Contacts of the strand formed by residues 367 - 374 (chain B) in PDB entry 5C16
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 ALA 367 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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324B LEU* 5.4 2.5 - - + -
336B LYS* 5.9 0.9 - - - -
337B LEU* 3.2 21.8 - - + +
339B ILE* 3.9 25.4 - - + -
361B GLU* 5.3 6.9 - - - +
364B TYR* 3.1 28.5 + - + +
365B PRO 3.3 3.7 - - - +
366B ASN* 1.3 81.2 - - - +
368B GLU* 1.3 61.8 + - - +
369B LEU 4.2 0.6 + - - -
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Residues in contact with GLU 368 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336B LYS* 3.0 30.8 + - + +
337B LEU 3.0 7.5 + - - +
338B ILE* 3.5 25.8 - - + +
339B ILE* 3.0 22.1 + - - +
367B ALA* 1.3 73.8 - - - +
369B LEU* 1.3 70.4 + - - +
370B VAL* 4.8 9.0 - - + +
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Residues in contact with LEU 369 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339B ILE* 3.2 28.2 - - + +
341B ASP* 4.0 7.9 - - + -
358B TYR* 3.8 19.5 - - + -
359B GLU* 3.3 44.4 - - + +
367B ALA 4.2 0.8 - - - -
368B GLU* 1.3 78.3 - - - +
370B VAL* 1.3 77.5 + - - +
371B PHE* 3.6 40.8 - - + -
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Residues in contact with VAL 370 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338B ILE* 5.3 6.5 - - + -
339B ILE 2.8 8.9 + - - +
340B PHE* 3.4 23.5 - - + +
341B ASP 3.0 24.3 + - - +
368B GLU* 4.8 14.8 - - + +
369B LEU* 1.3 85.6 - - - +
371B PHE* 1.3 74.3 + - - +
372B LEU 4.0 0.2 + - - -
422B ARG* 3.7 31.0 - - - +
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Residues in contact with PHE 371 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341B ASP* 3.4 28.3 - - + -
343B ARG 3.5 20.0 - - - +
344B GLN 4.4 0.7 - - - -
345B ASN* 3.4 45.8 - - + -
348B ALA* 3.6 20.9 - - + -
358B TYR* 4.0 26.0 - + - -
369B LEU* 3.6 18.6 - - + -
370B VAL* 1.3 84.5 - - - +
372B LEU* 1.3 63.3 + - - +
373B GLU* 3.5 19.0 - - - +
422B ARG* 4.2 5.7 + - - -
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Residues in contact with LEU 372 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340B PHE* 3.6 42.8 - - + -
341B ASP 2.9 13.6 + - - +
342B ALA* 3.7 13.2 - - - +
371B PHE* 1.3 76.5 - - - +
373B GLU* 1.3 72.3 + - - +
374B ILE* 3.3 18.5 + - + +
415B MET* 5.1 2.4 - - - +
419B GLY* 4.0 13.7 - - - +
422B ARG* 3.8 27.6 - - + +
423B ILE* 4.0 8.7 - - + -
448B LEU* 3.7 35.2 - - + -
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Residues in contact with GLU 373 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342B ALA 3.4 0.2 + - - -
343B ARG 3.1 12.4 + - - -
344B GLN* 3.5 30.1 + - - +
345B ASN* 3.0 27.2 + - - +
371B PHE* 3.7 17.2 - - - +
372B LEU* 1.3 80.4 - - - +
374B ILE* 1.3 62.7 + - - +
375B HIS* 3.4 17.7 + - + -
415B MET* 4.0 10.6 - - + +
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Residues in contact with ILE 374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342B ALA 2.9 18.9 + - - +
343B ARG* 3.8 7.5 - - - -
344B GLN* 3.9 4.1 + - - +
372B LEU* 3.5 22.7 - - + +
373B GLU* 1.3 76.6 - - - +
375B HIS* 1.3 65.7 + - - +
380B MET* 4.8 8.3 - - + -
412B TYR 5.7 0.2 - - - +
415B MET* 3.6 42.0 - - + +
416B LEU* 4.1 22.9 - - + +
419B GLY* 5.4 0.2 - - - -
444B ARG* 3.3 44.1 + - + -
447B GLN* 4.7 1.8 - - - +
448B LEU* 4.6 14.4 - - + -
503B GLN* 6.1 0.2 - - - +
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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