Contacts of the strand formed by residues 316 - 321 (chain A) in PDB entry 1U9J
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 THR 316 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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315A ARG* 1.3 69.8 - - - +
317A ARG* 1.3 65.0 + - - +
318A VAL* 3.6 1.8 + - + -
340A HIS* 3.0 11.3 + - - -
341A TYR* 3.5 32.4 - - + -
342A GLU 2.9 24.5 + - - +
384A ASP* 3.6 11.7 - - + +
385A VAL* 3.8 28.9 - - + -
551A ILE* 5.6 1.3 - - + +
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Residues in contact with ARG 317 (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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315A ARG 4.1 6.7 + - - +
316A THR* 1.3 72.9 - - - +
318A VAL* 1.3 60.4 + - - +
342A GLU* 3.4 13.8 - - + +
344A TYR* 3.8 30.5 + - + -
382A LYS* 3.2 40.9 + - - +
383A CYS* 3.4 19.6 - - + +
384A ASP* 2.7 43.6 + - - +
385A VAL 3.0 9.9 + - - -
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Residues in contact with VAL 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A THR* 4.1 6.3 - - + +
317A ARG* 1.3 74.8 - - - +
319A LEU* 1.3 59.7 + - - +
320A ILE* 3.7 15.8 + - + -
331A LEU* 5.1 1.6 - - + -
335A LEU* 4.1 26.5 - - + -
341A TYR* 3.7 33.7 - - + -
342A GLU 2.8 11.6 + - - +
343A VAL* 3.6 4.1 - - + +
344A TYR* 2.8 33.5 + - - +
383A CYS* 4.6 2.0 - - - -
385A VAL* 3.5 16.4 - - + +
387A LEU* 5.3 4.5 - - + -
551A ILE* 4.6 16.6 - - + -
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Residues in contact with LEU 319 (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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317A ARG 3.9 0.8 + - - -
318A VAL* 1.3 71.2 - - - +
320A ILE* 1.3 63.7 + - - +
321A LEU* 3.6 33.5 + - + -
344A TYR* 3.4 21.8 - - + +
346A LEU* 4.4 10.3 - - + -
365A VAL* 5.6 0.7 - - + -
376A ILE 4.9 0.4 - - - +
379A HIS* 4.0 25.4 - - + +
380A VAL* 4.0 19.7 - - + -
383A CYS* 3.9 22.7 - - + -
385A VAL 2.7 14.8 + - - +
386A VAL* 4.0 21.3 - - + +
387A LEU* 2.9 29.6 + - - +
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Residues in contact with ILE 320 (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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318A VAL* 4.1 13.2 - - + -
319A LEU* 1.3 73.0 - - - +
321A LEU* 1.3 62.5 + - - +
322A GLY 3.4 0.9 + - - -
323A VAL* 3.6 30.6 + - + +
328A GLY* 4.5 2.7 - - - +
331A LEU* 3.9 24.7 - - + -
332A THR* 3.7 23.3 - - - +
335A LEU* 4.6 6.1 - - + -
343A VAL* 3.8 16.2 - - + -
344A TYR 2.8 12.2 + - - +
345A GLY* 3.6 0.9 - - - -
346A LEU 2.9 25.1 + - - +
387A LEU* 3.8 13.0 - - + -
389A LEU* 3.7 25.1 - - + -
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Residues in contact with LEU 321 (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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319A LEU* 3.6 34.1 - - + -
320A ILE* 1.3 71.1 - - - +
322A GLY* 1.3 58.2 + - - +
346A LEU* 3.9 27.4 - - + -
369A ILE* 4.5 12.1 - - + -
376A ILE* 4.3 11.9 - - + -
386A VAL* 3.9 13.2 - - + -
387A LEU 3.0 10.5 + - - +
388A PRO* 4.2 10.1 - - + -
389A LEU* 2.9 32.6 + - - +
390A VAL* 3.7 4.3 + - + -
416A ILE* 3.7 45.8 - - + -
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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