Contacts of the strand formed by residues 325 - 335 (chain C) 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 GLU 325 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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260C LEU* 4.2 3.0 - - - +
301C ARG* 2.6 48.0 + - - -
311C VAL* 5.1 12.3 - - + -
312C ALA 3.6 3.8 - - - -
313C GLN* 3.8 23.9 + - + -
323C PRO* 3.3 19.0 + - - +
324C GLY* 1.3 73.9 - - - +
326C LEU* 1.3 59.9 + - - +
455C THR* 3.3 8.1 - - - -
456C PHE* 2.7 51.9 + - + +
457C SER* 5.5 1.0 + - - -
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Residues in contact with LEU 326 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260C LEU* 4.1 16.2 - - + -
262C LEU* 3.6 30.5 - - + -
311C VAL* 3.0 5.3 - - - -
312C ALA* 2.6 46.1 + - + +
325C GLU* 1.3 81.2 - - - +
327C VAL* 1.3 59.4 + - - +
328C LEU* 4.0 0.6 + - - -
428C LEU* 4.7 4.0 - - + -
429C ARG* 3.9 13.5 - - - +
430C SER* 3.8 31.2 - - - +
453C LEU* 4.3 13.9 - - + +
454C LEU 3.2 14.1 - - - +
455C THR* 3.6 21.3 - - + -
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Residues in contact with VAL 327 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309C VAL* 4.0 17.0 - - + -
310C TRP 3.1 15.9 - - - +
311C VAL* 3.8 10.5 - - + -
325C GLU 4.4 0.4 + - - -
326C LEU* 1.3 72.6 - - - +
328C LEU* 1.3 73.6 + - - +
361C LEU* 3.9 28.0 - - + +
453C LEU* 3.6 19.3 - - - +
454C LEU* 2.9 34.1 + - + +
455C THR 4.5 2.0 - - - +
456C PHE* 4.5 4.2 - - + +
459C PHE* 4.3 17.9 - - + -
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Residues in contact with LEU 328 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269C VAL* 4.3 11.0 - - + -
310C TRP* 2.4 43.5 + - + +
311C VAL 4.1 1.3 - - - -
312C ALA* 3.9 26.9 - - + +
327C VAL* 1.3 84.4 - - - +
329C ASP* 1.3 65.0 + - - +
330C HIS* 3.2 10.2 + - - +
361C LEU* 3.5 8.0 - - - +
419C LEU* 3.6 37.5 - - + -
423C TYR* 3.9 31.9 - - + -
428C LEU* 6.1 0.4 - - + -
453C LEU* 4.0 17.9 - - + -
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Residues in contact with ASP 329 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328C LEU* 1.3 75.7 - - - +
330C HIS* 1.3 64.2 + - - +
360C GLY 4.4 2.6 - - - +
361C LEU* 3.8 13.6 - - - +
362C GLU* 3.0 29.2 + - - +
363C ARG* 2.9 56.8 + - + +
423C TYR* 4.6 5.0 + - - +
431C ARG* 5.2 1.2 + - - -
447C PRO 5.3 1.4 - - - -
448C ASN* 4.1 7.3 - - - +
450C LEU* 3.1 42.1 - - + +
453C LEU* 4.1 7.6 - - + +
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Residues in contact with HIS 330 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309C VAL* 4.0 0.2 - - - -
310C TRP* 3.6 44.0 + + + -
328C LEU* 3.2 6.0 + - - +
329C ASP* 1.3 85.0 + - + +
331C ILE* 1.3 63.1 + - - +
361C LEU* 3.6 9.0 - - - +
363C ARG* 3.3 32.0 + - + +
365C VAL* 4.4 8.3 - - + -
415C LEU* 5.1 5.6 - - + -
419C LEU* 4.4 13.5 - - + +
448C ASN* 3.6 18.8 - - - -
416D GLN* 4.0 24.1 + - - +
417D LEU* 3.0 37.0 - - + +
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Residues in contact with ILE 331 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305C VAL 4.2 17.9 - - - +
306C GLY* 4.4 9.2 - - - -
308C PHE 3.1 17.0 - - - +
309C VAL* 3.4 17.0 - - + +
310C TRP* 5.2 0.4 - - - -
330C HIS* 1.3 78.8 - - - +
332C VAL* 1.3 67.0 + - - +
356C LEU* 4.8 11.0 - - + +
359C CYS* 4.5 11.2 - - - -
361C LEU* 3.5 26.9 - - + +
363C ARG 3.2 11.4 + - - +
364C ARG* 4.2 17.3 - - + -
365C VAL* 2.9 27.7 + - - +
459C PHE* 4.4 6.1 - - + -
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Residues in contact with VAL 332 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306C GLY* 5.5 0.4 - - - -
307C ASP 3.5 3.8 + - - -
308C PHE* 2.8 63.0 + - + +
310C TRP* 4.5 14.4 - - + -
331C ILE* 1.3 79.9 - - - +
333C GLU* 1.3 62.2 + - - +
365C VAL* 3.1 26.2 - - + +
367C LEU* 3.2 37.5 - - + -
412C LEU* 4.7 4.3 - - + -
415C LEU* 4.4 18.4 - - + -
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Residues in contact with GLU 333 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306C GLY* 3.3 28.9 + - - -
307C ASP* 3.5 22.1 + - - +
332C VAL* 1.3 73.4 - - - +
334C ARG* 1.3 61.3 + - - +
335C LYS* 4.2 6.0 + - + -
352C GLN* 2.6 37.6 + - - +
356C LEU* 4.6 12.2 - - + +
365C VAL 3.1 7.2 + - - +
366C TYR* 3.5 47.5 - - + +
367C LEU 3.1 23.5 + - - +
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Residues in contact with ARG 334 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277C GLU* 2.7 58.4 + - - +
307C ASP* 3.3 19.7 + - - +
308C PHE* 3.5 34.2 - - + -
332C VAL* 4.1 2.0 - - - +
333C GLU* 1.3 69.2 - - - +
335C LYS* 1.3 80.2 + - - +
336C ARG* 3.9 25.5 - - - +
339C ASP* 5.8 2.2 + - - -
367C LEU* 3.2 18.8 - - + +
369C GLU* 3.3 28.3 + - + +
405C ILE* 4.1 17.6 - - - +
408C SER* 5.9 4.2 - - - +
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Residues in contact with LYS 335 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277C GLU* 5.8 0.8 + - - -
307C ASP* 4.9 2.8 + - - -
333C GLU* 4.2 8.3 + - + +
334C ARG* 1.3 86.4 + - - +
336C ARG* 1.3 73.1 + - - +
337C LEU* 5.4 0.2 - - - +
339C ASP* 4.1 15.5 + - + +
340C LEU* 4.1 21.7 - - + +
343C SER* 3.4 22.2 - - - -
348C ARG* 3.5 16.0 - - - +
352C GLN* 3.3 33.9 + - - +
366C TYR* 4.3 18.8 - - + +
367C LEU 3.0 8.8 + - - +
368C VAL* 3.8 8.0 - - + +
369C GLU* 2.9 24.1 + - - +
55X T 6.1 2.0 - - - +
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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