Contacts of the strand formed by residues 358 - 365 (chain C) in PDB entry 5PAO
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 MET 358 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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213C ILE* 3.8 20.2 - - + +
216C GLY* 4.2 6.5 - - - +
217C LYS* 3.3 32.8 - - - +
218C VAL* 3.6 24.0 - - + +
219C CYS* 4.4 0.9 - - - -
342C SER* 3.1 8.4 - - - -
343C GLY 3.0 36.6 + - - +
347C LEU* 3.8 23.6 - - + -
354C ALA* 3.7 18.4 - - + -
356C GLU* 3.4 19.1 - - - +
357C LEU* 1.3 74.1 - - - +
359C VAL* 1.3 62.7 + - - +
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Residues in contact with VAL 359 (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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213C ILE* 4.3 2.0 - - - -
216C GLY* 3.3 3.7 - - - -
217C LYS* 2.8 40.9 + - + +
218C VAL 4.2 2.9 - - - +
219C CYS* 3.7 29.6 - - + -
220C PRO* 5.3 1.8 - - + -
224C CYS* 4.3 7.6 - - - -
340C LEU* 3.9 36.1 - - + -
341C VAL 3.3 11.9 - - - +
342C SER* 4.2 9.2 - - - -
358C MET* 1.3 76.4 - - - +
360C LEU* 1.3 63.8 + - - +
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Residues in contact with LEU 360 (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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213C ILE* 3.7 12.6 - - + -
214C VAL 3.8 2.0 - - - +
215C GLY 3.7 23.6 - - - +
216C GLY* 4.0 4.0 - - - -
339C SER 3.6 0.3 - - - +
340C LEU* 3.4 6.0 - - - -
341C VAL* 2.8 43.8 + - + +
359C VAL* 1.3 76.9 - - - +
361C ASN* 1.3 69.0 + - - +
362C VAL* 3.6 24.0 - - + -
397C LYS* 3.9 22.4 - - + -
398C ASP 3.5 42.0 - - - +
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Residues in contact with ASN 361 (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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338C PHE* 3.4 39.4 - - + +
339C SER* 3.2 20.8 + - - +
340C LEU* 3.5 17.4 - - + +
360C LEU* 1.3 79.8 - - - +
362C VAL* 1.3 62.5 + - - +
392C TYR* 3.7 18.4 + - - -
397C LYS* 5.2 0.5 - - - +
416C TRP* 6.2 0.4 - - - -
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Residues in contact with VAL 362 (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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337C ARG 3.7 0.3 - - - +
338C PHE* 3.3 4.9 - - - -
339C SER* 2.8 40.4 + - - +
341C VAL* 3.8 27.4 - - + -
360C LEU* 3.6 28.3 - - + -
361C ASN* 1.3 77.2 - - - +
363C PRO* 1.3 66.0 - - + +
364C ARG 4.0 0.3 + - - -
390C ALA* 4.0 17.3 - - + -
391C GLY* 3.8 22.2 - - - +
392C TYR* 4.5 3.6 - - + -
397C LYS 5.5 0.9 - - - +
398C ASP* 5.5 1.8 - - - -
408C HIS* 4.1 6.3 + - + -
437C TYR* 4.6 6.7 - - - +
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Residues in contact with PRO 363 (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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337C ARG* 3.3 38.8 - - + +
338C PHE* 3.7 17.5 - - + -
362C VAL* 1.3 85.4 - - + +
364C ARG* 1.3 62.0 + - - +
365C LEU* 3.5 6.9 - - + +
390C ALA* 3.2 3.8 - - - -
391C GLY 2.9 41.3 + - - +
392C TYR* 3.5 31.9 - - + +
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Residues in contact with ARG 364 (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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329C SER* 5.5 0.8 + - - -
333C LEU 4.6 2.0 + - - -
334C ALA* 3.6 47.6 + - - +
336C VAL 4.6 7.6 - - - +
337C ARG* 2.9 25.3 + - - +
339C SER* 6.0 1.1 - - - +
362C VAL 4.0 0.6 + - - -
363C PRO* 1.3 75.4 - - - +
365C LEU* 1.3 70.9 + - - +
366C MET 4.4 0.2 + - - -
388C PHE* 3.7 48.7 - - + +
389C CYS 3.6 5.2 - - - +
390C ALA* 3.9 6.1 - - + -
408C HIS* 4.9 8.4 - - + +
419C THR* 4.5 17.0 + - - +
439C ARG* 3.3 39.8 - - - +
441C SER* 5.5 0.8 + - - -
502C SO4 4.7 3.6 + - - -
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Residues in contact with LEU 365 (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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363C PRO* 3.5 21.1 - - + +
364C ARG* 1.3 85.6 + - - +
366C MET* 1.3 71.0 + - - +
367C THR* 3.6 1.0 + - - -
369C ASP* 4.3 3.8 - - + -
370C CYS* 3.9 22.7 - - + +
373C GLN* 3.8 21.1 - - - +
388C PHE* 4.8 3.3 - - - +
389C CYS 3.0 28.1 + - - +
390C ALA* 4.2 1.6 - - - -
391C GLY 4.2 3.1 - - - +
434C PHE* 3.6 51.6 - - + -
502C SO4 4.3 2.8 + - - -
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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