Contacts of the strand formed by residues 358 - 364 (chain B) in PDB entry 4P0S
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 358 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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392A GLN 5.8 2.9 - - - +
393A VAL* 5.4 9.4 - - + +
396A GLY* 6.1 3.8 - - - -
310B PRO 3.3 13.9 + - - +
311B THR* 3.7 15.9 - - + +
312B VAL 3.3 17.5 + - - +
356B GLY 4.3 0.2 - - - -
357B LYS* 1.3 66.8 - - - +
359B LEU* 1.3 63.4 + - - +
360B SER* 3.7 4.2 + - - +
420B GLU 5.7 2.5 - - - -
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Residues in contact with LEU 359 (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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312B VAL* 3.1 25.6 - - + +
314B VAL* 3.4 35.0 - - + +
347B VAL* 4.9 10.8 - - + +
350B ILE* 3.8 34.5 - - + -
351B THR* 6.1 0.9 - - - +
354B THR* 6.1 0.2 - - - +
357B LYS 2.8 10.4 + - - +
358B ALA* 1.3 72.3 - - - +
360B SER* 1.3 70.8 + - - +
361B LEU* 4.6 9.2 - - + +
420B GLU 4.4 4.9 + - - +
421B ALA* 3.7 20.6 - - + -
422B GLN* 2.9 27.2 + - - +
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Residues in contact with SER 360 (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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392A GLN* 3.7 15.8 + - - +
393A VAL* 5.2 0.5 - - - +
312B VAL 3.6 4.6 + - - -
313B LEU* 3.1 16.0 - - - +
314B VAL 3.0 24.4 + - - -
358B ALA* 4.4 4.5 + - - +
359B LEU* 1.3 82.5 + - - +
361B LEU* 1.3 59.7 + - - +
362B VAL* 5.7 0.4 - - - -
422B GLN* 3.4 14.2 + - - +
424B GLN* 6.3 0.2 - - - -
435B PHE* 5.4 1.8 - - - -
439B PHE* 3.5 35.2 - - - -
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Residues in contact with LEU 361 (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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314B VAL* 2.9 45.5 - - + +
316B LEU* 4.0 32.3 - - + -
321B PHE* 5.0 9.2 - - + -
343B LEU* 5.9 2.2 - - + -
346B PHE* 5.6 2.9 - - + -
347B VAL* 5.8 7.9 - - + -
350B ILE* 5.2 3.6 - - + -
359B LEU* 4.2 12.0 - - + -
360B SER* 1.3 70.3 - - - +
362B VAL* 1.3 70.5 + - - +
363B ILE* 4.6 13.2 - - + -
412B LEU* 6.1 1.1 - - + -
415B LEU* 5.4 11.7 - - + -
421B ALA* 5.9 2.5 - - + -
422B GLN* 2.8 22.2 + - - +
423B ALA* 3.6 6.7 - - + -
424B GLN* 3.5 25.1 + - - +
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Residues in contact with VAL 362 (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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313B LEU* 4.1 20.6 - - + -
314B VAL 3.4 6.0 + - - +
315B LEU* 3.8 6.2 - - + +
316B LEU* 3.0 26.5 + - - +
360B SER* 4.7 2.0 - - - +
361B LEU* 1.3 80.5 - - - +
363B ILE* 1.3 68.7 + - - +
364B VAL 3.9 1.0 + - - +
424B GLN* 4.2 20.4 - - + +
426B VAL* 3.3 36.3 - - + +
432B LEU* 4.4 18.8 - - + -
435B PHE* 4.5 13.7 - - + -
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Residues in contact with ILE 363 (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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316B LEU* 3.4 12.6 - - + +
317B ARG 4.4 1.8 - - - +
318B ALA* 3.8 22.2 - - + +
321B PHE* 3.7 48.0 - - + -
361B LEU* 4.6 14.1 - - + -
362B VAL* 1.3 81.0 - - - +
364B VAL* 1.3 55.1 - - - +
365B ASP* 3.7 4.2 + - + +
369B CYS* 5.7 6.3 - - + -
412B LEU* 4.5 7.6 - - + -
423B ALA* 6.2 0.7 - - + -
424B GLN 3.7 18.6 + - - +
425B ILE* 3.8 19.7 - - + +
426B VAL* 2.8 39.5 + - - +
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Residues in contact with VAL 364 (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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263B MET* 5.3 0.2 - - + -
315B LEU* 3.8 22.0 - - + -
316B LEU 3.6 3.9 + - - +
317B ARG* 4.2 11.2 + - + +
318B ALA* 2.9 22.8 + - - +
362B VAL 3.9 1.0 + - - -
363B ILE* 1.3 71.5 - - - +
365B ASP* 1.3 67.9 + - - +
366B GLN* 5.0 2.0 - - + +
426B VAL* 3.7 10.3 - - + -
428B SER 4.7 13.2 - - - +
429B TRP* 3.7 59.2 - - + +
432B LEU* 4.9 5.4 - - + -
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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