Contacts of the strand formed by residues 338 - 342 (chain A) in PDB entry 1UA4
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 338 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264A HIS* 3.8 10.1 + - - -
287A TYR* 2.9 17.3 + - + +
288A SER* 2.7 37.7 + - - +
289A VAL* 2.9 29.5 + - - +
336A VAL* 3.6 1.6 - - - +
337A LYS* 1.3 79.8 - - - +
339A ILE* 1.3 67.6 + - - +
340A HIS* 3.7 26.6 + - - +
349A ALA* 5.6 3.2 - - + +
350A LEU 3.5 4.5 - - - -
351A THR* 3.8 10.2 - - + +
353A TYR* 3.2 25.1 - - - +
358A VAL* 5.2 2.4 + - - +
361A ALA* 5.4 1.0 - - - +
362A LEU* 4.7 5.3 - - - +
443A SER 5.2 0.4 + - - -
446A ALA* 3.6 35.8 + - - +
447A PHE* 3.8 16.1 - - - +
450A GLU* 2.8 25.7 + - - -
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Residues in contact with ILE 339 (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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289A VAL* 3.4 15.9 - - + +
291A LEU* 4.2 17.5 - - + -
327A MET* 2.9 71.0 - - + +
330A LEU* 3.9 21.3 - - + -
331A ALA* 3.9 17.3 - - + +
336A VAL* 3.7 15.3 - - + +
337A LYS 5.6 0.2 - - - -
338A ARG* 1.3 80.4 - - - +
340A HIS* 1.3 60.3 + - - +
349A ALA* 3.2 3.4 - - - -
350A LEU* 2.9 28.2 + - + +
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Residues in contact with HIS 340 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A HIS* 5.1 0.7 - - - +
289A VAL 2.8 12.4 + - - +
290A GLY* 3.3 5.7 - - - -
291A LEU* 3.1 26.7 + - - +
338A ARG* 3.7 25.0 + - - +
339A ILE* 1.3 70.8 - - - +
341A PHE* 1.3 76.3 + - - +
342A HIS* 4.1 2.6 + - + -
347A TYR* 3.9 9.7 - + - +
348A LEU 3.6 4.3 - - - -
349A ALA* 4.5 1.6 - - + +
362A LEU* 3.3 25.9 - - + +
365A ALA* 4.7 0.4 - - + -
442A ILE* 3.5 32.4 - - + +
443A SER* 4.2 11.7 + - - -
446A ALA* 3.4 33.8 - - + +
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Residues in contact with PHE 341 (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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291A LEU* 3.3 18.4 - - + -
292A ASN 3.7 3.4 - - - -
293A GLU* 3.6 32.8 - - + -
296A LEU* 3.9 14.8 - - + -
312A LEU* 5.5 0.2 - - + -
318A VAL* 4.1 1.3 - - + -
323A VAL* 3.7 39.7 - - + -
327A MET* 3.9 19.1 - - + -
339A ILE 3.8 1.4 + - - -
340A HIS* 1.3 77.5 - - - +
342A HIS* 1.3 62.0 + - - +
343A THR* 3.6 38.6 - - + -
346A TYR* 4.0 12.6 - + - -
347A TYR* 3.3 3.5 - - - -
348A LEU* 2.8 50.3 + - + +
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Residues in contact with HIS 342 (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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266A GLU* 3.9 9.6 - - - -
291A LEU* 3.0 33.3 + - - -
292A ASN* 3.2 28.1 - - + +
293A GLU 3.8 0.5 + - - -
295A GLU* 5.1 1.3 - - - -
340A HIS* 4.5 3.0 + - - +
341A PHE* 1.3 78.6 - - - +
343A THR* 1.3 64.4 + - - +
346A TYR 4.2 0.2 - - - -
347A TYR* 3.6 25.8 - - + -
439A GLY* 3.7 10.6 - - - -
442A ILE* 4.0 16.0 - - + +
443A SER* 3.9 22.5 + - - -
1456A AMP 3.0 61.1 + + - +
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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