62.6 + - - +
344X PHE 2.9 20.8 - - - +
345X LYS* 5.0 0.2 - - - -
346X VAL* 4.9 5.9 - - + +
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Residues in contact with ASP 342 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24X LYS 5.0 3.3 - - - +
27X PHE* 3.3 55.5 - - + +
335X SER* 3.8 17.2 + - - -
338X GLY* 4.6 0.3 - - - -
339X ARG* 3.0 27.9 + - - +
341X ASP* 1.3 80.2 - - - +
343X PHE* 1.3 65.6 + - + +
344X PHE* 3.5 1.7 + - - -
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Residues in contact with PHE 343 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A PRO* 5.4 1.0 - - - +
232A ASP 3.3 26.7 - - - -
233A VAL* 3.3 22.9 - - + -
234A PRO* 3.3 21.3 - - + -
252A ALA* 4.2 7.0 - - + -
253A PRO* 4.1 10.3 - - + -
24X LYS 5.7 0.2 - - - +
25X SER* 4.8 13.4 - - - +
27X PHE* 4.0 35.4 - + - +
338X GLY* 3.7 30.5 - - - -
339X ARG 3.5 12.6 - - - -
340X LEU* 3.6 4.7 + - - +
341X ASP 3.5 0.2 - - - -
342X ASP* 1.3 79.2 - - + +
344X PHE* 1.3 90.2 + - + +
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Residues in contact with PHE 344 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A LEU* 3.9 22.5 - - + +
127A GLY 3.9 7.4 - - - +
128A ILE* 3.5 33.0 - - + -
129A PRO* 3.4 36.1 - - + -
131A GLN* 4.7 14.1 - - - -
133A TYR* 5.5 0.7 - - - -
234A PRO* 4.0 20.9 - - + -
250A TYR* 4.5 9.4 - + - -
340X LEU* 3.0 42.0 + - + +
341X ASP 2.9 23.2 - - - +
342X ASP 4.7 1.3 - - - -
343X PHE* 1.3 99.8 - - + +
345X LYS* 1.3 63.6 + - - +
346X VAL* 3.6 1.4 + - - +
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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