Contacts of the strand formed by residues 353 - 358 (chain C) in PDB entry 4PS1
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 LYS 353 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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310C PHE* 3.4 9.0 - - + +
340C PHE* 3.0 34.8 + - + +
341C THR* 5.2 1.6 - - - +
342C GLY 5.3 3.4 - - - +
348C LEU* 2.9 43.3 + - + -
349C ALA* 4.3 5.1 - - - +
350C GLY 4.3 1.0 - - - +
351C LYS 2.8 23.5 + - - +
352C PRO* 1.3 77.2 - - - +
354C VAL* 1.3 62.2 + - - +
355C PHE* 4.5 8.7 - - + -
395C ASP 5.7 0.2 - - - -
397C ALA 3.7 21.9 + - - -
398C ASP* 2.8 11.7 + - - +
399C PHE* 3.3 30.4 - - + -
400C LEU 2.9 24.8 + - - +
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Residues in contact with VAL 354 (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 CYS* 4.4 7.4 - - - -
310C PHE 2.8 15.7 + - - +
311C ILE* 3.1 17.8 - - + +
312C CYS 2.7 32.1 + - - +
352C PRO* 4.6 0.9 - - + -
353C LYS* 1.3 81.5 - - - +
355C PHE* 1.3 60.6 + - - +
356C PHE* 3.5 39.5 - - + -
400C LEU* 3.5 23.3 - - + +
439C ILE* 5.7 0.2 - - + -
474C LEU* 3.8 27.8 - - + -
476C PHE* 4.7 5.2 - - + -
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Residues in contact with PHE 355 (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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296C LEU* 5.1 1.1 - - + -
310C PHE* 4.1 9.2 - + - -
312C CYS* 3.2 38.8 - - + -
314C ILE* 5.0 2.5 - - + -
336C LEU* 4.2 10.8 - - + -
337C THR* 3.8 30.1 - - + -
340C PHE* 3.7 31.4 - + - -
353C LYS* 4.5 6.3 - - + -
354C VAL* 1.3 80.0 - - - +
356C PHE* 1.3 58.2 + - - +
357C ILE* 4.6 11.7 - - + -
399C PHE* 3.9 29.2 - + - -
400C LEU 2.9 8.4 + - - +
401C LEU* 3.5 21.5 - - + +
402C GLY* 2.7 31.7 + - - +
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Residues in contact with PHE 356 (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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274C PHE* 3.8 27.1 - + - -
311C ILE* 4.1 5.6 - - + -
312C CYS 3.0 6.1 + - - -
313C CYS* 3.4 26.5 - - + +
314C ILE 2.9 27.2 + - - +
354C VAL* 3.5 30.5 - - + -
355C PHE* 1.3 75.4 - - - +
357C ILE* 1.3 63.1 + - - +
358C GLN 4.0 0.2 - - - -
400C LEU* 5.0 0.7 - - + -
402C GLY* 3.4 7.6 - - - +
421C TYR* 3.6 21.8 - - + -
422C ILE* 4.7 10.0 - - + +
425C LEU* 3.6 40.4 - - + -
429C LEU* 5.3 0.2 - - + -
439C ILE* 4.6 14.8 - - + -
443C LEU* 4.3 12.3 - - + -
476C PHE* 5.9 1.1 - + - -
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Residues in contact with ILE 357 (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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314C ILE* 3.7 33.0 - - + +
323C ILE* 3.6 27.8 - - + -
333C ILE* 4.2 16.4 - - + -
336C LEU* 5.5 0.7 - - + -
337C THR* 6.1 0.2 - - + -
355C PHE* 4.6 13.2 - - + -
356C PHE* 1.3 81.8 - - - +
358C GLN* 1.3 59.4 + - - +
359C ALA* 3.7 9.4 + - + +
361C GLN* 5.0 0.2 - - - +
401C LEU* 3.8 24.2 - - + -
402C GLY 2.9 10.0 + - - +
403C MET* 3.8 27.3 - - + +
404C ALA* 3.1 26.7 + - - +
421C TYR* 4.4 3.6 - - - -
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Residues in contact with GLN 358 (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 ARG* 4.0 6.1 - - - +
266C ASP* 4.2 1.6 - - - +
314C ILE* 2.8 15.5 + - - +
315C LEU* 3.8 6.5 - - + -
316C SER 2.9 28.1 + - - +
356C PHE 4.0 1.0 - - - -
357C ILE* 1.3 70.7 - - - +
359C ALA* 1.3 64.4 + - - +
404C ALA* 3.2 20.6 - - + +
411C SER* 3.0 25.6 + - - -
412C TYR 4.2 3.3 + - - +
419C THR* 3.5 35.2 + - + +
421C TYR* 3.4 15.4 + - - +
422C ILE* 3.7 21.5 - - + -
462C GLN* 4.7 0.2 + - - -
405G 1U8 2.8 24.9 + - - +
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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