Contacts of the strand formed by residues 317 - 323 (chain A) in PDB entry 3RL8
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 ILE 317 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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316A LYS* 1.3 91.8 + - + +
318A MET* 1.3 64.3 + - - +
372A LEU* 4.0 19.7 - - + -
401A LYS* 3.8 21.1 - - + -
402A VAL 3.3 8.3 - - - +
403A ALA* 4.8 2.5 - - + -
366C GLN* 3.8 34.5 - - + +
367C ILE* 3.6 59.4 - - + +
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Residues in contact with MET 318 (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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316A LYS 3.8 0.4 + - - -
317A ILE* 1.3 75.5 - - - +
319A GLU* 1.3 73.4 + - - +
320A ILE* 4.1 5.1 + - + -
364A LYS* 3.7 44.2 - - + +
400A LEU 4.0 0.2 - - - +
401A LYS* 3.5 3.6 - - - +
402A VAL* 2.8 46.6 + - + +
404A LYS* 3.9 28.9 - - + -
367C ILE* 5.4 0.2 - - - -
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Residues in contact with GLU 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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318A MET* 1.3 81.5 - - - +
320A ILE* 1.3 66.0 + - - +
321A LYS* 5.5 3.8 - - - +
364A LYS* 4.6 6.6 - - - +
399A TYR* 2.8 35.3 + - + +
400A LEU 3.6 3.1 - - - -
401A LYS* 4.8 5.2 - - + -
341C HIS* 2.8 35.4 + - + +
350C VAL 4.1 1.3 - - - +
351C THR* 3.6 20.3 - - - +
367C ILE* 4.1 22.2 - - + +
368C GLY* 3.5 14.1 - - - -
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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 MET* 4.1 11.2 - - + +
319A GLU* 1.3 81.0 - - - +
321A LYS* 1.3 65.9 + - - +
322A LEU* 3.8 21.8 - - + -
362A ASP* 3.6 24.0 - - - +
364A LYS* 3.9 20.4 - - + +
365A LEU* 3.8 38.8 - - + +
398A VAL 3.8 0.7 - - - +
399A TYR* 3.4 4.2 - - - +
400A LEU* 2.8 50.5 + - + +
402A VAL* 3.9 26.0 - - + -
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Residues in contact with LYS 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 GLU* 4.4 3.3 + - - -
320A ILE* 1.3 78.3 - - - +
322A LEU* 1.3 68.4 + - - +
362A ASP* 4.0 10.4 + - - +
364A LYS* 5.5 3.3 - - - +
398A VAL 3.4 3.8 - - - +
399A TYR* 4.3 9.9 - - + -
323B ILE* 3.7 29.0 - - + +
396B ASP* 3.2 38.9 + - + +
397B PHE* 3.6 28.5 - - + -
334C ALA* 5.6 0.2 - - - +
340C GLN 4.6 1.0 + - - -
341C HIS* 3.0 62.6 + - - +
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Residues in contact with LEU 322 (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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320A ILE* 3.8 14.1 - - + -
321A LYS* 1.3 76.2 - - - +
323A ILE* 1.3 65.2 + - - +
324A LYS 4.0 0.2 - - - -
329A LEU* 3.9 30.7 - - + +
331A PHE* 4.9 1.6 - - + -
358A ALA* 4.0 9.4 - - + +
359A ALA* 4.1 24.5 - - + +
362A ASP* 3.3 41.3 - - + +
365A LEU* 5.5 1.3 - - + -
396A ASP 3.8 0.5 - - - +
397A PHE* 3.5 3.6 - - - -
398A VAL* 2.8 37.3 + - + +
400A LEU* 4.0 22.7 - - + -
323B ILE* 4.1 4.9 - - - +
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Residues in contact with ILE 323 (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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322A LEU* 1.3 76.7 - - - +
324A LYS* 1.3 73.4 + - - +
325A GLY* 4.6 0.2 - - - -
358A ALA* 3.1 21.3 - - - +
396A ASP* 3.5 8.7 - - + +
397A PHE* 3.8 12.8 - - + -
321B LYS* 3.3 52.5 - - + +
322B LEU* 3.7 16.6 - - - +
323B ILE* 3.8 18.3 - - + +
362B ASP* 5.7 1.3 - - - +
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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