Contacts of the strand formed by residues 495 - 500 (chain C) in PDB entry 5I94
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 495 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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220C ILE* 4.8 1.1 - - - -
226C PHE* 3.6 34.1 - - + -
230C ILE* 4.9 0.4 - - + -
264C VAL* 3.9 16.6 - - + -
265C CYS 3.5 14.4 - - - +
266C THR* 3.8 11.7 - - + +
267C ALA 4.3 0.7 - - - +
434C ALA* 3.1 13.8 - - - +
491C VAL* 2.9 51.8 + - + +
494C VAL* 1.3 92.5 - - + +
496C GLY* 1.3 62.3 + - - +
497C MET* 3.6 27.4 - - + -
520C LEU* 4.0 15.3 - - + -
526C PHE* 4.2 7.9 - - + -
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Residues in contact with GLY 496 (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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263C SER 3.9 0.2 - - - +
264C VAL* 3.7 0.2 - - - -
265C CYS 2.9 33.2 + - - +
427C SER 3.7 7.5 - - - +
430C ALA 3.7 23.6 - - - -
431C ALA* 3.7 2.8 - - - +
489C LEU 3.6 8.3 - - - -
490C VAL* 4.6 0.2 - - - -
491C VAL 4.8 0.2 - - - -
495C MET* 1.3 75.2 - - - +
497C MET* 1.3 65.2 + - - +
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Residues in contact with MET 497 (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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230C ILE* 4.8 1.1 - - - -
262C VAL* 3.8 8.5 - - + -
263C SER 3.1 14.6 - - - +
264C VAL* 3.5 19.5 - - + -
427C SER* 4.0 5.2 - - - -
430C ALA* 3.6 9.2 - - - +
487C ILE 4.5 0.2 - - - -
488C LEU* 3.7 1.4 - - - -
489C LEU* 2.8 53.6 + - + +
491C VAL* 6.1 0.7 - - + -
495C MET* 3.6 29.6 - - + -
496C GLY* 1.3 77.9 - - - +
498C MET* 1.3 62.0 + - - +
499C CYS* 3.6 21.1 - - - -
516C PHE* 3.3 36.3 - - + -
520C LEU* 4.3 1.6 - - - -
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Residues in contact with MET 498 (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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261C GLY 3.6 1.6 - - - +
262C VAL* 3.6 4.9 - - - +
263C SER 3.2 27.6 + - - -
281C PHE* 3.9 27.8 - - + -
283C LEU* 4.2 16.2 - - + -
286C CYS* 4.2 8.5 - - - -
423C CYS* 3.7 27.4 - - - +
426C ALA* 3.7 25.1 - - + +
427C SER* 3.9 2.4 - - - +
486C GLY* 4.1 0.7 - - - -
487C ILE 3.4 23.6 - - - +
488C LEU* 3.6 33.9 - - + +
497C MET* 1.3 75.5 - - - +
499C CYS* 1.3 72.7 + - - +
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Residues in contact with CYS 499 (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 TRP* 3.9 14.6 - - + -
261C GLY 3.4 4.3 - - - -
262C VAL* 4.5 3.1 - - - -
485C GLY 3.5 1.5 - - - +
486C GLY* 3.2 4.0 - - - -
487C ILE* 2.8 43.6 + - + +
489C LEU* 5.5 0.9 - - - -
497C MET* 3.6 28.0 - - - -
498C MET* 1.3 77.2 - - - +
500C TRP* 1.3 62.2 - - - +
513C GLY* 4.1 18.8 - - - -
516C PHE* 3.9 21.5 - - - -
517C CYS* 4.8 8.3 - - - -
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Residues in contact with TRP 500 (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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255C PHE* 3.8 17.3 - + - -
259C LEU* 3.5 38.8 - - + +
260C TRP* 3.0 10.1 + - - -
261C GLY 2.9 37.8 + - - -
276C ASP* 3.7 18.6 - - + -
279C VAL* 3.6 34.8 - - + -
281C PHE* 3.5 50.7 - + + +
423C CYS* 3.7 17.0 - - - -
484C ALA 3.0 27.0 + - - -
485C GLY 3.4 13.0 - - - -
486C GLY 3.9 0.7 - - - -
499C CYS* 1.3 77.7 - - - +
501C SER* 1.3 60.4 + - - +
502C PRO* 4.0 15.0 - - + +
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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