Contacts of the strand formed by residues 414 - 419 (chain C) in PDB entry 2R6C
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 ILE 414 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193C LEU* 4.6 17.9 - - + -
219C PHE* 3.8 25.1 - - + -
394C ALA* 4.5 12.6 - - + -
395C PHE 3.2 7.6 - - - +
396C LEU* 3.5 19.3 - - + -
413C GLU* 1.3 72.8 - - - +
415C ILE* 1.3 62.5 + - - +
416C ILE* 3.4 19.0 + - + +
425C GLY 3.8 0.3 - - - +
426C THR* 4.5 0.4 - - - -
427C VAL* 2.8 45.9 + - + +
429C LEU* 3.6 40.2 - - + -
438C PHE* 5.8 2.7 - - + -
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Residues in contact with ILE 415 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374C ARG 4.9 2.2 - - - +
375C PRO* 3.9 29.2 - - + +
393C VAL 3.6 0.2 - - - +
394C ALA* 3.3 1.3 - - - -
395C PHE* 2.7 51.1 + - + +
397C TYR* 4.6 5.6 - - + -
413C GLU* 4.1 22.4 - - + +
414C ILE* 1.3 72.4 - - - +
416C ILE* 1.3 61.6 + - - +
417C ALA* 3.1 25.0 + - + +
424C VAL* 6.4 0.2 - - + -
425C GLY* 4.1 5.6 - - - +
426C THR* 3.6 21.3 - - + +
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Residues in contact with ILE 416 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193C LEU* 3.7 29.4 - - + -
196C MET* 3.8 26.2 - - + -
197C THR* 3.8 17.0 - - + -
392C ILE* 4.4 11.7 - - + -
393C VAL 3.7 3.6 - - - -
394C ALA* 4.5 7.6 - - + +
414C ILE* 4.5 10.1 - - + +
415C ILE* 1.3 69.8 - - - +
417C ALA* 1.3 61.6 + - - +
418C LYS 4.1 15.3 - - - +
419C GLN* 4.1 17.7 - - + -
423C PRO 4.3 9.0 - - - +
424C VAL* 3.3 5.0 - - - +
425C GLY 3.1 33.5 + - - +
427C VAL* 4.4 4.9 - - + -
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Residues in contact with ALA 417 (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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376C MET* 6.0 0.7 - - - -
377C MET* 4.5 17.4 - - + +
393C VAL 2.9 8.0 + - - +
395C PHE* 3.8 32.8 - - + -
415C ILE* 3.1 9.6 + - + -
416C ILE* 1.3 75.0 - - - +
418C LYS* 1.3 63.1 + - - +
424C VAL* 3.3 21.5 - - - +
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Residues in contact with LYS 418 (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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377C MET* 4.2 16.4 - - + -
387C GLU* 3.0 29.7 + - + +
388C GLN* 4.2 3.2 - - - +
390C ALA 3.6 13.1 + - - +
391C ASP* 4.7 4.3 - - - +
392C ILE* 3.0 5.6 - - - +
393C VAL* 2.8 46.2 + - + +
416C ILE* 4.1 3.4 - - - +
417C ALA* 1.3 81.2 - - - +
419C GLN* 1.3 68.5 + - - +
420C ARG* 3.3 39.3 - - - +
424C VAL* 4.3 3.1 - - - -
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Residues in contact with GLN 419 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196C MET* 2.4 28.8 + - - +
197C THR* 3.2 26.3 - - - +
391C ASP 3.1 10.1 - - - -
392C ILE* 3.9 12.2 - - + +
416C ILE* 4.1 7.9 - - + -
418C LYS* 1.3 81.4 - - - +
420C ARG* 1.3 63.9 + - - +
421C ASN* 3.3 18.4 + - - +
422C GLY 3.6 22.6 - - - +
423C PRO* 2.7 41.5 + - - +
424C VAL* 4.2 7.4 - - - +
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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