Contacts of the strand formed by residues 355 - 360 (chain C) in PDB entry 2R2N
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 PHE 355 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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200C GLY 5.4 1.1 - - - -
201C ASN 4.9 1.3 - - - -
202C ASN* 3.5 37.7 - - + -
203C PRO 3.7 17.3 - - - +
205C GLY* 3.9 14.7 - - - +
233C TYR* 3.6 19.3 - + - -
350C PRO* 3.5 14.7 - - - +
352C ALA 5.1 0.8 + - - -
353C GLY 4.0 0.2 - - - -
354C MET* 1.3 97.8 - - + +
356C LEU* 1.3 59.9 + - - +
357C TRP 4.3 0.2 + - - -
399C ARG* 3.4 45.8 - - + -
400C ALA 3.4 1.3 - - - -
401C SER* 3.9 16.6 - - - -
402C PHE* 3.3 12.9 - - - -
428C KYN 4.9 0.9 - - - -
38D GLY 3.7 16.2 - - - -
39D GLY* 3.7 17.9 - - - -
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Residues in contact with LEU 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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203C PRO 4.6 0.9 - - - -
333C ILE* 4.2 33.7 - - + -
334C LEU* 3.9 20.0 - - + -
337C ALA* 4.3 19.7 - - + -
347C TRP* 4.0 11.9 - - + -
348C HIS 3.9 20.9 - - - +
350C PRO* 4.1 7.4 - - + -
355C PHE* 1.3 73.9 - - - +
357C TRP* 1.3 63.3 + - - +
358C ILE* 3.8 27.0 + - + +
398C LEU 3.5 2.1 - - - +
399C ARG* 3.5 2.4 - - - +
400C ALA* 2.7 42.6 + - + +
402C PHE* 3.9 6.3 - - + -
414C PHE* 4.5 0.4 - - + -
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Residues in contact with TRP 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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140C PRO* 3.6 26.5 - - + +
203C PRO* 3.5 41.1 - - + +
204C THR* 3.5 40.7 + - + +
206C ASN* 5.6 1.8 - - - -
347C TRP* 3.5 20.4 - - - +
348C HIS* 4.5 11.0 + + - +
350C PRO* 5.6 0.4 - - - +
355C PHE 4.2 0.8 + - - -
356C LEU* 1.3 76.0 - - - +
358C ILE* 1.3 61.2 + - - +
359C LYS 4.0 0.7 + - - -
384C GLY* 3.6 30.3 - - - -
387C PHE* 4.1 3.1 - + - -
388C TYR* 3.6 8.1 - - - -
397C TYR* 3.2 56.6 - + + -
398C LEU 3.5 18.4 - - - -
399C ARG* 4.1 10.1 - - + -
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Residues in contact with ILE 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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337C ALA* 5.5 0.2 - - + -
341C LEU* 4.4 9.6 - - + -
345C ALA* 3.6 28.3 - - + -
346C GLU 3.6 5.2 - - - +
347C TRP* 4.5 8.1 - - + -
356C LEU* 3.8 25.4 - - + +
357C TRP* 1.3 77.1 - - - +
359C LYS* 1.3 63.2 + - - +
360C VAL* 3.6 10.0 + - + +
381C MET* 3.6 29.6 - - + -
396C PRO 3.7 0.2 - - - +
397C TYR* 3.2 6.8 - - - -
398C LEU* 2.8 43.7 + - + +
400C ALA* 4.3 2.7 - - + -
414C PHE* 3.7 25.8 - - + -
417C LEU* 5.1 1.3 - - + -
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Residues in contact with LYS 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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345C ALA* 3.1 4.0 - - - -
346C GLU* 2.8 57.7 + - + +
357C TRP 4.0 0.6 + - - -
358C ILE* 1.3 69.7 - - - +
360C VAL* 1.3 65.9 + - - +
361C LYS* 3.6 2.6 + - + +
396C PRO* 3.7 27.8 - - + -
397C TYR* 3.3 41.7 + - + +
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Residues in contact with VAL 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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344C LEU 3.8 3.6 - - - +
345C ALA* 4.1 2.5 - - + -
358C ILE* 4.5 8.5 - - + +
359C LYS* 1.3 76.4 - - - +
361C LYS* 1.3 67.3 + - - +
362C GLY 3.8 0.7 + - - -
363C ILE* 3.5 36.9 - - + +
366C VAL* 4.1 10.3 - - + -
369C LEU* 5.0 0.7 - - + -
396C PRO* 2.9 36.4 + - - +
398C LEU* 3.8 29.2 - - + -
421C ILE* 3.9 34.5 - - + -
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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